Errors generated during make run.

[iajzenszmi]

(base) ian@ian-Aspire-One-753:~/vtk$ apt-cache search vtk cmake - cross-platform, open-source make system gdcm-doc - Grassroots DICOM documentation h5utils - HDF5 files visualization tools libocct-visualization-7.3 - Open CASCADE Technology graphical data visualization module libvtk-dicom-dev - DICOM for VTK - dev libvtk6-dev - VTK header files libvtk6-qt-dev - VTK header files, containing Qt files libvtk6.3 - VTK libraries libvtk6.3-qt - VTK libraries, Qt files libvtk7-dev - VTK header files libvtk7-java - Visualization Toolkit - A high level 3D visualization library - java libvtk7-jni - Visualization Toolkit - A high level 3D visualization library - java libvtk7-qt-dev - VTK header files, containing Qt files libvtk7.1p - VTK libraries libvtk7.1p-qt - VTK libraries, Qt files libvtkdicom0.8 - DICOM for VTK - lib libvtkgdcm-cil - Grassroots DICOM VTK CLI bindings libvtkgdcm-dev - Grassroots DICOM VTK development libraries and headers libvtkgdcm-java - Grassroots DICOM VTK Java bindings libvtkgdcm-tools - Grassroots DICOM VTK tools and utilities libvtkgdcm3.0 - Grassroots DICOM VTK runtime libraries mayavi2 - scientific visualization package for 2-D and 3-D data meshio-tools - command-line tools for meshio nifti2dicom - convert 3D medical images to DICOM 2D series nifti2dicom-dbg - convert 3D medical images to DICOM 2D series (debug symbols) octave-fpl - plot data on unstructured triangular and tetrahedral meshes in Octave python3-meshio - library for reading and writing mesh data (Python 3) python3-vtk-dicom - DICOM for VTK - Python python3-vtk7 - Python bindings for VTK python3-vtkgdcm - Grassroots DICOM VTK/Python bindings python3-vtkplotter - python module for 3D scientific visualization with VTK qnifti2dicom - convert 3D medical images to DICOM 2D series (gui) tcl-vtk7 - Tcl bindings for VTK vrrender - DICOM viewer vtk-dicom-tools - DICOM for VTK - tools vtk7 - Binaries for VTK7 vtk7-doc - VTK class reference documentation vtk7-examples - VTK examples vtkdata - Example data for VTK (base) ian@ian-Aspire-One-753:~/vtk$ sudo apt install libvtk7-dev [sudo] password for ian: Reading package lists... Done Building dependency tree
Reading state information... Done The following package was automatically installed and is no longer required: libllvm11 Use 'sudo apt autoremove' to remove it. The following additional packages will be installed: cython3 default-libmysqlclient-dev gdal-data hdf5-helpers libarmadillo-dev libarmadillo9 libarpack2-dev libavcodec-dev libavformat-dev libavutil-dev libboost-dev libboost1.71-dev libcfitsio-dev libcfitsio-doc libcfitsio8 libcharls-dev libcharls2 libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5 libeigen3-dev libepsilon-dev libepsilon1 libfreexl-dev libfreexl1 libfyba-dev libfyba0 libgdal-dev libgdal26 libgeos-3.8.0 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff5 libgif-dev libgl2ps-dev libglew-dev libglew2.1 libhdf4-0-alt libhdf4-alt-dev libhdf5-cpp-103 libhdf5-dev libjson-c-dev libjsoncpp-dev libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1 libminizip-dev libminizip1 libnetcdf-c++4 libnetcdf-cxx-legacy-dev libnetcdf-dev libnetcdf15 libogdi-dev libogdi4.1 libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libpq-dev libproj-dev libproj15 libqhull-dev libqhull-r7 libspatialite-dev libspatialite7 libsqlite3-dev libswresample-dev libswscale-dev libtheora-dev liburiparser-dev liburiparser1 libvtk7-java libvtk7-jni libvtk7.1p libvtk7.1p-qt libwebp-dev libxerces-c-dev libxerces-c3.2 libxml2-dev libxss-dev libzstd-dev proj-bin proj-data python3-autobahn python3-automat python3-cbor python3-constantly python3-hamcrest python3-hyperlink python3-incremental python3-lz4 python3-mpi4py python3-openssl python3-png python3-pyasn1 python3-pyasn1-modules python3-pyqrcode python3-service-identity python3-snappy python3-trie python3-twisted python3-twisted-bin python3-txaio python3-u-msgpack python3-ubjson python3-vtk7 python3-wsaccel python3-zope.interface tcl tcl-dev tcl-vtk7 tcl8.6 tcl8.6-dev tk tk-dev tk8.6 tk8.6-dev unixodbc-dev vtk7 x11proto-scrnsaver-dev Suggested packages: cython-doc libitpp-dev libboost-doc libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libeigen3-doc libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin glew-utils libhdf4-doc hdf4-tools libhdf5-doc netcdf-bin netcdf-doc ogdi-bin postgresql-doc-12 sqlite3-doc vtk7-doc vtk7-examples java-virtual-machine libxerces-c-doc python-openssl-doc python3-openssl-dbg python-trie-doc python3-pampy python3-qt4 python3-serial python3-wxgtk2.8 python3-twisted-bin-dbg python-txaio-doc mayavi2 tcl-doc tcl-tclreadline tcl8.6-doc tk-doc tk8.6-doc The following NEW packages will be installed: cython3 default-libmysqlclient-dev gdal-data hdf5-helpers libarmadillo-dev libarmadillo9 libarpack2-dev libavcodec-dev libavformat-dev libavutil-dev libboost-dev libboost1.71-dev libcfitsio-dev libcfitsio-doc libcfitsio8 libcharls-dev libcharls2 libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5 libeigen3-dev libepsilon-dev libepsilon1 libfreexl-dev libfreexl1 libfyba-dev libfyba0 libgdal-dev libgdal26 libgeos-3.8.0 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff5 libgif-dev libgl2ps-dev libglew-dev libglew2.1 libhdf4-0-alt libhdf4-alt-dev libhdf5-cpp-103 libhdf5-dev libjson-c-dev libjsoncpp-dev libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1 libminizip-dev libminizip1 libnetcdf-c++4 libnetcdf-cxx-legacy-dev libnetcdf-dev libnetcdf15 libogdi-dev libogdi4.1 libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libpq-dev libproj-dev libproj15 libqhull-dev libqhull-r7 libspatialite-dev libspatialite7 libsqlite3-dev libswresample-dev libswscale-dev libtheora-dev liburiparser-dev liburiparser1 libvtk7-dev libvtk7-java libvtk7-jni libvtk7.1p libvtk7.1p-qt libwebp-dev libxerces-c-dev libxerces-c3.2 libxml2-dev libxss-dev libzstd-dev proj-bin proj-data python3-autobahn python3-automat python3-cbor python3-constantly python3-hamcrest python3-hyperlink python3-incremental python3-lz4 python3-mpi4py python3-openssl python3-png python3-pyasn1 python3-pyasn1-modules python3-pyqrcode python3-service-identity python3-snappy python3-trie python3-twisted python3-twisted-bin python3-txaio python3-u-msgpack python3-ubjson python3-vtk7 python3-wsaccel python3-zope.interface tcl tcl-dev tcl-vtk7 tcl8.6 tcl8.6-dev tk tk-dev tk8.6 tk8.6-dev unixodbc-dev vtk7 x11proto-scrnsaver-dev 0 to upgrade, 127 to newly install, 0 to remove and 19 not to upgrade. Need to get 115 MB of archives. After this operation, 683 MB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://archive.ubuntu.com/ubuntu focal/universe amd64 cython3 amd64 0.29.14-0.1ubuntu3 [1,474 kB] Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 default-libmysqlclient-dev amd64 1.0.5ubuntu2 [3,932 B] Get:3 http://archive.ubuntu.com/ubuntu focal/universe amd64 gdal-data all 3.0.4+dfsg-1build3 [186 kB] Get:4 http://archive.ubuntu.com/ubuntu focal/universe amd64 hdf5-helpers amd64 1.10.4+repack-11ubuntu1 [13.6 kB] Get:5 http://archive.ubuntu.com/ubuntu focal/universe amd64 libarmadillo9 amd64 1:9.800.4+dfsg-1build1 [93.2 kB] Get:6 http://archive.ubuntu.com/ubuntu focal/universe amd64 libarpack2-dev amd64 3.7.0-3 [105 kB] Get:7 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhdf5-cpp-103 amd64 1.10.4+repack-11ubuntu1 [120 kB] Get:8 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhdf5-dev amd64 1.10.4+repack-11ubuntu1 [2,589 kB] Get:9 http://archive.ubuntu.com/ubuntu focal/universe amd64 libarmadillo-dev amd64 1:9.800.4+dfsg-1build1 [374 kB] Get:10 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 libavutil-dev amd64 7:4.2.4-1ubuntu0.1 [365 kB] Get:11 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 libswresample-dev amd64 7:4.2.4-1ubuntu0.1 [70.6 kB] Get:12 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 libavcodec-dev amd64 7:4.2.4-1ubuntu0.1 [5,415 kB] Get:13 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 libavformat-dev amd64 7:4.2.4-1ubuntu0.1 [1,182 kB] Get:14 http://archive.ubuntu.com/ubuntu focal/main amd64 libboost1.71-dev amd64 1.71.0-6ubuntu6 [9,068 kB] Get:15 http://archive.ubuntu.com/ubuntu focal/main amd64 libboost-dev amd64 1.71.0.0ubuntu2 [3,596 B]
Get:16 http://archive.ubuntu.com/ubuntu focal/universe amd64 libcfitsio8 amd64 3.470-3 [466 kB]
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Get:21 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libcurl4-gnutls-dev amd64 7.68.0-1ubuntu2.7 [319 kB]
Get:22 http://archive.ubuntu.com/ubuntu focal/universe amd64 libdap25 amd64 3.20.5-1 [435 kB]
Get:23 http://archive.ubuntu.com/ubuntu focal/universe amd64 libdapserver7v5 amd64 3.20.5-1 [23.0 kB]
Get:24 http://archive.ubuntu.com/ubuntu focal/universe amd64 libdapclient6v5 amd64 3.20.5-1 [92.2 kB]
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Get:26 http://archive.ubuntu.com/ubuntu focal/universe amd64 libdap-dev amd64 3.20.5-1 [745 kB]
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Get:33 http://archive.ubuntu.com/ubuntu focal/universe amd64 proj-data all 6.3.1-1 [7,647 kB]
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Get:35 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgeotiff5 amd64 1.5.1-2 [53.1 kB]
Get:36 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhdf4-0-alt amd64 4.2.14-1ubuntu1 [268 kB]
Get:37 http://archive.ubuntu.com/ubuntu focal/universe amd64 libminizip1 amd64 1.1-8build1 [20.2 kB]
Get:38 http://archive.ubuntu.com/ubuntu focal/universe amd64 liburiparser1 amd64 0.9.3-2 [39.3 kB]
Get:39 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkmlbase1 amd64 1.3.0-8build1 [45.4 kB]
Get:40 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkmldom1 amd64 1.3.0-8build1 [152 kB]
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Get:42 http://archive.ubuntu.com/ubuntu focal/universe amd64 libnetcdf15 amd64 1:4.7.3-1 [341 kB]
Get:43 http://archive.ubuntu.com/ubuntu focal/universe amd64 libogdi4.1 amd64 4.1.0+ds-1build1 [198 kB]
Get:44 http://archive.ubuntu.com/ubuntu focal/universe amd64 libspatialite7 amd64 4.3.0a-6build1 [1,286 kB]
Get:45 http://archive.ubuntu.com/ubuntu focal/universe amd64 libxerces-c3.2 amd64 3.2.2+debian-1build3 [878 kB]
Get:46 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgdal26 amd64 3.0.4+dfsg-1build3 [6,156 kB]
Get:47 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgeos-dev amd64 3.8.0-1build1 [92.3 kB]
Get:48 http://archive.ubuntu.com/ubuntu focal/main amd64 libgif-dev amd64 5.1.9-1 [20.6 kB]
Get:49 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgl2ps-dev amd64 1.4.0+dfsg1-2 [239 kB]
Get:50 http://archive.ubuntu.com/ubuntu focal/universe amd64 libglew2.1 amd64 2.1.0-4 [155 kB]
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Get:52 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkmlconvenience1 amd64 1.3.0-8build1 [44.7 kB]
Get:53 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkmlregionator1 amd64 1.3.0-8build1 [19.8 kB]
Get:54 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkmlxsd1 amd64 1.3.0-8build1 [27.1 kB]
Get:55 http://archive.ubuntu.com/ubuntu focal/universe amd64 libminizip-dev amd64 1.1-8build1 [26.7 kB]
Get:56 http://archive.ubuntu.com/ubuntu focal/universe amd64 libnetcdf-c++4 amd64 4.2-11build2 [33.6 kB]
Get:57 http://archive.ubuntu.com/ubuntu focal/universe amd64 libnetcdf-dev amd64 1:4.7.3-1 [45.7 kB]
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Get:59 http://archive.ubuntu.com/ubuntu focal/universe amd64 libogdi-dev amd64 4.1.0+ds-1build1 [22.1 kB]
Get:60 http://archive.ubuntu.com/ubuntu focal/main amd64 libpoppler-dev amd64 0.86.1-0ubuntu1 [5,336 B]
Get:61 http://archive.ubuntu.com/ubuntu focal/main amd64 libpoppler-private-dev amd64 0.86.1-0ubuntu1 [174 kB]
Get:62 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpq-dev amd64 12.9-0ubuntu0.20.04.1 [136 kB]
Get:63 http://archive.ubuntu.com/ubuntu focal/universe amd64 libqhull-r7 amd64 2015.2-4 [149 kB]
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Get:65 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsqlite3-dev amd64 3.31.1-4ubuntu0.2 [696 kB]
Get:66 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 libswscale-dev amd64 7:4.2.4-1ubuntu0.1 [175 kB]
Get:67 http://archive.ubuntu.com/ubuntu focal/main amd64 libtheora-dev amd64 1.1.1+dfsg.1-15ubuntu2 [178 kB]
Get:68 http://archive.ubuntu.com/ubuntu focal/universe amd64 liburiparser-dev amd64 0.9.3-2 [12.0 kB]
Get:69 http://archive.ubuntu.com/ubuntu focal/universe amd64 libeigen3-dev all 3.3.7-2 [815 kB]
Get:70 http://archive.ubuntu.com/ubuntu focal/universe amd64 libepsilon-dev amd64 0.9.2+dfsg-4 [48.6 kB]
Get:71 http://archive.ubuntu.com/ubuntu focal/universe amd64 libfreexl-dev amd64 1.0.5-3 [30.9 kB]
Get:72 http://archive.ubuntu.com/ubuntu focal/universe amd64 libproj-dev amd64 6.3.1-1 [1,092 kB]
Get:73 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgeotiff-dev amd64 1.5.1-2 [76.8 kB]
Get:74 http://archive.ubuntu.com/ubuntu focal/universe amd64 libhdf4-alt-dev amd64 4.2.14-1ubuntu1 [369 kB]
Get:75 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libjson-c-dev amd64 0.13.1+dfsg-7ubuntu0.3 [46.9 kB]
Get:76 http://archive.ubuntu.com/ubuntu focal/universe amd64 libkml-dev amd64 1.3.0-8build1 [933 kB]
Get:77 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libopenjp2-7-dev amd64 2.3.1-1ubuntu4.20.04.1 [26.7 kB]
Get:78 http://archive.ubuntu.com/ubuntu focal/universe amd64 libspatialite-dev amd64 4.3.0a-6build1 [1,387 kB]
Get:79 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libwebp-dev amd64 0.6.1-2ubuntu0.20.04.1 [266 kB]
Get:80 http://archive.ubuntu.com/ubuntu focal/universe amd64 libxerces-c-dev amd64 3.2.2+debian-1build3 [1,694 kB]
Get:81 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libzstd-dev amd64 1.4.4+dfsg-3ubuntu0.1 [286 kB]
Get:82 http://archive.ubuntu.com/ubuntu focal/main amd64 unixodbc-dev amd64 2.3.6-0.1build1 [225 kB]
Get:83 http://archive.ubuntu.com/ubuntu focal/universe amd64 libgdal-dev amd64 3.0.4+dfsg-1build3 [8,093 kB]
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Get:85 http://archive.ubuntu.com/ubuntu focal/universe amd64 libvtk7.1p amd64 7.1.1+dfsg2-2ubuntu1 [36.7 MB]
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Get:87 http://archive.ubuntu.com/ubuntu focal/universe amd64 libvtk7-java amd64 7.1.1+dfsg2-2ubuntu1 [2,225 kB]
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Get:90 http://archive.ubuntu.com/ubuntu focal/universe amd64 libvtk7.1p-qt amd64 7.1.1+dfsg2-2ubuntu1 [98.8 kB]
Get:91 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-cbor amd64 1.0.0-1.1build1 [20.5 kB]
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Get:93 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-openssl all 19.0.0-1build1 [43.3 kB]
Get:94 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-pyqrcode all 1.2.1-4 [30.3 kB]
Get:95 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-pyasn1 all 0.4.2-3build1 [46.7 kB]
Get:96 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-pyasn1-modules all 0.2.1-0.2build1 [32.9 kB]
Get:97 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-service-identity all 18.1.0-5build1 [10.7 kB]
Get:98 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-snappy amd64 0.5.3-1.1build1 [16.9 kB]
Get:99 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-trie all 0.2+ds-2 [7,520 B]
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Get:101 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-constantly all 15.1.0-1build1 [8,244 B]
Get:102 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-hyperlink all 19.0.0-1 [33.5 kB]
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Get:104 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-zope.interface amd64 4.7.1-1 [85.2 kB]
Get:105 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-twisted-bin amd64 18.9.0-11ubuntu0.20.04.1 [11.1 kB]
Get:106 http://archive.ubuntu.com/ubuntu focal/main amd64 python3-hamcrest all 1.9.0-3 [24.9 kB]
Get:107 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 python3-twisted all 18.9.0-11ubuntu0.20.04.1 [1,931 kB]
Get:108 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-txaio all 2.10.0-2 [18.8 kB]
Get:109 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-u-msgpack all 2.1-1build1 [7,576 B]
Get:110 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-ubjson amd64 0.14.0-2build1 [33.0 kB]
Get:111 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-wsaccel amd64 0.6.2-2build1 [41.4 kB]
Get:112 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-autobahn all 17.10.1+dfsg1-6 [157 kB]
Get:113 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-mpi4py amd64 3.0.3-4build2 [500 kB]
Get:114 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-vtk7 amd64 7.1.1+dfsg2-2ubuntu1 [255 kB]
Get:115 http://archive.ubuntu.com/ubuntu focal/main amd64 tcl8.6 amd64 8.6.10+dfsg-1 [14.8 kB]
Get:116 http://archive.ubuntu.com/ubuntu focal/main amd64 tcl8.6-dev amd64 8.6.10+dfsg-1 [905 kB]
Get:117 http://archive.ubuntu.com/ubuntu focal/universe amd64 tcl amd64 8.6.9+1 [5,112 B]
Get:118 http://archive.ubuntu.com/ubuntu focal/universe amd64 tcl-dev amd64 8.6.9+1 [5,760 B]
Get:119 http://archive.ubuntu.com/ubuntu focal/universe amd64 tcl-vtk7 amd64 7.1.1+dfsg2-2ubuntu1 [151 kB]
Get:120 http://archive.ubuntu.com/ubuntu focal/main amd64 tk8.6 amd64 8.6.10-1 [12.5 kB]
Get:121 http://archive.ubuntu.com/ubuntu focal/main amd64 tk8.6-dev amd64 8.6.10-1 [711 kB]
Get:122 http://archive.ubuntu.com/ubuntu focal/universe amd64 tk amd64 8.6.9+1 [3,240 B]
Get:123 http://archive.ubuntu.com/ubuntu focal/universe amd64 tk-dev amd64 8.6.9+1 [3,076 B]
Get:124 http://archive.ubuntu.com/ubuntu focal/universe amd64 vtk7 amd64 7.1.1+dfsg2-2ubuntu1 [173 kB]
Get:125 http://archive.ubuntu.com/ubuntu focal/universe amd64 libvtk7-dev amd64 7.1.1+dfsg2-2ubuntu1 [2,241 kB]
Get:126 http://archive.ubuntu.com/ubuntu focal/universe amd64 python3-png all 0.0.20+ds-2 [46.9 kB]
Get:127 http://archive.ubuntu.com/ubuntu focal/universe amd64 proj-bin amd64 6.3.1-1 [88.8 kB]
Fetched 115 MB in 29s (3,987 kB/s)
Extracting templates from packages: 100% Selecting previously unselected package cython3. (Reading database ... 314039 files and directories currently installed.) Preparing to unpack .../000-cython3_0.29.14-0.1ubuntu3_amd64.deb ... Unpacking cython3 (0.29.14-0.1ubuntu3) ... Selecting previously unselected package default-libmysqlclient-dev:amd64. Preparing to unpack .../001-default-libmysqlclient-dev_1.0.5ubuntu2_amd64.deb ... Unpacking default-libmysqlclient-dev:amd64 (1.0.5ubuntu2) ... Selecting previously unselected package gdal-data. Preparing to unpack .../002-gdal-data_3.0.4+dfsg-1build3_all.deb ... Unpacking gdal-data (3.0.4+dfsg-1build3) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../003-hdf5-helpers_1.10.4+repack-11ubuntu1_amd64.deb ... Unpacking hdf5-helpers (1.10.4+repack-11ubuntu1) ... Selecting previously unselected package libarmadillo9. Preparing to unpack .../004-libarmadillo9_1%3a9.800.4+dfsg-1build1_amd64.deb ... 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(base) ian@ian-Aspire-One-753:~/vtk$ cd ~/fluidity (base) ian@ian-Aspire-One-753:~/fluidity$ ls fluidity (base) ian@ian-Aspire-One-753:~/fluidity$ cd fluidity (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ls 4.1.19.tar.gz config.guess docker horizontal_adaptivity libmba3d Makefile.in preprocessor aclocal.m4 config.log error_measures hyperlight libspud manual python acx_blas.m4 config.sub examples include libvtkfortran mayavi README acx_lapack.m4 configure femtools INSTALL libwm ocean_forcing schemas assemble configure.in fldecomp install-sh LICENSE parameterisation sediments AUTHORS debian fluidity-4.1.19 libadaptivity m4 petsc_makefile spatialindex-1.8.0 bathymetry debug forward_interfaces libjudy main petsc_makefile_old tests climatology diagnostics h5hut libmba2d main.cpp population_balance tools (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ./configure Hostname: ian-Aspire-One-753 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu configure: Fishing for legacy fortran compiler. checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes configure: Fishing for modern Fortran compiler checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) checking for gawk... gawk configure: * Assuming that gfortran can process both free and fixed form fortran files. checking for icc... no checking for ecc... no checking for suncc... no checking for pgcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for icpc... no checking for icc... no checking for ecc... no checking for sunCC... no checking for pgCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of long int... 8 checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for python... yes checking for python3... /home/ian/miniconda3/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for a version of Python >= '3.6'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/ian/miniconda3/include/python3.9 checking for Python library path... -L/home/ian/miniconda3/lib -lpython3.9 checking for Python site-packages path... /home/ian/miniconda3/lib/python3.9/site-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes Failed to locate Numpy configure: Failed to import (optional) python module assess configure: checking the position of the stars to help find a versions of BLAS checking for builtin sgemm... no checking for sgemm in -lmkl_def... no checking for sgemm in -lmkl_ipf... no checking for sgemm in -lmkl_em64t... no configure: trying Intel MKL < 7: checking for lsame in -lmkl_lapack... no configure: Intel MKL < 7... no checking for sgemm in -lacml... no checking for sgemm in -lf77blas... no checking for sgemm in -lveclib... no configure: trying PhiPACK: checking for sgemm in -lblas... yes checking for dgemm in -ldgemm... no configure: PhiPACK... no checking for sgemm in -lcxml... no checking for sgemm in -ldxml... no checking for sgemm in -lscs... no checking for sgemm in -lcomplib.sgimath... no configure: trying IBM ESSL: checking for sgemm in -lblas... yes checking for sgemm in -lessl... no configure: IBM ESSL... no checking for sgemm in -lblas... yes checking for dsyev in -lmkl_lapack... no checking for dsyev in -lsunperf... no checking for dsyev in BLAS library... no checking for dsyev in -llapack... yes checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking for library containing utInit... no checking "Checking for -funroll-loops"... -funroll-loops works checking "Checking for -fno-realloc-lhs"... -fno-realloc-lhs works, adding to FCFLAGS checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... ranlib configure: Setting optimisation flags for gfortran checking for malloc in -ltcmalloc... no configure: WARNING: No tcmalloc support available. checking for mpif90... mpif90 checking for mpicc... mpicc checking for mpicxx... mpicxx checking if we can compile and link without using -lmpi... yes checking netcdf automagic... no checking for nc_create in -lnetcdf... yes checking for Fortran flag to compile .f90 files... none checking netcdff automagic... no checking for nccre in -lnetcdff... no checking for Fortran flag to compile .f files... none checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes configure: WARNING: No PETSC_DIR set - trying to autodetect configure: Using PETSC_DIR=/usr/lib/petsc configure: Detected PETSc version "3"."12" configure: PETSc modules are working. configure: PETSc program succesfully compiled and linked. checking for library containing PCHYPRESetType... none required checking if we can compile and link without using -lparmetis... no checking metis automagic... no checking for METIS_PartGraphKway in -lmetis... no checking parmetis automagic... no checking for ParMETIS_V3_AdaptiveRepart in -lparmetis... no checking parmetis.h usability... no checking parmetis.h presence... no checking for parmetis.h... no checking how to run the C++ preprocessor... mpicxx -E checking zoltan automagic... no checking for Zoltan_Create in -lzoltan... no configure: Fluidity can be built without zoltan by configuring with the --enable-sam flag. This gives limited functionality when using parallel adaptivity. See the manual for more details. configure: error: in /home/ian/fluidity/fluidity': configure: error: "Could not link with Zoltan library." Seeconfig.log' for more details (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ apt-cache search Zoltan libtrilinos-zoltan-dev - parallel dynamic load balancing - development files libtrilinos-zoltan12 - parallel dynamic load balancing - runtime files libtrilinos-zoltan2-12 - Trilinos next generation load balancing package - runtime files libtrilinos-zoltan2-dev - Trilinos next generation load balancing package - development files pysph-doc - documentation and examples for PySPH pysph-viewer - viewer for PySPH - framework for Smoothed Particle Hydrodynamics python3-pysph - open source framework for Smoothed Particle Hydrodynamics (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ sudo apt install ibtrilinos-zoltan-dev Reading package lists... Done Building dependency tree
Reading state information... Done E: Unable to locate package ibtrilinos-zoltan-dev (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ sudo apt install libtrilinos-zoltan-dev Reading package lists... Done Building dependency tree
Reading state information... Done The following package was automatically installed and is no longer required: libllvm11 Use 'sudo apt autoremove' to remove it. The following additional packages will be installed: libtrilinos-zoltan12 trilinos-dev Suggested packages: trilinos-doc The following NEW packages will be installed: libtrilinos-zoltan-dev libtrilinos-zoltan12 trilinos-dev 0 to upgrade, 3 to newly install, 0 to remove and 19 not to upgrade. Need to get 423 kB of archives. After this operation, 1,253 kB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://archive.ubuntu.com/ubuntu focal/universe amd64 libtrilinos-zoltan12 amd64 12.14.1-3 [379 kB] Get:2 http://archive.ubuntu.com/ubuntu focal/universe amd64 trilinos-dev amd64 12.14.1-3 [12.4 kB] Get:3 http://archive.ubuntu.com/ubuntu focal/universe amd64 libtrilinos-zoltan-dev amd64 12.14.1-3 [31.5 kB] Fetched 423 kB in 2s (186 kB/s)
Selecting previously unselected package libtrilinos-zoltan12:amd64. (Reading database ... 340308 files and directories currently installed.) Preparing to unpack .../libtrilinos-zoltan12_12.14.1-3_amd64.deb ... Unpacking libtrilinos-zoltan12:amd64 (12.14.1-3) ... Selecting previously unselected package trilinos-dev:amd64. Preparing to unpack .../trilinos-dev_12.14.1-3_amd64.deb ... Unpacking trilinos-dev:amd64 (12.14.1-3) ... Selecting previously unselected package libtrilinos-zoltan-dev:amd64. Preparing to unpack .../libtrilinos-zoltan-dev_12.14.1-3_amd64.deb ... Unpacking libtrilinos-zoltan-dev:amd64 (12.14.1-3) ... Setting up libtrilinos-zoltan12:amd64 (12.14.1-3) ... Setting up trilinos-dev:amd64 (12.14.1-3) ... Setting up libtrilinos-zoltan-dev:amd64 (12.14.1-3) ... Processing triggers for libc-bin (2.31-0ubuntu9.2) ... (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ./configure Hostname: ian-Aspire-One-753 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu configure: * Fishing for legacy fortran compiler. checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes configure: Fishing for modern Fortran compiler checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) checking for gawk... gawk configure: Assuming that gfortran can process both free and fixed form fortran files. checking for icc... no checking for ecc... no checking for suncc... no checking for pgcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for icpc... no checking for icc... no checking for ecc... no checking for sunCC... no checking for pgCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of long int... 8 checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for python... yes checking for python3... /home/ian/miniconda3/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for a version of Python >= '3.6'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/ian/miniconda3/include/python3.9 checking for Python library path... -L/home/ian/miniconda3/lib -lpython3.9 checking for Python site-packages path... /home/ian/miniconda3/lib/python3.9/site-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes Failed to locate Numpy configure: Failed to import (optional) python module assess configure: checking the position of the stars to help find a versions of BLAS checking for builtin sgemm... no checking for sgemm in -lmkl_def... no checking for sgemm in -lmkl_ipf... no checking for sgemm in -lmkl_em64t... no configure: trying Intel MKL < 7: checking for lsame in -lmkl_lapack... no configure: Intel MKL < 7... no checking for sgemm in -lacml... no checking for sgemm in -lf77blas... no checking for sgemm in -lveclib... no configure: trying PhiPACK: checking for sgemm in -lblas... yes checking for dgemm in -ldgemm... no configure: PhiPACK... no checking for sgemm in -lcxml... no checking for sgemm in -ldxml... no checking for sgemm in -lscs... no checking for sgemm in -lcomplib.sgimath... no configure: trying IBM ESSL: checking for sgemm in -lblas... yes checking for sgemm in -lessl... no configure: IBM ESSL... no checking for sgemm in -lblas... yes checking for dsyev in -lmkl_lapack... no checking for dsyev in -lsunperf... no checking for dsyev in BLAS library... no checking for dsyev in -llapack... yes checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking for library containing utInit... no checking "Checking for -funroll-loops"... -funroll-loops works checking "Checking for -fno-realloc-lhs"... -fno-realloc-lhs works, adding to FCFLAGS checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... ranlib configure: Setting optimisation flags for gfortran checking for malloc in -ltcmalloc... no configure: WARNING: No tcmalloc support available. checking for mpif90... mpif90 checking for mpicc... mpicc checking for mpicxx... mpicxx checking if we can compile and link without using -lmpi... yes checking netcdf automagic... no checking for nc_create in -lnetcdf... yes checking for Fortran flag to compile .f90 files... none checking netcdff automagic... no checking for nccre in -lnetcdff... no checking for Fortran flag to compile .f files... none checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes configure: WARNING: No PETSC_DIR set - trying to autodetect configure: Using PETSC_DIR=/usr/lib/petsc configure: Detected PETSc version "3"."12" configure: PETSc modules are working. configure: PETSc program succesfully compiled and linked. checking for library containing PCHYPRESetType... none required checking if we can compile and link without using -lparmetis... no checking metis automagic... no checking for METIS_PartGraphKway in -lmetis... no checking parmetis automagic... no checking for ParMETIS_V3_AdaptiveRepart in -lparmetis... no checking parmetis.h usability... no checking parmetis.h presence... no checking for parmetis.h... no checking how to run the C++ preprocessor... mpicxx -E checking zoltan automagic... no checking for Zoltan_Create in -lzoltan... no configure: Fluidity can be built without zoltan by configuring with the --enable-sam flag. This gives limited functionality when using parallel adaptivity. See the manual for more details. configure: error: in /home/ian/fluidity/fluidity': configure: error: "Could not link with Zoltan library." Seeconfig.log' for more details (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ./configure --enable-sam Hostname: ian-Aspire-One-753 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu configure: Fishing for legacy fortran compiler. checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes configure: Fishing for modern Fortran compiler checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) checking for gawk... gawk configure: Assuming that gfortran can process both free and fixed form fortran files. checking for icc... no checking for ecc... no checking for suncc... no checking for pgcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for icpc... no checking for icc... no checking for ecc... no checking for sunCC... no checking for pgCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of long int... 8 checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for python... yes checking for python3... /home/ian/miniconda3/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for a version of Python >= '3.6'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/ian/miniconda3/include/python3.9 checking for Python library path... -L/home/ian/miniconda3/lib -lpython3.9 checking for Python site-packages path... /home/ian/miniconda3/lib/python3.9/site-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes Failed to locate Numpy configure: Failed to import (optional) python module assess configure: checking the position of the stars to help find a versions of BLAS checking for builtin sgemm... no checking for sgemm in -lmkl_def... no checking for sgemm in -lmkl_ipf... no checking for sgemm in -lmkl_em64t... no configure: trying Intel MKL < 7: checking for lsame in -lmkl_lapack... no configure: Intel MKL < 7... no checking for sgemm in -lacml... no checking for sgemm in -lf77blas... no checking for sgemm in -lveclib... no configure: trying PhiPACK: checking for sgemm in -lblas... yes checking for dgemm in -ldgemm... no configure: PhiPACK... no checking for sgemm in -lcxml... no checking for sgemm in -ldxml... no checking for sgemm in -lscs... no checking for sgemm in -lcomplib.sgimath... no configure: trying IBM ESSL: checking for sgemm in -lblas... yes checking for sgemm in -lessl... no configure: IBM ESSL... no checking for sgemm in -lblas... yes checking for dsyev in -lmkl_lapack... no checking for dsyev in -lsunperf... no checking for dsyev in BLAS library... no checking for dsyev in -llapack... yes checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking for library containing utInit... no checking "Checking for -funroll-loops"... -funroll-loops works checking "Checking for -fno-realloc-lhs"... -fno-realloc-lhs works, adding to FCFLAGS checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... ranlib configure: Setting optimisation flags for gfortran checking for malloc in -ltcmalloc... no configure: WARNING: No tcmalloc support available. checking for mpif90... mpif90 checking for mpicc... mpicc checking for mpicxx... mpicxx checking if we can compile and link without using -lmpi... yes checking netcdf automagic... no checking for nc_create in -lnetcdf... yes checking for Fortran flag to compile .f90 files... none checking netcdff automagic... no checking for nccre in -lnetcdff... no checking for Fortran flag to compile .f files... none checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes configure: WARNING: No PETSC_DIR set - trying to autodetect configure: Using PETSC_DIR=/usr/lib/petsc configure: Detected PETSc version "3"."12" configure: PETSc modules are working. configure: PETSc program succesfully compiled and linked. checking for library containing PCHYPRESetType... none required checking if we can compile and link without using -lparmetis... no checking metis automagic... no checking for METIS_PartGraphKway in -lmetis... no checking parmetis automagic... no checking for ParMETIS_V3_AdaptiveRepart in -lparmetis... no checking parmetis.h usability... no checking parmetis.h presence... no checking for parmetis.h... no checking how to run the C++ preprocessor... mpicxx -E checking what voodoo is required to get 64 bit reals....... -fdefault-real-8 -fdefault-double-8 configure: Turning on double 8 byte floating point numbers checking for compiler stream I/O support.... yes checking for compiler signal handling support.... yes configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% configure: Configuring libadaptivity configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ~/fluidity/fluidity/libadaptivity ~/fluidity/fluidity Hostname: ian-Aspire-One-753 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu configure: Fishing for legacy fortran compiler. checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath configure: Fishing for modern Fortran compiler checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath configure: Assuming that gfortran can process both free and fixed form fortran files. checking for icc... no checking for ecc... no checking for suncc... no checking for pgcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for icpc... no checking for icc... no checking for ecc... no checking for sunCC... no checking for pgCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of long int... 8 checking how to get verbose linking output from gfortran... (cached) -v checking for Fortran 77 libraries of gfortran... (cached) -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gfortran... (cached) -v checking for Fortran libraries of gfortran... (cached) -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore configure: checking the position of the stars to help find a versions of BLAS checking for builtin sgemm... no checking for sgemm in -lmkl_def... no checking for sgemm in -lmkl_ipf... no checking for sgemm in -lmkl_em64t... no configure: trying Intel MKL < 7: checking for lsame in -lmkl_lapack... no configure: Intel MKL < 7... no checking for sgemm in -lacml... no checking for sgemm in -lf77blas... no checking for sgemm in -lveclib... no configure: trying PhiPACK: checking for sgemm in -lblas... yes checking for dgemm in -ldgemm... no configure: PhiPACK... no checking for sgemm in -lcxml... no checking for sgemm in -ldxml... no checking for sgemm in -lscs... no checking for sgemm in -lcomplib.sgimath... no configure: trying IBM ESSL: checking for sgemm in -lblas... yes checking for sgemm in -lessl... no configure: IBM ESSL... no checking for sgemm in -lblas... yes checking for dsyev in -lmkl_lapack... no checking for dsyev in -lsunperf... no checking for dsyev in BLAS library... no checking for dsyev in -llapack... yes checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking how to run the C++ preprocessor... g++ -E checking iostream usability... yes checking iostream presence... yes checking for iostream... yes configure: Checking for VTK automagic. configure: VTK automagic works. checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... ranlib configure: Setting optimisation flags for gfortran checking for mpif90... mpif90 checking for mpicc... mpicc checking for mpicxx... mpicxx checking if we can compile and link without using -lmpi... yes checking what voodoo is required to get 64 bit reals....... -fdefault-real-8 configure: Turning on double 8 byte floating point numbers configure: creating ./config.status config.status: creating Makefile config.status: creating load_balance/Makefile config.status: creating adapt3d/Makefile config.status: creating metric_field/Makefile config.status: creating tests/Makefile config.status: creating include/config.h ~/fluidity/fluidity configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% configure: Configuring libjudy configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% checking whether to enable maintainer-specific portions of Makefiles... no checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking which flavor to build... product checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether time.h and sys/time.h may both be included... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for working volatile... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of void ... 8 Detected 64-bit Build Environment checking for error_at_line... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for getpagesize... yes checking for working mmap... yes checking whether lstat dereferences a symlink specified with a trailing slash... yes checking whether stat accepts an empty string... no checking for vprintf... yes checking for _doprnt... no checking for getpagesize... (cached) yes checking for gettimeofday... yes checking for memset... yes checking for munmap... yes checking for pow... no checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strstr... yes checking for strtoul... yes checking for uname... yes checking for ar... ar checking for ld... ld checking for ranlib... ranlib checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... ld checking if the linker (ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for ld option to reload object files... -r checking how to recognize dependent libraries... pass_all checking for ar... (cached) ar checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating ./config.status config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands checking size of void ... 8 configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% configure: Configuring libspud configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... 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(cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate configure: Fishing for legacy fortran compiler. checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fPIC checking if gfortran PIC flag -fPIC works... yes checking if gfortran static flag -static works... yes checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath configure: Fishing for modern Fortran compiler checking whether we are using the GNU Fortran compiler... (cached) yes checking whether gfortran accepts -g... (cached) yes checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath configure: *** Assuming that gfortran can process both free and fixed form fortran files. checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking how to run the C preprocessor... gcc -E checking size of long int... 8 checking how to get verbose linking output from gfortran... (cached) -v checking for Fortran libraries of gfortran... (cached) -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... (cached) ranlib configure: Setting optimisation flags configure: creating ./config.status config.status: creating Makefile config.status: creating src/tests/Makefile config.status: creating examples/Makefile config.status: creating bin/spud-preprocess config.status: creating diamond/setup.py config.status: creating diamond/diamond/plugins.py config.status: creating diamond/diamond/preprocess.py config.status: executing libtool commands configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% configure: Configuring spatialindex configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% checking build system type... x86_64-unknown-linux-gnu checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking how to run the C++ preprocessor... mpicxx -E checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... yes checking host system type... x86_64-unknown-linux-gnu checking how to print strings... printf checking for gcc... mpicc checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from mpicc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... mpicc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC -DPIC checking if mpicc PIC flag -fPIC -DPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking if mpicc supports -c -o file.o... (cached) yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... mpicxx -E checking for ld used by mpicxx... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -DPIC works... yes checking if mpicxx static flag -static works... no checking if mpicxx supports -c -o file.o... yes checking if mpicxx supports -c -o file.o... (cached) yes checking whether the mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether build environment is sane... yes /home/ian/fluidity/fluidity/spatialindex-1.8.0/missing: Unknown --is-lightweight' option Try/home/ian/fluidity/fluidity/spatialindex-1.8.0/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for style of include used by make... GNU checking whether make supports nested variables... yes checking dependency style of mpicc... gcc3 checking dependency style of mpicxx... gcc3 checking whether to enable maintainer-specific portions of Makefiles... no checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for stdint.h... (cached) yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking wether debug information is enabled... no checking for gettimeofday... yes checking for memset... yes checking for memcpy... yes checking for bcopy... yes checking for srand48... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating include/Makefile config.status: creating src/Makefile config.status: creating src/libspatialindex.pc config.status: creating src/capi/Makefile config.status: creating src/spatialindex/Makefile config.status: creating src/storagemanager/Makefile config.status: creating src/rtree/Makefile config.status: creating src/mvrtree/Makefile config.status: creating src/tprtree/Makefile config.status: creating src/tools/Makefile config.status: creating test/Makefile config.status: creating test/rtree/Makefile config.status: creating test/mvrtree/Makefile config.status: creating test/tprtree/Makefile config.status: executing libtool commands config.status: executing depfiles commands checking for a sed that does not truncate output... /usr/bin/sed checking for h5pcc... /usr/bin/h5pcc checking for HDF5 type... parallel checking for HDF5 libraries... yes (version 1.10.4) checking hdf5.h usability... yes checking hdf5.h presence... no configure: WARNING: hdf5.h: accepted by the compiler, rejected by the preprocessor! configure: WARNING: hdf5.h: proceeding with the compiler's result checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... yes checking for main in -lhdf5_hl... yes checking for matching HDF5 Fortran wrapper... /usr/bin/h5pfc configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% configure: Configuring h5hut configure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

• making misc files ...

libtoolize: putting auxiliary files in '..'. libtoolize: linking file '../ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: linking file 'm4/libtool.m4' libtoolize: linking file 'm4/ltoptions.m4' libtoolize: linking file 'm4/ltsugar.m4' libtoolize: linking file 'm4/ltversion.m4' libtoolize: linking file 'm4/lt~obsolete.m4'

• running aclocal ...

• running autoheader ...

• running autoconf ...

• running automake ... configure.ac:138: installing '../compile' configure.ac:13: installing '../missing' examples/H5/Makefile.am: installing '../depcomp' src/Python/Makefile.am:6: installing '../py-compile' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of mpicc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking dependency style of mpicxx... gcc3 checking for mpif90... mpif90 checking whether we are using the GNU Fortran compiler... yes checking whether mpif90 accepts -g... yes checking whether /usr/bin/mpicxx supports C++11 features by default... yes checking for /usr/bin/mpicc option to accept ISO C99... none needed checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking whether make sets $(MAKE)... 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BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from /usr/bin/mpicc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... /usr/bin/mpicc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if /usr/bin/mpicc supports -fno-rtti -fno-exceptions... no checking for /usr/bin/mpicc option to produce PIC... -fPIC -DPIC checking if /usr/bin/mpicc PIC flag -fPIC -DPIC works... yes checking if /usr/bin/mpicc static flag -static works... no checking if /usr/bin/mpicc supports -c -o file.o... yes checking if /usr/bin/mpicc supports -c -o file.o... (cached) yes checking whether the /usr/bin/mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... 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(cached) yes checking whether the /usr/bin/mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for /usr/bin/mpif90 option to produce PIC... -fPIC checking if /usr/bin/mpif90 PIC flag -fPIC works... yes checking if /usr/bin/mpif90 static flag -static works... no checking if /usr/bin/mpif90 supports -c -o file.o... yes checking if /usr/bin/mpif90 supports -c -o file.o... (cached) yes checking whether the /usr/bin/mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for size_t... yes checking for ssize_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for ptrdiff_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for compress2 in -lz... yes checking for H5open in -lhdf5... yes checking checking whether hdf5 lib supports parallel IO... yes checking for lustre API ... checking looking in /usr ... ... no checking looking in /usr/local ... ... no checking looking in /usr/local/lustre ... ... no checking looking in /opt/lustre ... ... no configure: WARNING: Couldn't locate the lustre API... building without support for lustre striping! checking if C interface enabled... yes checking if fortran interface enabled... yes checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking if python interface is enabled... no checking if large indices are enabled... no checking if parallel interface enabled... yes checking if we have to compile the VTK to H5hut grid converter... no checking if we have to compile the H5hut examples... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/h5core/Makefile config.status: creating src/include/Makefile config.status: creating src/include/h5core/Makefile config.status: creating src/C/Makefile config.status: creating src/Fortran/Makefile config.status: creating src/Python/Makefile config.status: creating test/Makefile config.status: creating doc/Makefile config.status: creating tools/Makefile config.status: creating tools/h5hutcc config.status: creating tools/vtk2h5grid/Makefile config.status: creating examples/H5/Makefile config.status: creating examples/H5Part/Makefile config.status: creating examples/H5Block/Makefile config.status: creating examples/H5Fed/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands

Summary:

Host OS: linux-gnu Host CPU: x86_64 Host vendor: unknown CC = /usr/bin/mpicc CXX = /usr/bin/mpicxx FC = /usr/bin/mpif90 CFLAGS = -Wall -O3 FFLAGS = -Wall -O3 AM_CPPFLAGS = -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK AM_LDFLAGS = -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi LIBS = -lhdf5 -lz -lhdf5_hl -lhdf5 -lsz -lz -ldl -lm -lm HDF5_PREFIX =
LUSTREROOT =

checking arpack automagic... no checking for dsaupd in -larpack... no configure: Checking for VTK automagic. configure: VTK automagic works. checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep configure: creating ./config.status config.status: creating Makefile config.status: creating debug/Makefile config.status: creating bathymetry/Makefile config.status: creating ocean_forcing/Makefile config.status: creating ocean_forcing/tests/Makefile config.status: creating sediments/Makefile config.status: creating population_balance/Makefile config.status: creating hyperlight/Makefile config.status: creating femtools/Makefile config.status: creating femtools/tests/Makefile config.status: creating forward_interfaces/Makefile config.status: creating horizontal_adaptivity/Makefile config.status: creating horizontal_adaptivity/tests/Makefile config.status: creating preprocessor/Makefile config.status: creating error_measures/Makefile config.status: creating error_measures/tests/Makefile config.status: creating parameterisation/Makefile config.status: creating parameterisation/tests/Makefile config.status: creating fldecomp/Makefile config.status: creating assemble/Makefile config.status: creating assemble/tests/Makefile config.status: creating diagnostics/Makefile config.status: creating main/Makefile config.status: creating tools/Makefile config.status: creating tools/version-info config.status: creating python/setup.py config.status: creating climatology/Makefile config.status: creating libmba2d/Makefile config.status: creating libmba3d/Makefile config.status: creating libjudy/Makefile config.status: creating libjudy/src/Makefile config.status: creating libjudy/src/JudyCommon/Makefile config.status: creating libjudy/src/Judy1/Makefile config.status: creating libjudy/src/JudyL/Makefile config.status: creating libjudy/src/JudySL/Makefile config.status: creating libjudy/src/JudyHS/Makefile config.status: creating libwm/Makefile config.status: creating libvtkfortran/Makefile config.status: creating tests/tools.mk config.status: creating include/config.h (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ls 4.1.19.tar.gz config.guess docker include LICENSE ocean_forcing sediments aclocal.m4 config.log error_measures INSTALL ltmain.sh parameterisation spatialindex-1.8.0 acx_blas.m4 config.status examples install-sh m4 petsc_makefile tests acx_lapack.m4 config.sub femtools libadaptivity main petsc_makefile_old tools assemble configure fldecomp libjudy main.cpp population_balance AUTHORS configure.in fluidity-4.1.19 libmba2d Makefile preprocessor bathymetry debian forward_interfaces libmba3d Makefile.in py-compile climatology debug h5hut libspud manual python CMakeFiles depcomp horizontal_adaptivity libvtkfortran mayavi README compile diagnostics hyperlight libwm missing schemas (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ make DEFINE __FLUIDITY_VERSION MKDIR lib echo ' MAKE libspud'; make -s -C libspud && make -s -C libspud install-libspud && cd libspud/python && python3 setup.py build && cd ../.. && cp libspud/python/build/lib/libspud.so python/ MAKE libspud libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/spud.cpp -fPIC -DPIC -o .libs/spud.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/spud.cpp -o spud.o >/dev/null 2>&1 libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/spud_interfaces.cpp -fPIC -DPIC -o .libs/spud_interfaces.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/spud_interfaces.cpp -o spud_interfaces.o >/dev/null 2>&1 libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinystr.cpp -fPIC -DPIC -o .libs/tinystr.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinystr.cpp -o tinystr.o >/dev/null 2>&1 libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxml.cpp -fPIC -DPIC -o .libs/tinyxml.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxml.cpp -o tinyxml.o >/dev/null 2>&1 libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxmlerror.cpp -fPIC -DPIC -o .libs/tinyxmlerror.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxmlerror.cpp -o tinyxmlerror.o >/dev/null 2>&1 libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxmlparser.cpp -fPIC -DPIC -o .libs/tinyxmlparser.o libtool: compile: g++ -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -c src/tinyxmlparser.cpp -o tinyxmlparser.o >/dev/null 2>&1 libtool: compile: gfortran -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -ffast-math -frecord-marker=4 -I/usr/include -ffree-line-length-none -ffixed-line-length-none -c src/fspud.f90 -fPIC -o .libs/fspud.o libtool: compile: gfortran -Iinclude -DUSING_GFORTRAN=1 -DNDEBUG=1 -O3 -ffast-math -frecord-marker=4 -I/usr/include -ffree-line-length-none -ffixed-line-length-none -c src/fspud.f90 -o fspud.o >/dev/null 2>&1 libtool: link: gfortran -shared -fPIC .libs/spud.o .libs/spud_interfaces.o .libs/tinystr.o .libs/tinyxml.o .libs/tinyxmlerror.o .libs/tinyxmlparser.o .libs/fspud.o -lpthread -lstdc++ -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lquadmath -lm -lc -lgcc_s -O3 -Wl,-soname -Wl,libspud.so.0 -o .libs/libspud.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libspud.so.0" && ln -s "libspud.so.0.0.0" "libspud.so.0") libtool: link: (cd ".libs" && rm -f "libspud.so" && ln -s "libspud.so.0.0.0" "libspud.so") libtool: link: ar cru .libs/libspud.a spud.o spud_interfaces.o tinystr.o tinyxml.o tinyxmlerror.o tinyxmlparser.o fspud.o ar: u' modifier ignored sinceD' is the default (see `U') libtool: link: ranlib .libs/libspud.a libtool: link: ( cd ".libs" && rm -f "libspud.la" && ln -s "../libspud.la" "libspud.la" ) running build running build_py creating build creating build/lib creating build/lib/diamond copying diamond/attributewidget.py -> build/lib/diamond copying diamond/dialogs.py -> build/lib/diamond copying diamond/triangle_reader.py -> build/lib/diamond copying diamond/datawidget.py -> build/lib/diamond copying diamond/config.py -> build/lib/diamond copying diamond/preprocess.py -> build/lib/diamond copying diamond/plist.py -> build/lib/diamond copying diamond/descriptionwidget.py -> build/lib/diamond copying diamond/schemausage.py -> build/lib/diamond copying diamond/tree.py -> build/lib/diamond copying diamond/mixedtree.py -> build/lib/diamond copying diamond/plugins.py -> build/lib/diamond copying diamond/diffview.py -> build/lib/diamond copying diamond/scherror.py -> build/lib/diamond copying diamond/init__.py -> build/lib/diamond copying diamond/debug.py -> build/lib/diamond copying diamond/choice.py -> build/lib/diamond copying diamond/databuttonswidget.py -> build/lib/diamond copying diamond/pygtkconsole.py -> build/lib/diamond copying diamond/commentwidget.py -> build/lib/diamond copying diamond/interface.py -> build/lib/diamond copying diamond/useview.py -> build/lib/diamond copying diamond/datatype.py -> build/lib/diamond copying diamond/sliceview.py -> build/lib/diamond copying diamond/schema.py -> build/lib/diamond running build_scripts creating build/scripts-3.9 copying and adjusting bin/diamond -> build/scripts-3.9 changing mode of build/scripts-3.9/diamond from 664 to 775 /home/ian/fluidity/fluidity/libspud running build running build_ext building 'libspud' extension creating build creating build/temp.linux-x86_64-3.9 gcc -pthread -B /home/ian/miniconda3/compiler_compat -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /home/ian/miniconda3/include -fPIC -O2 -isystem /home/ian/miniconda3/include -fPIC -I/home/ian/fluidity/fluidity/libspud/include -I/home/ian/miniconda3/include/python3.9 -c libspud.c -o build/temp.linux-x86_64-3.9/libspud.o libspud.c: In function ‘set_option_aux_string’: libspud.c:12:27: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 12 | #define PyString_AsString PyUnicode_AsUTF8 | ^~~~ libspud.c:565:17: note: in expansion of macro ‘PyString_AsString’ 565 | char val = PyString_AsString(pystring); | ^~~~~ libspud.c: In function ‘libspud_set_option’: libspud.c:716:9: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 716 | shape[0] = PyString_GET_SIZE(secondArg); | ^~~~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from libspud.c:1: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ libspud.c:716:9: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 716 | shape[0] = PyString_GET_SIZE(secondArg); | ^~~~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from libspud.c:1: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE ) PyUnicode_AsUnicode( | ^~~~~~~ libspud.c:716:9: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 716 | shape[0] = PyString_GET_SIZE(secondArg); | ^~~~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from libspud.c:1: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ creating build/lib.linux-x86_64-3.9 gcc -pthread -B /home/ian/miniconda3/compiler_compat -Wl,--sysroot=/ -shared -Wl,-rpath,/home/ian/miniconda3/lib -Wl,-rpath-link,/home/ian/miniconda3/lib -L/home/ian/miniconda3/lib -Wl,-rpath,/home/ian/miniconda3/lib -Wl,-rpath-link,/home/ian/miniconda3/lib -L/home/ian/miniconda3/lib build/temp.linux-x86_64-3.9/libspud.o -L/home/ian/fluidity/fluidity/libspud -lspud -o build/lib.linux-x86_64-3.9/libspud.cpython-39-x86_64-linux-gnu.so CXX main.cpp mpicxx -I/home/ian/miniconda3/include/python3.9 -I/usr/lib/petscdir/petsc3.12/x86_64-linux-gnu-real/include -I/usr/include/hypre -I/usr/include/suitesparse -I/usr/include/superlu -I/usr/include/superlu-dist -I/usr/include/scotch -I/usr/include/hdf5/openmpi -I/home/ian/fluidity/fluidity/include/ -DHAVE_PETSC -I/usr/include/vtk-7.1 -I/usr/include/freetype2 -I/usr/include -I/usr/include/x86_64-linux-gnu -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/include/python3.8 -I/usr/include/hdf5/openmpi -I/usr/include/jsoncpp -I/usr/include/libxml2 -I/usr/include/tcl -DHAVE_VTK -I/home/ian/miniconda3/include/python3.9 -O3 -I./include -c main.cpp MKDIR lib MAKE libadaptivity ar: creating ../lib/libadaptivity.a a - Debug.o a - AdaptProgress.o a - write_log.o a - adapt1.o a - addedg.o a - addele.o a - addfac.o a - addnd.o a - adfrnd.o a - adptvy.o a - angedg.o a - angfac.o a - chkfac.o a - chkgmy.o a - cmlced.o a - cmneds.o a - cmnnod.o a - cnctel.o a - cnctfc.o a - dofacs.o a - edg2fc.o a - edg3nd.o a - edg4nd.o a - edgdst.o a - edgeig.o a - edgels.o a - edgfnc.o a - edginf.o a - edgtst.o a - elmdiv.o a - elmeig.o a - elmfnc.o a - elminf.o a - elmtst.o a - elnods.o a - elstst.o a - facinf.o a - facnrm.o a - fc2edg.o a - fchsnd.o a - fixeig.o a - fndedg.o a - fndelm.o a - fndsrf.o a - getflg.o a - getmsh.o a - getsiz.o a - gtfrfl.o a - gtndfl.o a - hasedg.o a - adaptmem.o a - hasnod.o a - inipwr.o a - inirls.o a - initim.o a - initls.o a - intfld.o a - intrpl.o a - lenedg.o a - lisbig.o a - lstels.o a - lstfac.o a - lstnds.o a - lstout.o a - minang.o a - mk1ele.o a - mkadpt.o a - mkecls.o a - mkfixd.o a - mkfrnt.o a - mkncls.o a - mknels.o a - mshout.o a - ndcnct.o a - nodeig.o a - nodfcs.o a - nodmov.o a - nodtst.o a - nxtid.o a - oppedg.o a - ordnds.o a - qlyout.o a - rmfrnd.o a - rmvedg.o a - rmvele.o a - rmvfac.o a - rmvnd.o a - rmvnxt.o a - rspnse.o a - second.o a - sectlp.o a - setflg.o a - setgmy.o a - shredg.o a - shwhst.o a - shwtim.o a - spledg.o a - stchfr.o a - stfrfl.o a - stfrgm.o a - stndfl.o a - mtetin.o a - tetvol.o a - undstt.o a - vals3d.o a - invrse.o a - chkint.o a - assval.o a - nwcnel.o a - wchfac.o a - chgeds.o a - Adaptivity.o a - expected_elements.o a - Flag_Handling.o ./src/Mesh.cpp: In member function ‘samfloat_t Mesh::idealElementDensity(unsigned int)’: ./src/Mesh.cpp:785:1: warning: control reaches end of non-void function [-Wreturn-type] 785 | } | ^ a - MetricTensor.o a - ErrorMeasure.o a - DiscreteGeometryConstraints.o MKDIR lib echo ' MAKE libvtkfortran'; make -s -C libvtkfortran 2>make.log 2>&1 && cp libvtkfortran/libvtkfortran.a lib/ && cp libvtkfortran/*.mod include/ MAKE libvtkfortran MKDIR lib echo ' MAKE libspatialindex'; make -s -C spatialindex-1.8.0 && make -s -C spatialindex-1.8.0 install >> make.log 2>&1 MAKE libspatialindex Making all in src Making all in storagemanager libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Buffer.lo -MD -MP -MF .deps/Buffer.Tpo -c Buffer.cc -o Buffer.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT DiskStorageManager.lo -MD -MP -MF .deps/DiskStorageManager.Tpo -c DiskStorageManager.cc -o DiskStorageManager.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT MemoryStorageManager.lo -MD -MP -MF .deps/MemoryStorageManager.Tpo -c MemoryStorageManager.cc -o MemoryStorageManager.o MemoryStorageManager.cc: In member function 'virtual void SpatialIndex::StorageManager::MemoryStorageManager::loadByteArray(SpatialIndex::id_type, uint32_t&, byte*)': MemoryStorageManager.cc:70:14: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=] 70 | catch (std::out_of_range) | ^~~~ MemoryStorageManager.cc: In member function 'virtual void SpatialIndex::StorageManager::MemoryStorageManager::storeByteArray(SpatialIndex::id_type&, uint32_t, const byte)': MemoryStorageManager.cc:106:15: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=] 106 | catch (std::out_of_range) | ^~~~ MemoryStorageManager.cc: In member function 'virtual void SpatialIndex::StorageManager::MemoryStorageManager::deleteByteArray(SpatialIndex::id_type)': MemoryStorageManager.cc:126:14: warning: catching polymorphic type 'class std::out_of_range' by value [-Wcatch-value=] 126 | catch (std::out_of_range) | ^~~~ libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT RandomEvictionsBuffer.lo -MD -MP -MF .deps/RandomEvictionsBuffer.Tpo -c RandomEvictionsBuffer.cc -o RandomEvictionsBuffer.o libtool: link: ar cru .libs/libstoragemanager.a Buffer.o DiskStorageManager.o MemoryStorageManager.o RandomEvictionsBuffer.o ar: u' modifier ignored sinceD' is the default (see U') libtool: link: ranlib .libs/libstoragemanager.a libtool: link: ( cd ".libs" && rm -f "libstoragemanager.la" && ln -s "../libstoragemanager.la" "libstoragemanager.la" ) Making all in spatialindex libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Point.lo -MD -MP -MF .deps/Point.Tpo -c Point.cc -o Point.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Region.lo -MD -MP -MF .deps/Region.Tpo -c Region.cc -o Region.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT LineSegment.lo -MD -MP -MF .deps/LineSegment.Tpo -c LineSegment.cc -o LineSegment.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT MovingPoint.lo -MD -MP -MF .deps/MovingPoint.Tpo -c MovingPoint.cc -o MovingPoint.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT MovingRegion.lo -MD -MP -MF .deps/MovingRegion.Tpo -c MovingRegion.cc -o MovingRegion.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT TimePoint.lo -MD -MP -MF .deps/TimePoint.Tpo -c TimePoint.cc -o TimePoint.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT TimeRegion.lo -MD -MP -MF .deps/TimeRegion.Tpo -c TimeRegion.cc -o TimeRegion.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT SpatialIndexImpl.lo -MD -MP -MF .deps/SpatialIndexImpl.Tpo -c SpatialIndexImpl.cc -o SpatialIndexImpl.o libtool: link: ar cru .libs/liblibrary.a Point.o Region.o LineSegment.o MovingPoint.o MovingRegion.o TimePoint.o TimeRegion.o SpatialIndexImpl.o ar:u' modifier ignored since D' is the default (seeU') libtool: link: ranlib .libs/liblibrary.a libtool: link: ( cd ".libs" && rm -f "liblibrary.la" && ln -s "../liblibrary.la" "liblibrary.la" ) Making all in rtree libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT BulkLoader.lo -MD -MP -MF .deps/BulkLoader.Tpo -c BulkLoader.cc -o BulkLoader.o BulkLoader.cc: In member function 'void SpatialIndex::RTree::ExternalSorter::sort()': BulkLoader.cc:221:20: warning: catching polymorphic type 'class Tools::EndOfStreamException' by value [-Wcatch-value=] 221 | catch (Tools::EndOfStreamException) | ^~~~~~~~ BulkLoader.cc:247:21: warning: catching polymorphic type 'class Tools::EndOfStreamException' by value [-Wcatch-value=] 247 | catch (Tools::EndOfStreamException) | ^~~~~~~~ BulkLoader.cc: In member function 'void SpatialIndex::RTree::BulkLoader::createLevel(SpatialIndex::RTree::RTree*, Tools::SmartPointer, uint32_t, uint32_t, uint32_t, uint32_t, Tools::SmartPointer, uint32_t, uint32_t)': BulkLoader.cc:397:51: warning: catching polymorphic type 'class Tools::EndOfStreamException' by value [-Wcatch-value=] 397 | try { r = es->getNextRecord(); } catch (Tools::EndOfStreamException) { break; } | ^~~~~~~~ BulkLoader.cc:433:19: warning: catching polymorphic type 'class Tools::EndOfStreamException' by value [-Wcatch-value=] 433 | catch (Tools::EndOfStreamException) { bMore = false; break; } | ^~~~~~~~ libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Index.lo -MD -MP -MF .deps/Index.Tpo -c Index.cc -o Index.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Leaf.lo -MD -MP -MF .deps/Leaf.Tpo -c Leaf.cc -o Leaf.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Node.lo -MD -MP -MF .deps/Node.Tpo -c Node.cc -o Node.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT RTree.lo -MD -MP -MF .deps/RTree.Tpo -c RTree.cc -o RTree.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Statistics.lo -MD -MP -MF .deps/Statistics.Tpo -c Statistics.cc -o Statistics.o libtool: link: ar cru .libs/librtree.a BulkLoader.o Index.o Leaf.o Node.o RTree.o Statistics.o ar: u' modifier ignored sinceD' is the default (see U') libtool: link: ranlib .libs/librtree.a libtool: link: ( cd ".libs" && rm -f "librtree.la" && ln -s "../librtree.la" "librtree.la" ) Making all in mvrtree libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Index.lo -MD -MP -MF .deps/Index.Tpo -c Index.cc -o Index.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Leaf.lo -MD -MP -MF .deps/Leaf.Tpo -c Leaf.cc -o Leaf.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Node.lo -MD -MP -MF .deps/Node.Tpo -c Node.cc -o Node.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT MVRTree.lo -MD -MP -MF .deps/MVRTree.Tpo -c MVRTree.cc -o MVRTree.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Statistics.lo -MD -MP -MF .deps/Statistics.Tpo -c Statistics.cc -o Statistics.o libtool: link: ar cru .libs/libmvrtree.a Index.o Leaf.o Node.o MVRTree.o Statistics.o ar:u' modifier ignored since D' is the default (seeU') libtool: link: ranlib .libs/libmvrtree.a libtool: link: ( cd ".libs" && rm -f "libmvrtree.la" && ln -s "../libmvrtree.la" "libmvrtree.la" ) Making all in tprtree libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Index.lo -MD -MP -MF .deps/Index.Tpo -c Index.cc -o Index.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Leaf.lo -MD -MP -MF .deps/Leaf.Tpo -c Leaf.cc -o Leaf.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Node.lo -MD -MP -MF .deps/Node.Tpo -c Node.cc -o Node.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT TPRTree.lo -MD -MP -MF .deps/TPRTree.Tpo -c TPRTree.cc -o TPRTree.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Statistics.lo -MD -MP -MF .deps/Statistics.Tpo -c Statistics.cc -o Statistics.o libtool: link: ar cru .libs/libtprtree.a Index.o Leaf.o Node.o TPRTree.o Statistics.o ar: u' modifier ignored sinceD' is the default (see U') libtool: link: ranlib .libs/libtprtree.a libtool: link: ( cd ".libs" && rm -f "libtprtree.la" && ln -s "../libtprtree.la" "libtprtree.la" ) Making all in tools libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Tools.lo -MD -MP -MF .deps/Tools.Tpo -c Tools.cc -o Tools.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT rand48.lo -MD -MP -MF .deps/rand48.Tpo -c rand48.cc -o rand48.o libtool: link: ar cru .libs/libtools.a Tools.o rand48.o ar:u' modifier ignored since D' is the default (seeU') libtool: link: ranlib .libs/libtools.a libtool: link: ( cd ".libs" && rm -f "libtools.la" && ln -s "../libtools.la" "libtools.la" ) Making all in capi libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT BoundsQuery.lo -MD -MP -MF .deps/BoundsQuery.Tpo -c BoundsQuery.cc -o BoundsQuery.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT CountVisitor.lo -MD -MP -MF .deps/CountVisitor.Tpo -c CountVisitor.cc -o CountVisitor.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT CustomStorage.lo -MD -MP -MF .deps/CustomStorage.Tpo -c CustomStorage.cc -o CustomStorage.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT DataStream.lo -MD -MP -MF .deps/DataStream.Tpo -c DataStream.cc -o DataStream.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Error.lo -MD -MP -MF .deps/Error.Tpo -c Error.cc -o Error.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT IdVisitor.lo -MD -MP -MF .deps/IdVisitor.Tpo -c IdVisitor.cc -o IdVisitor.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Index.lo -MD -MP -MF .deps/Index.Tpo -c Index.cc -o Index.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT LeafQuery.lo -MD -MP -MF .deps/LeafQuery.Tpo -c LeafQuery.cc -o LeafQuery.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT ObjVisitor.lo -MD -MP -MF .deps/ObjVisitor.Tpo -c ObjVisitor.cc -o ObjVisitor.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT sidx_api.lo -MD -MP -MF .deps/sidx_api.Tpo -c sidx_api.cc -o sidx_api.o libtool: compile: mpicxx -DPACKAGE_NAME=\"spatialindex\" -DPACKAGE_TARNAME=\"spatialindex-src\" -DPACKAGE_VERSION=\"1.8.0\" -DPACKAGE_STRING=\"spatialindex_1.8.0\" -DPACKAGE_BUGREPORT=\"mhadji@gmail.com\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DPACKAGE=\"spatialindex-src\" -DVERSION=\"1.8.0\" -DHAVE_FCNTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_PTHREAD_H=1 -DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_TIME_H=1 -DHAVE_STDINT_H=1 -DHAVE_FEATURES_H=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_MEMSET=1 -DHAVE_MEMCPY=1 -DHAVE_BCOPY=1 -DHAVE_SRAND48=1 -I. -I../../include -I../../include/capi -D_GNU_SOURCE -Wall -Wno-long-long -pedantic -std=c++98 -O2 -DNDEBUG -MT Utility.lo -MD -MP -MF .deps/Utility.Tpo -c Utility.cc -o Utility.o libtool: link: ar cru .libs/libsidxc.a BoundsQuery.o CountVisitor.o CustomStorage.o DataStream.o Error.o IdVisitor.o Index.o LeafQuery.o ObjVisitor.o sidx_api.o Utility.o ar: u' modifier ignored sinceD' is the default (see U') libtool: link: ranlib .libs/libsidxc.a libtool: link: ( cd ".libs" && rm -f "libsidxc.la" && ln -s "../libsidxc.la" "libsidxc.la" ) Making all in . libtool: link: (cd .libs/libspatialindex.lax/liblibrary.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/spatialindex/.libs/liblibrary.a") libtool: link: (cd .libs/libspatialindex.lax/libstoragemanager.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/storagemanager/.libs/libstoragemanager.a") libtool: link: (cd .libs/libspatialindex.lax/librtree.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/rtree/.libs/librtree.a") libtool: link: (cd .libs/libspatialindex.lax/libmvrtree.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/mvrtree/.libs/libmvrtree.a") libtool: link: (cd .libs/libspatialindex.lax/libtprtree.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/tprtree/.libs/libtprtree.a") libtool: link: (cd .libs/libspatialindex.lax/libtools.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/tools/.libs/libtools.a") copying selected object files to avoid basename conflicts... libtool: link: ln .libs/libspatialindex.lax/libmvrtree.a/Index.o .libs/libspatialindex.lax/lt1-Index.o || cp .libs/libspatialindex.lax/libmvrtree.a/Index.o .libs/libspatialindex.lax/lt1-Index.o libtool: link: ln .libs/libspatialindex.lax/libmvrtree.a/Leaf.o .libs/libspatialindex.lax/lt2-Leaf.o || cp .libs/libspatialindex.lax/libmvrtree.a/Leaf.o .libs/libspatialindex.lax/lt2-Leaf.o libtool: link: ln .libs/libspatialindex.lax/libmvrtree.a/Node.o .libs/libspatialindex.lax/lt3-Node.o || cp .libs/libspatialindex.lax/libmvrtree.a/Node.o .libs/libspatialindex.lax/lt3-Node.o libtool: link: ln .libs/libspatialindex.lax/libmvrtree.a/Statistics.o .libs/libspatialindex.lax/lt4-Statistics.o || cp .libs/libspatialindex.lax/libmvrtree.a/Statistics.o .libs/libspatialindex.lax/lt4-Statistics.o libtool: link: ln .libs/libspatialindex.lax/libtprtree.a/Index.o .libs/libspatialindex.lax/lt5-Index.o || cp .libs/libspatialindex.lax/libtprtree.a/Index.o .libs/libspatialindex.lax/lt5-Index.o libtool: link: ln .libs/libspatialindex.lax/libtprtree.a/Leaf.o .libs/libspatialindex.lax/lt6-Leaf.o || cp .libs/libspatialindex.lax/libtprtree.a/Leaf.o .libs/libspatialindex.lax/lt6-Leaf.o libtool: link: ln .libs/libspatialindex.lax/libtprtree.a/Node.o .libs/libspatialindex.lax/lt7-Node.o || cp .libs/libspatialindex.lax/libtprtree.a/Node.o .libs/libspatialindex.lax/lt7-Node.o libtool: link: ln .libs/libspatialindex.lax/libtprtree.a/Statistics.o .libs/libspatialindex.lax/lt8-Statistics.o || cp .libs/libspatialindex.lax/libtprtree.a/Statistics.o .libs/libspatialindex.lax/lt8-Statistics.o libtool: link: ar cru .libs/libspatialindex.a .libs/libspatialindex.lax/liblibrary.a/LineSegment.o .libs/libspatialindex.lax/liblibrary.a/MovingPoint.o .libs/libspatialindex.lax/liblibrary.a/MovingRegion.o .libs/libspatialindex.lax/liblibrary.a/Point.o .libs/libspatialindex.lax/liblibrary.a/Region.o .libs/libspatialindex.lax/liblibrary.a/SpatialIndexImpl.o .libs/libspatialindex.lax/liblibrary.a/TimePoint.o .libs/libspatialindex.lax/liblibrary.a/TimeRegion.o .libs/libspatialindex.lax/libstoragemanager.a/Buffer.o .libs/libspatialindex.lax/libstoragemanager.a/DiskStorageManager.o .libs/libspatialindex.lax/libstoragemanager.a/MemoryStorageManager.o .libs/libspatialindex.lax/libstoragemanager.a/RandomEvictionsBuffer.o .libs/libspatialindex.lax/librtree.a/BulkLoader.o .libs/libspatialindex.lax/librtree.a/Index.o .libs/libspatialindex.lax/librtree.a/Leaf.o .libs/libspatialindex.lax/librtree.a/Node.o .libs/libspatialindex.lax/librtree.a/RTree.o .libs/libspatialindex.lax/librtree.a/Statistics.o .libs/libspatialindex.lax/lt1-Index.o .libs/libspatialindex.lax/lt2-Leaf.o .libs/libspatialindex.lax/libmvrtree.a/MVRTree.o .libs/libspatialindex.lax/lt3-Node.o .libs/libspatialindex.lax/lt4-Statistics.o .libs/libspatialindex.lax/lt5-Index.o .libs/libspatialindex.lax/lt6-Leaf.o .libs/libspatialindex.lax/lt7-Node.o .libs/libspatialindex.lax/lt8-Statistics.o .libs/libspatialindex.lax/libtprtree.a/TPRTree.o .libs/libspatialindex.lax/libtools.a/Tools.o .libs/libspatialindex.lax/libtools.a/rand48.o ar:u' modifier ignored since D' is the default (seeU') libtool: link: ranlib .libs/libspatialindex.a libtool: link: rm -fr .libs/libspatialindex.lax .libs/libspatialindex.lax libtool: link: ( cd ".libs" && rm -f "libspatialindex.la" && ln -s "../libspatialindex.la" "libspatialindex.la" ) libtool: link: (cd .libs/libspatialindex_c.lax/libsidxc.a && ar x "/home/ian/fluidity/fluidity/spatialindex-1.8.0/src/capi/.libs/libsidxc.a") libtool: link: ar cru .libs/libspatialindex_c.a .libs/libspatialindex_c.lax/libsidxc.a/BoundsQuery.o .libs/libspatialindex_c.lax/libsidxc.a/CountVisitor.o .libs/libspatialindex_c.lax/libsidxc.a/CustomStorage.o .libs/libspatialindex_c.lax/libsidxc.a/DataStream.o .libs/libspatialindex_c.lax/libsidxc.a/Error.o .libs/libspatialindex_c.lax/libsidxc.a/IdVisitor.o .libs/libspatialindex_c.lax/libsidxc.a/Index.o .libs/libspatialindex_c.lax/libsidxc.a/LeafQuery.o .libs/libspatialindex_c.lax/libsidxc.a/ObjVisitor.o .libs/libspatialindex_c.lax/libsidxc.a/Utility.o .libs/libspatialindex_c.lax/libsidxc.a/sidx_api.o ar: u' modifier ignored sinceD' is the default (see `U') libtool: link: ranlib .libs/libspatialindex_c.a libtool: link: rm -fr .libs/libspatialindex_c.lax libtool: link: ( cd ".libs" && rm -f "libspatialindex_c.la" && ln -s "../libspatialindex_c.la" "libspatialindex_c.la" ) Making all in include MKDIR lib echo ' MAKE h5hut'; make -s -C h5hut install-exec install-data && cp include/H5hut.f90 femtools/H5hut.F90 MAKE h5hut Making install-exec in src Making install-exec in Fortran libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c H5.c -o H5.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5_attribs.lo -MD -MP -MF .deps/H5_attribs.Tpo -c H5_attribs.c -o H5_attribs.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5_model.lo -MD -MP -MF .deps/H5_model.Tpo -c H5_model.c -o H5_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5Part_model.lo -MD -MP -MF .deps/H5Part_model.Tpo -c H5Part_model.c -o H5Part_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5Part_io.lo -MD -MP -MF .deps/H5Part_io.Tpo -c H5Part_io.c -o H5Part_io.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5Block_model.lo -MD -MP -MF .deps/H5Block_model.Tpo -c H5Block_model.c -o H5Block_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5Block_attribs.lo -MD -MP -MF .deps/H5Block_attribs.Tpo -c H5Block_attribs.c -o H5Block_attribs.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT H5Block_io.lo -MD -MP -MF .deps/H5Block_io.Tpo -c H5Block_io.c -o H5Block_io.o libtool: link: ar cr .libs/libH5hutF.a H5.o H5_attribs.o H5_model.o H5Part_model.o H5Part_io.o H5Block_model.o H5Block_attribs.o H5Block_io.o libtool: link: ranlib .libs/libH5hutF.a libtool: link: ( cd ".libs" && rm -f "libH5hutF.la" && ln -s "../libH5hutF.la" "libH5hutF.la" ) /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libH5hutF.la '/home/ian/fluidity/fluidity/h5hut/../lib' libtool: install: /usr/bin/install -c .libs/libH5hutF.lai /home/ian/fluidity/fluidity/h5hut/../lib/libH5hutF.la libtool: install: /usr/bin/install -c .libs/libH5hutF.a /home/ian/fluidity/fluidity/h5hut/../lib/libH5hutF.a libtool: install: chmod 644 /home/ian/fluidity/fluidity/h5hut/../lib/libH5hutF.a libtool: install: ranlib /home/ian/fluidity/fluidity/h5hut/../lib/libH5hutF.a libtool: finish: PATH="/home/ian/miniconda3/bin:/home/ian/miniconda3/condabin:/home/ian/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sbin" ldconfig -n /home/ian/fluidity/fluidity/h5hut/../lib

Libraries have been installed in: /home/ian/fluidity/fluidity/h5hut/../lib

If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following:

• add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution
• add LIBDIR to the 'LD_RUN_PATH' environment variable during linking
• use the '-Wl,-rpath -Wl,LIBDIR' linker flag
• have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages.

Making install-exec in h5core libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_attachments.lo -MD -MP -MF .deps/h5_attachments.Tpo -c h5_attachments.c -o h5_attachments.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_attribs.lo -MD -MP -MF .deps/h5_attribs.Tpo -c h5_attribs.c -o h5_attribs.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_err.lo -MD -MP -MF .deps/h5_err.Tpo -c h5_err.c -o h5_err.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_log.lo -MD -MP -MF .deps/h5_log.Tpo -c h5_log.c -o h5_log.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_file.lo -MD -MP -MF .deps/h5_file.Tpo -c h5_file.c -o h5_file.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_model.lo -MD -MP -MF .deps/h5_model.Tpo -c h5_model.c -o h5_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_syscall.lo -MD -MP -MF .deps/h5_syscall.Tpo -c h5_syscall.c -o h5_syscall.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5u_io.lo -MD -MP -MF .deps/h5u_io.Tpo -c h5u_io.c -o h5u_io.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5b_io.lo -MD -MP -MF .deps/h5b_io.Tpo -c h5b_io.c -o h5b_io.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5u_model.lo -MD -MP -MF .deps/h5u_model.Tpo -c h5u_model.c -o h5u_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5b_model.lo -MD -MP -MF .deps/h5b_model.Tpo -c h5b_model.c -o h5b_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5b_attribs.lo -MD -MP -MF .deps/h5b_attribs.Tpo -c h5b_attribs.c -o h5b_attribs.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_hdf5.lo -MD -MP -MF private/.deps/h5_hdf5.Tpo -c private/h5_hdf5.c -o private/h5_hdf5.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5_init.lo -MD -MP -MF .deps/h5_init.Tpo -c h5_init.c -o h5_init.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_hsearch.lo -MD -MP -MF private/.deps/h5_hsearch.Tpo -c private/h5_hsearch.c -o private/h5_hsearch.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_maps.lo -MD -MP -MF private/.deps/h5_maps.Tpo -c private/h5_maps.c -o private/h5_maps.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_fcmp.lo -MD -MP -MF private/.deps/h5_fcmp.Tpo -c private/h5_fcmp.c -o private/h5_fcmp.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_qsort.lo -MD -MP -MF private/.deps/h5_qsort.Tpo -c private/h5_qsort.c -o private/h5_qsort.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_qsort_r.lo -MD -MP -MF private/.deps/h5_qsort_r.Tpo -c private/h5_qsort_r.c -o private/h5_qsort_r.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_io.lo -MD -MP -MF private/.deps/h5_io.Tpo -c private/h5_io.c -o private/h5_io.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5_lustre.lo -MD -MP -MF private/.deps/h5_lustre.Tpo -c private/h5_lustre.c -o private/h5_lustre.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_adjacencies.lo -MD -MP -MF .deps/h5t_adjacencies.Tpo -c h5t_adjacencies.c -o h5t_adjacencies.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_map.lo -MD -MP -MF .deps/h5t_map.Tpo -c h5t_map.c -o h5t_map.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_model.lo -MD -MP -MF .deps/h5t_model.Tpo -c h5t_model.c -o h5t_model.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_octree.lo -MD -MP -MF .deps/h5t_octree.Tpo -c h5t_octree.c -o h5t_octree.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_io.lo -MD -MP -MF .deps/h5t_io.Tpo -c h5t_io.c -o h5t_io.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_retrieve.lo -MD -MP -MF .deps/h5t_retrieve.Tpo -c h5t_retrieve.c -o h5t_retrieve.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_store.lo -MD -MP -MF .deps/h5t_store.Tpo -c h5t_store.c -o h5t_store.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT h5t_tags.lo -MD -MP -MF .deps/h5t_tags.Tpo -c h5t_tags.c -o h5t_tags.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_core.lo -MD -MP -MF private/.deps/h5t_core.Tpo -c private/h5t_core.c -o private/h5t_core.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_core_trim.lo -MD -MP -MF private/.deps/h5t_core_trim.Tpo -c private/h5t_core_trim.c -o private/h5t_core_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_core_tetm.lo -MD -MP -MF private/.deps/h5t_core_tetm.Tpo -c private/h5t_core_tetm.c -o private/h5t_core_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_access_tetm.lo -MD -MP -MF private/.deps/h5t_access_tetm.Tpo -c private/h5t_access_tetm.c -o private/h5t_access_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_access_trim.lo -MD -MP -MF private/.deps/h5t_access_trim.Tpo -c private/h5t_access_trim.c -o private/h5t_access_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_adjacencies_tetm.lo -MD -MP -MF private/.deps/h5t_adjacencies_tetm.Tpo -c private/h5t_adjacencies_tetm.c -o private/h5t_adjacencies_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_adjacencies_trim.lo -MD -MP -MF private/.deps/h5t_adjacencies_trim.Tpo -c private/h5t_adjacencies_trim.c -o private/h5t_adjacencies_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_model_tetm.lo -MD -MP -MF private/.deps/h5t_model_tetm.Tpo -c private/h5t_model_tetm.c -o private/h5t_model_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_model_trim.lo -MD -MP -MF private/.deps/h5t_model_trim.Tpo -c private/h5t_model_trim.c -o private/h5t_model_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_retrieve_tetm.lo -MD -MP -MF private/.deps/h5t_retrieve_tetm.Tpo -c private/h5t_retrieve_tetm.c -o private/h5t_retrieve_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_retrieve_trim.lo -MD -MP -MF private/.deps/h5t_retrieve_trim.Tpo -c private/h5t_retrieve_trim.c -o private/h5t_retrieve_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_io_trim.lo -MD -MP -MF private/.deps/h5t_io_trim.Tpo -c private/h5t_io_trim.c -o private/h5t_io_trim.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_io_tetm.lo -MD -MP -MF private/.deps/h5t_io_tetm.Tpo -c private/h5t_io_tetm.c -o private/h5t_io_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_ref_elements.lo -MD -MP -MF private/.deps/h5t_ref_elements.Tpo -c private/h5t_ref_elements.c -o private/h5t_ref_elements.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_store_tetm.lo -MD -MP -MF private/.deps/h5t_store_tetm.Tpo -c private/h5t_store_tetm.c -o private/h5t_store_tetm.o libtool: compile: /usr/bin/mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/include -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -I/usr/include -I/usr/include/hdf5/openmpi -DFC_MANGLING_LOWERCASE_SINGLE_UNDERSCORE -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wall -O3 -MT private/h5t_store_trim.lo -MD -MP -MF private/.deps/h5t_store_trim.Tpo -c private/h5t_store_trim.c -o private/h5t_store_trim.o libtool: link: ar cr .libs/libH5hut.a h5_attachments.o h5_attribs.o h5_err.o h5_log.o h5_file.o h5_model.o h5_syscall.o h5u_io.o h5b_io.o h5u_model.o h5b_model.o h5b_attribs.o private/h5_hdf5.o h5_init.o private/h5_hsearch.o private/h5_maps.o private/h5_fcmp.o private/h5_qsort.o private/h5_qsort_r.o private/h5_io.o private/h5_lustre.o h5t_adjacencies.o h5t_map.o h5t_model.o h5t_octree.o h5t_io.o h5t_retrieve.o h5t_store.o h5t_tags.o private/h5t_core.o private/h5t_core_trim.o private/h5t_core_tetm.o private/h5t_access_tetm.o private/h5t_access_trim.o private/h5t_adjacencies_tetm.o private/h5t_adjacencies_trim.o private/h5t_model_tetm.o private/h5t_model_trim.o private/h5t_retrieve_tetm.o private/h5t_retrieve_trim.o private/h5t_io_trim.o private/h5t_io_tetm.o private/h5t_ref_elements.o private/h5t_store_tetm.o private/h5t_store_trim.o libtool: link: ranlib .libs/libH5hut.a libtool: link: ( cd ".libs" && rm -f "libH5hut.la" && ln -s "../libH5hut.la" "libH5hut.la" ) /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libH5hut.la '/home/ian/fluidity/fluidity/h5hut/../lib' libtool: install: /usr/bin/install -c .libs/libH5hut.lai /home/ian/fluidity/fluidity/h5hut/../lib/libH5hut.la libtool: install: /usr/bin/install -c .libs/libH5hut.a /home/ian/fluidity/fluidity/h5hut/../lib/libH5hut.a libtool: install: chmod 644 /home/ian/fluidity/fluidity/h5hut/../lib/libH5hut.a libtool: install: ranlib /home/ian/fluidity/fluidity/h5hut/../lib/libH5hut.a libtool: finish: PATH="/home/ian/miniconda3/bin:/home/ian/miniconda3/condabin:/home/ian/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sbin" ldconfig -n /home/ian/fluidity/fluidity/h5hut/../lib

Libraries have been installed in: /home/ian/fluidity/fluidity/h5hut/../lib

If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following:

• add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution
• add LIBDIR to the 'LD_RUN_PATH' environment variable during linking
• use the '-Wl,-rpath -Wl,LIBDIR' linker flag
• have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages.

Making install-exec in C Making install-exec in include Making install-exec in h5core Making install-exec in Python Python is disabled Making install-exec in test Making install-exec in tools Making install-exec in doc Making install-exec in examples/H5 Making install-exec in examples/H5Part Making install-exec in examples/H5Block Making install-exec in examples/H5Fed Making install-data in src Making install-data in Fortran /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../include' /usr/bin/install -c -m 644 ../../src/include/H5hut.f90 ../../src/include/H5_const.f90 ../../src/include/H5_file.f90 ../../src/include/H5_model.f90 ../../src/include/H5_file_attribs.f90 ../../src/include/H5_step_attribs.f90 ../../src/include/H5_err.f90 ../../src/include/H5_log.f90 ../../src/include/H5Part_model.f90 ../../src/include/H5Part_io.f90 ../../src/include/H5Block_model.f90 ../../src/include/H5Block_attribs.f90 ../../src/include/H5Block_io.f90 ../../src/include/H5hut.f '/home/ian/fluidity/fluidity/h5hut/../include' /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../include' /usr/bin/install -c -m 644 ../../src/include/H5hut.f '/home/ian/fluidity/fluidity/h5hut/../include' Making install-data in h5core Making install-data in C /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../include' /usr/bin/install -c -m 644 ../../src/include/H5Block_attribs.h ../../src/include/H5Block_io.h ../../src/include/H5Block_model.h ../../src/include/H5Fed_adjacency.h ../../src/include/H5Fed_model.h ../../src/include/H5Fed_retrieve.h ../../src/include/H5Fed_store.h ../../src/include/H5Fed_tags.h ../../src/include/H5Part_io.h ../../src/include/H5Part_model.h ../../src/include/H5_attachments.h ../../src/include/H5_err.h ../../src/include/H5_file.h ../../src/include/H5_file_attribs.h ../../src/include/H5_log.h ../../src/include/H5_model.h ../../src/include/H5_step_attribs.h ../../src/include/H5hut.h '/home/ian/fluidity/fluidity/h5hut/../include' Making install-data in include Making install-data in h5core /usr/bin/mkdir -p '/home/ian/fluidity/fluidity/h5hut/../include/h5core' /usr/bin/install -c -m 644 h5_attachments.h h5_err.h h5_file.h h5_file_attribs.h h5_log.h h5_model.h h5_step_attribs.h h5_syscall.h h5_types.h h5b_attribs.h h5b_model.h h5b_io.h h5t_adjacencies.h h5t_map.h h5t_model.h h5t_octree.h h5t_retrieve.h h5t_store.h h5t_tags.h h5u_io.h h5u_model.h '/home/ian/fluidity/fluidity/h5hut/../include/h5core' Making install-data in Python Python is disabled Making install-data in test Making install-data in tools Making install-data in doc Making install-data in examples/H5 Making install-data in examples/H5Part Making install-data in examples/H5Block Making install-data in examples/H5Fed MKDIR lib echo ' MAKE libjudy'; make -s -C libjudy > make.log && make -s -C libjudy install >> make.log MAKE libjudy INSTALL local scripts BUILD libfluidity MKDIR lib MAKE debug CXX C++_Debug.cpp FC Debug_Parameters.F90 FC Debug.F90 FC Diagnostic_Output.F90 MAKE libwm CXX Wm4Command.cpp CXX Wm4FoundationPCH.cpp CXX Wm4Math.cpp CXX Wm4Memory.cpp CXX Wm4System.cpp Wm4System.cpp: In static member function ‘static double Wm4::System::GetTime()’: Wm4System.cpp:127:19: warning: ‘int ftime(timeb)’ is deprecated [-Wdeprecated-declarations] 127 | ftime(&kTB); | ^ In file included from Wm4System.cpp:29: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb timebuf) | ^~~~~ Wm4System.cpp:127:19: warning: ‘int ftime(timeb)’ is deprecated [-Wdeprecated-declarations] 127 | ftime(&kTB); | ^ In file included from Wm4System.cpp:29: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb __timebuf) | ^~~~~ Wm4System.cpp:132:15: warning: ‘int ftime(timeb)’ is deprecated [-Wdeprecated-declarations] 132 | ftime(&kTB); | ^ In file included from Wm4System.cpp:29: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb timebuf) | ^~~~~ Wm4System.cpp:132:15: warning: ‘int ftime(timeb)’ is deprecated [-Wdeprecated-declarations] 132 | ftime(&kTB); | ^ In file included from Wm4System.cpp:29: /usr/include/x86_64-linux-gnu/sys/timeb.h:39:12: note: declared here 39 | extern int ftime (struct timeb timebuf) | ^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12, inlined from ‘static const char Wm4::System::GetPath(const char, const char)’ at Wm4System.cpp:633:23, inlined from ‘static const char Wm4::System::GetPath(const char, const char)’ at Wm4System.cpp:577:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* builtin_strncpy_chk(char, const char, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return builtin_strncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static const char Wm4::System::GetPath(const char, const char)’: Wm4System.cpp:629:30: note: length computed here 629 | size_t uiDLength = strlen(acDirectory); | ~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12, inlined from ‘static const char Wm4::System::GetEnv(const char)’ at Wm4System.cpp:853:19, inlined from ‘static void Wm4::System::Initialize()’ at Wm4System.cpp:645:35: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char builtin___strncpy_chk(char, const char, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return builtin_strncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static void Wm4::System::Initialize()’: Wm4System.cpp:929:29: note: length computed here 929 | size_t uiSrcLen = strlen(acSrc); | ~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12, inlined from ‘static void Wm4::System::Initialize()’ at Wm4System.cpp:648:15: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char __builtin___strncpy_chk(char, const char, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return builtin___strncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static void Wm4::System::Initialize()’: Wm4System.cpp:929:29: note: length computed here 929 | size_t uiSrcLen = strlen(acSrc); | ~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12, inlined from ‘static const char Wm4::System::GetPath(const char, const char)’ at Wm4System.cpp:633:23, inlined from ‘static const char Wm4::System::GetPath(const char, const char)’ at Wm4System.cpp:577:13, inlined from ‘static const char Wm4::System::GetPath(const char, int)’ at Wm4System.cpp:744:50: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char builtin___strncpy_chk(char, const char, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return builtin_strncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static const char Wm4::System::GetPath(const char, int)’: Wm4System.cpp:629:30: note: length computed here 629 | size_t uiDLength = strlen(acDirectory); | ~~^~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12, inlined from ‘static const char Wm4::System::GetEnv(const char)’ at Wm4System.cpp:853:19: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char __builtin___strncpy_chk(char, const char, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return builtin___strncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static const char Wm4::System::GetEnv(const char)’: Wm4System.cpp:929:29: note: length computed here 929 | size_t uiSrcLen = strlen(acSrc); | ~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncpy(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcpy(char, size_t, const char)’ at Wm4System.cpp:937:12: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char builtin_strncpy(char, const char, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return _builtinstrncpy_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static char Wm4::System::Strcpy(char, size_t, const char)’: Wm4System.cpp:929:29: note: length computed here 929 | size_t uiSrcLen = strlen(acSrc); | ~~^~~ In file included from /usr/include/string.h:495, from /usr/include/c++/9/cstring:42, from Wm4System.h:31, from Wm4System.cpp:17: In function ‘char strncat(char, const char, size_t)’, inlined from ‘static char Wm4::System::Strcat(char, size_t, const char)’ at Wm4System.cpp:972:12: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:136:34: warning: ‘char builtin_strncat(char, const char, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 136 | return builtin___strncat_chk (dest, src, len, bos (dest)); | ~~~~~~^~~~~~~~ Wm4System.cpp: In static member function ‘static char Wm4::System::Strcat(char, size_t, const char)’: Wm4System.cpp:962:29: note: length computed here 962 | size_t uiSrcLen = strlen(acSrc); | ~~^~~ CXX Wm4Vector2.cpp CXX Wm4Vector3.cpp CXX Wm4Intersector.cpp CXX Wm4Intersector1.cpp CXX Wm4IntrQuad2Quad2.cpp CXX Wm4IntrTetrahedron3Tetrahedron3.cpp CXX Wm4IntrTriangle2Triangle2.cpp MAKE femtools FC Integer_hash_table.F90 FC Integer_set.F90 FC Data_structures.F90 FC Global_Parameters.F90 FC Futils.F90 FC Element_Numbering.F90 FC MPI_Interfaces.F90 FC Parallel_Tools.F90 FC Polynomials.F90 FC Grundmann_Moeller_Quadrature.F90 FC Reference_Counting.F90 FC Vector_Tools.F90 FC Wandzura_Quadrature.F90 FC Quadrature.F90 FC Elements.F90 FC Embed_Python_Fortran.F90 FC Halo_Data_Types.F90 FC Picker_Data_Types.F90 FC ieee_arithmetic_dummy.F90 FC Superconvergence.F90 FC Shape_Functions.F90 FC qsortd.F90 FC Halos_Base.F90 FC Halos_Debug.F90 FC Halos_Allocates.F90 FC Memory_Diagnostics.F90 FC Sparse_Tools.F90 FC Fields_Data_Types.F90 FC Tensors.F90 FC Fields_Base.F90 FC CV_Faces.F90 FC EventCounter.F90 FC Transform_elements.F90 FC FETools.F90 FC Adjacency_Lists.F90 FC Linked_Lists.F90 FC Halos_Communications.F90 FC Halos_Numbering.F90 FC Halos_Ownership.F90 FC Global_Numbering.F90 FC Halos_Repair.F90 FC Pickers_Base.F90 FC Pickers_Deallocates.F90 FC Fields_Allocates.F90 FC Element_set.F90 FC Fields_Manipulation.F90 FC Parallel_fields.F90 FC Unittest_tools.F90 FC Metric_tools.F90 FC Tetrahedron_intersection.F90 FC Unify_meshes.F90 FC Supermesh.F90 FC Intersection_finder.F90 FC Fields_Calculations.F90 FC Fields.F90 FC Profiler_Fortran.F90 FC Petsc_Tools.F90 FC Sparse_Tools_Petsc.F90 FC State.F90 FC Boundary_Conditions.F90 FC Sparsity_Patterns.F90 FC Dgtools.F90 FC Halos_Derivation.F90 FC VTK_interfaces.F90 FC Halos_Diagnostics.F90 FC Halos_Registration.F90 FC Halos.F90 FC Coordinates.F90 FC Quadrature_Test.F90 FC Shape_Functions_Test.F90 FC Signal_Vars.F90 FC Signals.F90 FC signal_handlers.F90 FC Timers.F90 FC Field_Options.F90 FC C_Interfaces_Fortran.F90 FC Sparse_Matrices_Fields.F90 FC FEFields.F90 FC Read_Triangle.F90 FC MeshDiagnostics.F90 FC Multigrid.F90 FC Solvers.F90 FC Sparsity_Patterns_Meshes.F90 CC ieee_arithmetic_C99.c FC Detector_Data_Types.F90 FC Node_Owner_Finder_Fortran.F90 FC Pickers_Allocates.F90 FC Pickers_Inquire.F90 FC Pickers.F90 FC Detector_Tools.F90 FC Detector_Parallel.F90 FC Merge_tensors.F90 FC Surface_Labels.F90 FC Node_boundary.F90 FC Vector_set.F90 FC Field_derivatives.F90 FC H5hut.F90 FC Mixing_Statistics.F90 FC Detector_Move_Lagrangian.F90 FC Time_Period.F90 FC Particles.F90 FC State_Fields.F90 FC Surface_Integrals.F90 FC Write_State.F90 FC Diagnostic_variables.F90 FC CVTools.F90 FC CV_Options.F90 FC CV_Shape_Functions.F90 FC CV_Face_Values.F90 FC CV_Upwind_Values.F90 FC Node_Ownership.F90 FC Interpolation.F90 FC Streamfunction.F90 FC Diagnostic_Fields.F90 FC SampleNetCDF_fortran.F90 FC AuxilaryOptions.F90 CXX ISCopyIndices.cpp FC Colouring.F90 CXX vecset.cpp CXX intvecset.cpp CXX eleset.cpp FC Matrix_Norms.F90 CC embed_python.c embed_python.c: In function ‘set_vector_result_double_array’: embed_python.c:316:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:316:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:316:28: note: each undeclared identifier is reported only once for each function it appears in embed_python.c:316:43: error: expected expression before ‘)’ token 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^ embed_python.c:320:7: warning: implicit declaration of function ‘PyArray_DIMS’ [-Wimplicit-function-declaration] 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^~~~ embed_python.c:320:27: error: subscripted value is neither array nor pointer nor vector 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^ embed_python.c:320:62: error: subscripted value is neither array nor pointer nor vector 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^ embed_python.c:322:39: error: subscripted value is neither array nor pointer nor vector 322 | natt, dim, PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1]); | ^ embed_python.c:322:64: error: subscripted value is neither array nor pointer nor vector 322 | natt, dim, PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1]); | ^ embed_python.c:328:44: warning: implicit declaration of function ‘PyArray_GETPTR2’ [-Wimplicit-function-declaration] 328 | result[i][j(dim) + d] = ((double)PyArray_GETPTR2(pArray, j, d)); | ^~~~~~~ embed_python.c:328:35: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 328 | result[i][j(dim) + d] = ((double)PyArray_GETPTR2(pArray, j, d)); | ^ embed_python.c: In function ‘set_tensor_result_double’: embed_python.c:367:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:367:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:367:43: error: expected expression before ‘)’ token 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^ embed_python.c:372:27: error: subscripted value is neither array nor pointer nor vector 372 | if (PyArray_DIMS(pArray)[0] != dim[0] || PyArray_DIMS(pArray)[1] != dim[1]) { | ^ embed_python.c:372:64: error: subscripted value is neither array nor pointer nor vector 372 | if (PyArray_DIMS(pArray)[0] != dim[0] || PyArray_DIMS(pArray)[1] != dim[1]) { | ^ embed_python.c:374:32: error: subscripted value is neither array nor pointer nor vector 374 | (int) PyArray_DIMS(pArray)[0], (int) PyArray_DIMS(pArray)[1], dim[0], dim[1]); | ^ embed_python.c:374:63: error: subscripted value is neither array nor pointer nor vector 374 | (int) PyArray_DIMS(pArray)[0], (int) PyArray_DIMS(pArray)[1], dim[0], dim[1]); | ^ embed_python.c:380:67: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 380 | (*(double)result)[i(dim[0]dim[1]) + jjdim[0] + ii] = ((double)PyArray_GETPTR2(pArray, ii, jj)); | ^ embed_python.c: In function ‘set_tensor_result_double_array’: embed_python.c:390:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^~~~~ | PyCoroObject embed_python.c:390:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^~~~~ | PyCoroObject embed_python.c:390:43: error: expected expression before ‘)’ token 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^ embed_python.c:397:27: error: subscripted value is neither array nor pointer nor vector 397 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^ embed_python.c:397:62: error: subscripted value is neither array nor pointer nor vector 397 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^ embed_python.c:397:99: error: subscripted value is neither array nor pointer nor vector 397 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^ embed_python.c:399:49: error: subscripted value is neither array nor pointer nor vector 399 | natt, dim[0], dim[1], PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^ embed_python.c:399:74: error: subscripted value is neither array nor pointer nor vector 399 | natt, dim[0], dim[1], PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^ embed_python.c:399:99: error: subscripted value is neither array nor pointer nor vector 399 | natt, dim[0], dim[1], PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^ embed_python.c:407:22: warning: implicit declaration of function ‘PyArray_GETPTR3’ [-Wimplicit-function-declaration] 407 | ((double)PyArray_GETPTR3(pArray, j, ii, jj)); | ^~~~~~~ embed_python.c:407:13: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 407 | ((double)PyArray_GETPTR3(pArray, j, ii, jj)); | ^ embed_python.c: In function ‘set_dict_from_fields’: embed_python.c:467:3: error: unknown type name ‘npy_intp’ 467 | npy_intp dims[] = {dim, dim}; | ^~~~ embed_python.c:479:22: warning: implicit declaration of function ‘PyArray_SimpleNew’ [-Wimplicit-function-declaration] 479 | PyObject pVec = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~ embed_python.c:479:49: error: ‘NPY_DOUBLE’ undeclared (first use in this function) 479 | PyObject pVec = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~~ embed_python.c:483:17: warning: implicit declaration of function ‘PyArray_DATA’; did you mean ‘PyAPI_DATA’? [-Wimplicit-function-declaration] 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^~~~ | PyAPI_DATA embed_python.c:483:31: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^~~~~ | PyCoroObject embed_python.c:483:45: error: expected expression before ‘)’ token 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^ embed_python.c:497:40: error: expected expression before ‘)’ token 497 | ((double)PyArray_DATA((PyArrayObject)pTens))[k + ldim] = field_vals[i][kdim + l + offset]; | ^ embed_python.c: In function ‘set_dict_from_old_atts’: embed_python.c:538:3: error: unknown type name ‘npy_intp’ 538 | npy_intp dims[] = {0, dim, dim}; | ^~~~ embed_python.c:552:41: error: ‘NPY_DOUBLE’ undeclared (first use in this function) 552 | pAtt = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~~ embed_python.c:554:13: warning: implicit declaration of function ‘PyArray_GETPTR1’ [-Wimplicit-function-declaration] 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^~~~~~~ embed_python.c:554:30: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^~~~~ | PyCoroObject embed_python.c:554:44: error: expected expression before ‘)’ token 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^ embed_python.c:570:44: error: expected expression before ‘)’ token 570 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, k)) = att_vals[ai + k]; | ^ embed_python.c:578:46: error: expected expression before ‘)’ token 578 | ((double)PyArray_GETPTR2((PyArrayObject)pAtt, d, k)) = att_vals[ai + k]; | ^ embed_python.c:596:46: error: expected expression before ‘)’ token 596 | ((double)PyArray_GETPTR2((PyArrayObject)pAtt, l, k)) = att_vals[ai + l]; | ^ embed_python.c:606:48: error: expected expression before ‘)’ token 606 | ((double)PyArray_GETPTR3((PyArrayObject)pAtt, d, l, k)) = att_vals[ai + l]; | ^ embed_python.c: In function ‘set_field_from_python_fields’: embed_python.c:640:3: warning: implicit declaration of function ‘import_array’ [-Wimplicit-function-declaration] 640 | import_array(); | ^~~~ embed_python.c: In function ‘string_frompython’: embed_python.c:1512:3: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ embed_python.c:1512:3: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE ) PyUnicode_AsUnicode( | ^~~~~~~ embed_python.c:1512:3: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ make[1]: [Makefile:127: embed_python.o] Error 1 make: *** [Makefile:244: lib/libfluidity.a] Error 2 (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$

[Patol75]

Pasting hundreds, if not thousands of lines from a terminal into a GitHub issue without saying hello or anything else is the opposite of what you want to do if you expect help from the developers. I invite you to start again and to describe in simple words the setup you are using and the issue you are facing, which seems to be Python-related (embed_python.c:316:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’?).

[iajzenszmi]

Hello I am using the Ubuntu operating system to run fluidity. All the dependencies have been installed. The problems are output at the tail of the listing and are as follows make[1]: [Makefile:127: embed_python.o] Error 1 make: [Makefile:244: lib/libfluidity.a] Error 2

Here is the run listing of the ./configure and make commands and the resulting output. following a listing of the members of the fluidity directory. Seasons greetings.

(base) ian@ian-Aspire-One-753:~$ cd fluidity (base) ian@ian-Aspire-One-753:~/fluidity$ ls fluidity (base) ian@ian-Aspire-One-753:~/fluidity$ cd fluidity (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ls 4.1.19.tar.gz debug libjudy missing aclocal.m4 depcomp libmba2d ocean_forcing acx_blas.m4 diagnostics libmba3d parameterisation acx_lapack.m4 docker libspud petsc_makefile assemble error_measures libvtkfortran petsc_makefile_old AUTHORS examples libwm population_balance bathymetry femtools LICENSE preprocessor bin fldecomp ltmain.sh py-compile climatology fluidity-4.1.19 m4 python CMakeFiles forward_interfaces main README compile h5hut main.cpp schemas config.guess horizontal_adaptivity main.o sediments config.log hyperlight Makefile spatialindex-1.8.0 config.status include Makefile.in tests config.sub INSTALL make.log tools configure install-sh manual configure.in lib mayavi debian libadaptivity
(base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ ./configure Hostname: ian-Aspire-One-753 checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu configure: Fishing for legacy fortran compiler. checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU Fortran 77 compiler... yes checking whether gfortran accepts -g... yes configure: Fishing for modern Fortran compiler checking for ifort... no checking for ifc... no checking for efc... no checking for sunf95... no checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) checking for gawk... gawk configure: ** Assuming that gfortran can process both free and fixed form fortran files. checking for icc... no checking for ecc... no checking for suncc... no checking for pgcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for icpc... no checking for icc... no checking for ecc... no checking for sunCC... no checking for pgCC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of long int... 8 checking how to get verbose linking output from gfortran... -v checking for Fortran libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking how to get verbose linking output from gfortran... -v checking for Fortran 77 libraries of gfortran... -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for python... yes checking for python3... /home/ian/miniconda3/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for a version of Python >= '3.6'... yes checking for the distutils Python package... yes checking for Python include path... -I/home/ian/miniconda3/include/python3.9 checking for Python library path... -L/home/ian/miniconda3/lib -lpython3.9 checking for Python site-packages path... /home/ian/miniconda3/lib/python3.9/site-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic checking consistency of all components of python development environment... yes Numpy is /home/ian/miniconda3/lib/python3.9/site-packages/numpy/core/include configure: Failed to import (optional) python module assess configure: checking the position of the stars to help find a versions of BLAS checking for builtin sgemm... no checking for sgemm in -lmkl_def... no checking for sgemm in -lmkl_ipf... no checking for sgemm in -lmkl_em64t... no configure: trying Intel MKL < 7: checking for lsame in -lmkl_lapack... no configure: Intel MKL < 7... no checking for sgemm in -lacml... no checking for sgemm in -lf77blas... no checking for sgemm in -lveclib... no configure: trying PhiPACK: checking for sgemm in -lblas... yes checking for dgemm in -ldgemm... no configure: PhiPACK... no checking for sgemm in -lcxml... no checking for sgemm in -ldxml... no checking for sgemm in -lscs... no checking for sgemm in -lcomplib.sgimath... no configure: trying IBM ESSL: checking for sgemm in -lblas... yes checking for sgemm in -lessl... no configure: IBM ESSL... no checking for sgemm in -lblas... yes checking for dsyev in -lmkl_lapack... no checking for dsyev in -lsunperf... no checking for dsyev in BLAS library... no checking for dsyev in -llapack... yes checking for main in -lstdc++... yes checking for main in -lm... yes checking for main in -lpthread... yes checking for library containing utInit... no checking "Checking for -funroll-loops"... -funroll-loops works checking "Checking for -fno-realloc-lhs"... -fno-realloc-lhs works, adding to FCFLAGS checking how do we get fortran 77 to allow long lines... -ffree-line-length-none -ffixed-line-length-none checking for a BSD-compatible install... /usr/bin/install -c checking for gmake... make checking for ar... ar checking for ranlib... ranlib configure: Setting optimisation flags for gfortran checking for malloc in -ltcmalloc... no configure: WARNING: No tcmalloc support available. checking for mpif90... mpif90 checking for mpicc... mpicc checking for mpicxx... mpicxx checking if we can compile and link without using -lmpi... yes checking netcdf automagic... no checking for nc_create in -lnetcdf... yes checking for Fortran flag to compile .f90 files... none checking netcdff automagic... no checking for nccre in -lnetcdff... no checking for Fortran flag to compile .f files... none checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes configure: WARNING: No PETSC_DIR set - trying to autodetect configure: Using PETSC_DIR=/usr/lib/petsc configure: Detected PETSc version "3"."12" configure: PETSc modules are working. configure: PETSc program succesfully compiled and linked. checking for library containing PCHYPRESetType... none required checking if we can compile and link without using -lparmetis... no checking metis automagic... no checking for METIS_PartGraphKway in -lmetis... no checking parmetis automagic... no checking for ParMETIS_V3_AdaptiveRepart in -lparmetis... no checking parmetis.h usability... no checking parmetis.h presence... no checking for parmetis.h... no checking how to run the C++ preprocessor... mpicxx -E checking zoltan automagic... no checking for Zoltan_Create in -lzoltan... no configure: Fluidity can be built without zoltan by configuring with the --enable-sam flag. This gives limited functionality when using parallel adaptivity. See the manual for more details. configure: error: in /home/ian/fluidity/fluidity': configure: error: "Could not link with Zoltan library." Seeconfig.log' for more details (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ make INSTALL local scripts BUILD libfluidity MKDIR lib MAKE debug MAKE libwm MAKE femtools CC embed_python.c embed_python.c: In function ‘set_vector_result_double_array’: embed_python.c:316:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:316:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:316:28: note: each undeclared identifier is reported only once for each function it appears in embed_python.c:316:43: error: expected expression before ‘)’ token 316 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^ embed_python.c:320:7: warning: implicit declaration of function ‘PyArray_DIMS’ [-Wimplicit-function-declaration] 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^~~~ embed_python.c:320:27: error: subscripted value is neither array nor pointer nor vector 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^ embed_python.c:320:62: error: subscripted value is neither array nor pointer nor vector 320 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim) { | ^ embed_python.c:322:39: error: subscripted value is neither array nor pointer nor vector 322 | natt, dim, PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1]); | ^ embed_python.c:322:64: error: subscripted value is neither array nor pointer nor vector 322 | natt, dim, PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1]); | ^ embed_python.c:328:44: warning: implicit declaration of function ‘PyArray_GETPTR2’ [-Wimplicit-function-declaration] 328 | result[i][j(dim) + d] = ((double)PyArray_GETPTR2(pArray, j, d)); | ^~~~~~~ embed_python.c:328:35: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 328 | result[i][j(dim) + d] = ((double)PyArray_GETPTR2(pArray, j, d)); | ^ embed_python.c: In function ‘set_tensor_result_double’: embed_python.c:367:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:367:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^~~~~ | PyCoroObject embed_python.c:367:43: error: expected expression before ‘)’ token 367 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 2, 2); | ^ embed_python.c:372:27: error: subscripted value is neither array nor pointer nor vector 372 | if (PyArray_DIMS(pArray)[0] != dim[0] || PyArray_DIMS(pArray)[1] != dim[1]) { | ^ embed_python.c:372:64: error: subscripted value is neither array nor pointer nor vector 372 | if (PyArray_DIMS(pArray)[0] != dim[0] || PyArray_DIMS(pArray)[1] != dim[1]) { | ^ embed_python.c:374:32: error: subscripted value is neither array nor pointer nor vector 374 | (int) PyArray_DIMS(pArray)[0], (int) PyArray_DIMS(pArray)[1], dim[0], dim[1]); | ^ embed_python.c:374:63: error: subscripted value is neither array nor pointer nor vector 374 | (int) PyArray_DIMS(pArray)[0], (int) PyArray_DIMS(pArray)[1], dim[0], dim[1]); | ^

embed_python.c:380:67: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 380 | (*(double*)result)[i(dim[0]dim[1]) + jjdim[0] + ii] = ((double)PyArray_GETPTR2(pArray, ii, jj)); | ^

embed_python.c: In function ‘set_tensor_result_double_array’: embed_python.c:390:3: error: unknown type name ‘PyArrayObject’; did you mean ‘PyCoroObject’? 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^~~~~ | PyCoroObject embed_python.c:390:28: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^~~~~ | PyCoroObject embed_python.c:390:43: error: expected expression before ‘)’ token 390 | PyArrayObject pArray = (PyArrayObject )PyArray_ContiguousFromObject(pResult, NPY_DOUBLE, 3, 3); | ^ embed_python.c:397:27: error: subscripted value is neither array nor pointer nor vector 397 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^ embed_python.c:397:62: error: subscripted value is neither array nor pointer nor vector 397 | if (PyArray_DIMS(pArray)[0] != natt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^ embed_python.c:397:99: error: subscripted value is neither array nor pointer nor vector 397 | tt || PyArray_DIMS(pArray)[1] != dim[0] || PyArray_DIMS(pArray)[2] != dim[1]) { | ^

embed_python.c:399:49: error: subscripted value is neither array nor pointer nor vector 399 | natt, dim[0], dim[1], PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^ embed_python.c:399:74: error: subscripted value is neither array nor pointer nor vector 399 | dim[0], dim[1], PyArray_DIMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^

embed_python.c:399:99: error: subscripted value is neither array nor pointer nor vector 399 | IMS(pArray)[0], PyArray_DIMS(pArray)[1], PyArray_DIMS(pArray)[2]); | ^

embed_python.c:407:22: warning: implicit declaration of function ‘PyArray_GETPTR3’ [-Wimplicit-function-declaration] 407 | ((double)PyArray_GETPTR3(pArray, j, ii, jj)); | ^~~~~~~ embed_python.c:407:13: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 407 | ((double)PyArray_GETPTR3(pArray, j, ii, jj)); | ^ embed_python.c: In function ‘set_dict_from_fields’: embed_python.c:467:3: error: unknown type name ‘npy_intp’ 467 | npy_intp dims[] = {dim, dim}; | ^~~~ embed_python.c:479:22: warning: implicit declaration of function ‘PyArray_SimpleNew’ [-Wimplicit-function-declaration] 479 | PyObject pVec = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~ embed_python.c:479:49: error: ‘NPY_DOUBLE’ undeclared (first use in this function) 479 | PyObject pVec = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~~ embed_python.c:483:17: warning: implicit declaration of function ‘PyArray_DATA’; did you mean ‘PyAPI_DATA’? [-Wimplicit-function-declaration] 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^~~~ | PyAPI_DATA embed_python.c:483:31: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^~~~~ | PyCoroObject embed_python.c:483:45: error: expected expression before ‘)’ token 483 | ((double)PyArray_DATA((PyArrayObject)pVec))[k] = field_vals[i][k + offset]; | ^ embed_python.c:497:40: error: expected expression before ‘)’ token 497 | ((double)PyArray_DATA((PyArrayObject)pTens))[k + ldim] = field_vals[i][kdim + l + offset]; | ^ embed_python.c: In function ‘set_dict_from_old_atts’: embed_python.c:538:3: error: unknown type name ‘npy_intp’ 538 | npy_intp dims[] = {0, dim, dim}; | ^~~~ embed_python.c:552:41: error: ‘NPY_DOUBLE’ undeclared (first use in this function) 552 | pAtt = PyArray_SimpleNew(1, dims, NPY_DOUBLE); | ^~~~~~ embed_python.c:554:13: warning: implicit declaration of function ‘PyArray_GETPTR1’ [-Wimplicit-function-declaration] 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^~~~~~~ embed_python.c:554:30: error: ‘PyArrayObject’ undeclared (first use in this function); did you mean ‘PyCoroObject’? 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^~~~~ | PyCoroObject embed_python.c:554:44: error: expected expression before ‘)’ token 554 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, d)) = att_vals[ai + d]; | ^ embed_python.c:570:44: error: expected expression before ‘)’ token 570 | ((double)PyArray_GETPTR1((PyArrayObject)pAtt, k)) = att_vals[ai + k]; | ^ embed_python.c:578:46: error: expected expression before ‘)’ token 578 | ((double)PyArray_GETPTR2((PyArrayObject)pAtt, d, k)) = att_vals[ai + k]; | ^ embed_python.c:596:46: error: expected expression before ‘)’ token 596 | ((double)PyArray_GETPTR2((PyArrayObject)pAtt, l, k)) = att_vals[ai + l]; | ^ embed_python.c:606:48: error: expected expression before ‘)’ token 606 | ((double)PyArray_GETPTR3((PyArrayObject)pAtt, d, l, k)) = att_vals[ai + l]; | ^ embed_python.c: In function ‘set_field_from_python_fields’: embed_python.c:640:3: warning: implicit declaration of function ‘import_array’ [-Wimplicit-function-declaration] 640 | import_array(); | ^~~~ embed_python.c: In function ‘string_frompython’: embed_python.c:1512:3: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ embed_python.c:1512:3: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE ) PyUnicode_AsUnicode( | ^~~~~~~ embed_python.c:1512:3: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 1512 | pResult_len = PyString_Size(pResult); | ^~~ In file included from /home/ian/miniconda3/include/python3.9/unicodeobject.h:1026, from /home/ian/miniconda3/include/python3.9/Python.h:97, from embed_python.c:35: /home/ian/miniconda3/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject op) { | ^~~~~~ make[1]: [Makefile:127: embed_python.o] Error 1 make: [Makefile:244: lib/libfluidity.a] Error 2 (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$

[stephankramer]

Looks like your configure failed. It ends with an error:

configure: Fluidity can be built without zoltan by configuring with the --enable-sam flag. This gives limited functionality when using parallel adaptivity. See the manual for more details.
configure: error: in /home/ian/fluidity/fluidity': configure: error: "Could not link with Zoltan library." See config.log' for more details

In that case there's not point in trying to move on to the make step, you first need to complete the configure step successfully. If you're not interested in adaptivity you can try to configure with the --enable-sam flag as suggested, otherwise you need to figure out what is wrong with your zoltan library. What version of Ubuntu are you using? Are you using fluidity's ppa and do you have the fluidity-dev package installed?

[iajzenszmi]

I have made fluidity to work and pass its tests. The run listing is as follows. All dependencies had to be installed to make it work. (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ make test INSTALL local scripts BUILD libfluidity MKDIR lib MAKE debug MAKE libwm MAKE femtools MAKE bathymetry MAKE ocean_forcing MAKE sediments MAKE parameterisation MAKE forward_interfaces MAKE horizontal_adaptivity MAKE preprocessor MAKE population_balance MAKE error_measures MAKE assemble MAKE diagnostics MAKE main MAKE options_check MAKE register_diagnostics BUILDING fluidity_library INSTALL local scripts BUILD libfluidity MKDIR lib MAKE debug MAKE libwm MAKE femtools MAKE bathymetry MAKE ocean_forcing MAKE sediments MAKE parameterisation MAKE forward_interfaces MAKE horizontal_adaptivity MAKE preprocessor MAKE population_balance MAKE error_measures MAKE assemble MAKE diagnostics MAKE main MAKE options_check MAKE register_diagnostics BUILDING fluidity_library BUILD fldecomp MKDIR bin BUILD fluidity tools MAKE climatology BUILD fluidity MKDIR bin LD ./bin/fluidity Test criteria:

length: short parallel: any tags to include: None tags to exclude: ['zoltan', '2dadapt', 'exodusii', 'assess']

fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity fluidity

which fluidity: /home/ian/fluidity/fluidity/bin/fluidity Revision: main:1ccc702b296ae4badb15fba1b76b4673d90b3757 Compile date: Dec 12 2021 05:15:59 OpenMP Support no Adaptivity support yes 2D adaptivity support no 3D MBA support no CGAL support no MPI support yes Double precision yes NetCDF support yes Signal handling support yes Stream I/O support yes PETSc support yes Hypre support yes ARPACK support no Python support yes Numpy support yes VTK support yes Zoltan support no Memory diagnostics no FEMDEM support no Hyperlight support no libsupermesh support no

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/viscosity_2d_p0_parallel_localassembly' rm -rf .ele .edge .node .poly .halo .vtu .pvtu fluidity. .s .d.1 *.stat \ matrixdump matrixdump.info heat flredecomp* cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/viscosity_2d_p0_parallel_local_assembly'

There are not enough slots available in the system to satisfy the 16 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

viscosity_2d_p0_parallel_local_assembly: Running viscosity_2d_p0_parallel_local_assembly: Calling 'make input': viscosity_2d_p0_parallel_local_assembly: mpiexec -n 16 ../../bin/flredecomp -i 1 -o 16 -v -l heat heat_flredecomp && mpiexec -n 16 ../../bin/fluidity -v2 -l heat_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/parallel_coarsening_2d' gmsh -2 src/square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/parallel_coarsening_2d' parallel_coarsening_2d: Running parallel_coarsening_2d: Calling 'make input': Error: parallel_coarsening_2d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_diagnostic_field_fromarray' rm -rf mesh/.msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp circle? *~ circle? checkpoint* circle?? gmsh -2 -bin mesh/mesh.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_diagnostic_field_from_array' particle_diagnostic_field_from_array: Running particle_diagnostic_field_from_array: Calling 'make input': Error: particle_diagnostic_field_from_array.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp' tar -xvjf src/cube.tar.bz2 cube.ele cube.face cube.node ../../bin/triangle2gmsh cube Warning: Failed to import vtk module Warning: Failed to import vtk module Warning: Failed to import vtktools module Warning: Failed to import vtk module Reading .node file Reading .face file Reading .ele file make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp' make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp' rm -f cube?*.ele cube?.face cube_?.halo cube_?.node rm -f .log .err test_flredecomp.flml rm -f test_flredecompCoordinateMesh make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp'

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

flredecomp: Running flredecomp: Calling 'make input': flredecomp: make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp_repart' tar -xvjf src/cube.tar.bz2 cube.ele cube.face cube.node ../../bin/triangle2gmsh cube Warning: Failed to import vtk module Warning: Failed to import vtk module Warning: Failed to import vtktools module Warning: Failed to import vtk module Reading .node file Reading .face file Reading .ele file make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_repart' make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomprepart' rm -f cube?.ele cube_?.face cube?*.halo cube?.node rm -f .log .err test_flredecomp_repart.flml rm -f test_flredecomp make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_repart'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

---

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

flredecomp_repart: Running flredecomp_repart: Calling 'make input': flredecomp_repart: make clean-run mpiexec -n 4 -np 2 ../../bin/flredecomp -i 1 -o 2 -v -l test test_flredecomp mpiexec -n 4 ../../bin/flredecomp -i 2 -o 4 -v -l test_flredecomp test_flredecomp_repart

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_attributes_checkpointparallel' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp particleattributes? ~ particleattributes?_checkpoint particle_attributescheckpoint?_checkpoint .h5part P4* particle_attributescheckpoint? gmsh -2 -bin square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_attributes_checkpoint_parallel' particle_attributes_checkpoint_parallel: Running particle_attributes_checkpoint_parallel: Calling 'make input': Error: particle_attributes_checkpoint_parallel.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_attributes_checkpoint_parallelflredecomp' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. particleattributes? ~ .h5part P4* particle_attributescheckpoint? rm -f particle_attributes_1_checkpoint.flml rm -f particle_attributes_checkpoint_1_checkpoint.flml rm -f particle-attributes-flredecomp.flml gmsh -format msh2 -2 -bin square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_attributes_checkpoint_parallel_flredecomp' particle_attributes_checkpoint_parallel_flredecomp: Running particle_attributes_checkpoint_parallel_flredecomp: Calling 'make input': Error: particle_attributes_checkpoint_parallel_flredecomp.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp_1d' ../../bin/interval --dx=0.0008 0 1 line make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_1d' make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp1d' rm -f line?.bound line_?.ele line?*.halo line?.node rm -f .log .err test_flredecomp.flml rm -f test_flredecompCoordinateMesh make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_1d'

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

flredecomp_1d: Running flredecomp_1d: Calling 'make input': flredecomp_1d: make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_prescribed_vortex_flow3d' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp Sphere? *~ Sphere? checkpoint* Sphere?? gmsh -3 -bin mesh3D.geo -o mesh3D.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_prescribed_vortex_flow_3d' particle_prescribed_vortex_flow_3d: Running particle_prescribed_vortex_flow_3d: Calling 'make input': Error: particle_prescribed_vortex_flow_3d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_prescribed_vortexflow' rm -rf mesh/.msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp circle? *~ circle? checkpoint* circle?? gmsh -2 -bin mesh/mesh.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_prescribed_vortex_flow' particle_prescribed_vortex_flow: Running particle_prescribed_vortex_flow: Calling 'make input': Error: particle_prescribed_vortex_flow.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp_2d' tar -xvjf src/square.tar.bz2 square.edge square.ele square.node ../../bin/triangle2gmsh square Warning: Failed to import vtk module Warning: Failed to import vtk module Warning: Failed to import vtktools module Warning: Failed to import vtk module Reading .node file Reading .edge file Reading .ele file make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_2d' make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/flredecomp2d' rm -f square?.edge square_?.ele square?*.halo square?.node rm -f .log .err test_flredecomp.flml rm -f test_flredecompCoordinateMesh make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/flredecomp_2d'

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

flredecomp_2d: Running flredecomp_2d: Calling 'make input': flredecomp_2d: make clean-run; mpiexec -n 4 ../../bin/flredecomp -i 1 -o 4 -v -l test test_flredecomp

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/lagrangian_detectors_3d1e2' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .detectors .dat lagrangiandetectors[01] flredecomp *h5part gmsh -3 -bin src/box.geo -o box.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/lagrangian_detectors_3d_1e2' lagrangian_detectors_3d_1e2: Running lagrangian_detectors_3d_1e2: Calling 'make input': Error: lagrangian_detectors_3d_1e2.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/parallel_refinement3d' rm -rf fluidity. cube.msh refinep refine refine.stat adapted_state metric_input gradation_metric bounding_box adapted_quality rm -rf matrixdump* gmsh -3 src/cube.geo -algo front3d -o cube.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/parallel_refinement_3d' parallel_refinement_3d: Running parallel_refinement_3d: Calling 'make input': Error: parallel_refinement_3d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/mixing_stats_test' rm -f .stat .vtu .pvtu .convergence checkpoint .err .log
rm -f mixing_stats_test_serial.flml mixing_stats_test_parallel.flml rm -f .halo .node .ele .face .msh rm -rf mixing_stats_testparallel? \ matrixdump matrixdump.info rm -rf flredecomp* sed "s/mixing_stats_test/mixing_stats_test_serial/" mixing_stats_test.flml > mixing_stats_test_serial.flml sed "s/mixing_stats_test/mixing_stats_test_parallel/" mixing_stats_test.flml > mixing_stats_test_parallel.flml gmsh -bin -3 src/pseudo_2d_square.geo -o pseudo_2d_square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:4: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/mixing_stats_test' mixing_stats_test: Running mixing_stats_test: Calling 'make input': Error: mixing_stats_test.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/parallel_refinement_2d' gmsh -2 src/square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/parallel_refinement_2d' parallel_refinement_2d: Running parallel_refinement_2d: Calling 'make input': Error: parallel_refinement_2d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/parallel_coarsening3d' rm -rf fluidity. cube.msh coarsenp coarsen coarsen.stat adapted_state metric_input gradation_metric bounding_box rm -rf matrixdump gmsh -3 src/cube.geo -algo front3d -o cube.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/parallel_coarsening_3d' parallel_coarsening_3d: Running parallel_coarsening_3d: Calling 'make input': Error: parallel_coarsening_3d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/Stokes_slab_detachment' rm -r -f Benchmark_Case_1a .pvtu .vtu .stat .detectors .dat fluidity. state matrixdump* log .pyc ~ flredecomp Parallel make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/Stokes_slab_detachment'

There are not enough slots available in the system to satisfy the 3 slots that were requested by the application:

../../bin/flredecomp

Either request fewer slots for your application, or make more slots available for use.

A "slot" is the Open MPI term for an allocatable unit where we can launch a process. The number of slots available are defined by the environment in which Open MPI processes are run:

1. Hostfile, via "slots=N" clauses (N defaults to number of processor cores if not provided)
2. The --host command line parameter, via a ":N" suffix on the hostname (N defaults to 1 if not provided)
3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)
4. If none of a hostfile, the --host command line parameter, or an RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number of hardware threads instead of the number of processor cores, use the --use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the number of available slots when deciding the number of processes to launch.

Stokes_slab_detachment: Running Stokes_slab_detachment: Calling 'make input': Stokes_slab_detachment: mpiexec -n 3 ../../bin/flredecomp -i 1 -o 3 -v -l Slab-detachment Parallel_NP3_Slab-detachment && mpiexec -n 3 ../../bin/fluidity -v2 -l Parallel_NP3_Slab-detachment.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/pvtu2vtu_dg' rm -rf output square.msh pvtu2vtu_flredecomp rm -rf flredecomp. fluidity. gmsh -2 -bin src/square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/pvtu2vtu_dg' pvtu2vtu_dg: Running pvtu2vtu_dg: Calling 'make input': Error: pvtu2vtu_dg.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/parallel_vertical_extrapolation' rm -rf output input1_NP input2_NP fluidity. flredecomp.* cube.msh gmsh -3 src/cube.geo -o cube.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/parallel_vertical_extrapolation' parallel_vertical_extrapolation: Running parallel_vertical_extrapolation: Calling 'make input': Error: parallel_vertical_extrapolation.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/square-convection-parallel-trivial' rm -f square-structured-linear.msh rm -f square-convection?*.vtu square-convection?checkpoint.msh square-convection?checkpoint.flml square-convection?_?_checkpoint.vtu square-convection.detectors square-convection.stat fluidity.err-0 fluidity.log-0 matrixdump matrixdump.info rm -rf flredecomp rm -f adaptedmesh?.vtu boundingbox?_?.vtu finalmetric?.vtu gmon.out gradationmetric?.vtu interpolation_metricfinal?.vtu interpolation_metrichessian?_?.vtu interpolation_metricmerge?_?.vtu interpolation_metricmetric?_?.vtu metricinput?_?.vtu rm -fr .halo .msh checkpoint .detectors.h5part square-convection_ fluidity.[le] cp src/.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/square-convection-parallel-trivial'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

square-convection-parallel-trivial: Running square-convection-parallel-trivial: Calling 'make input': square-convection-parallel-trivial: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l square-convection square-convection_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l square-convection_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/detectors_mesh_movement_parallel' rm -f .ele .edge .face .node .halo .pvtu .vtu .detectors.h5part .stat rm -f gmsh.log gmsh_err.log rm -f matrixdump matrixdump.info rm -f fluidity.err- fluidity.log- rm -rf detectors_? rm -rf flredecomp* cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/detectors_mesh_movement_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

detectors_mesh_movement_parallel: Running detectors_mesh_movement_parallel: Calling 'make input': detectors_mesh_movement_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l detectors_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/viscosity_2d_p0parallel' rm -fr .ele .edge .node .poly .halo .vtu .pvtu \ fluidity. .s .d.1 *.stat heat \ matrixdump matrixdump.info rm -rf flredecomp* cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/viscosity_2d_p0_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

viscosity_2d_p0_parallel: Running viscosity_2d_p0_parallel: Calling 'make input': viscosity_2d_p0_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l heat_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/column-parallel' rm -f .ele .edge .msh .node .face .poly .pvtu .vtu .s .stat .log- .err- matrixdump log err rm -rf column-parallel_ *.halo gmsh -3 -o column.msh src/column.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/column-parallel' column-parallel: Running column-parallel: Calling 'make input': Error: column-parallel.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/heat_2ddg' rm -fr .ele .edge .node .poly .halo .vtu .pvtu fluidity. .s .d.1 *.stat heat[01] \ matrixdump matrixdump.info rm -rf flredecomp cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/heat_2d_dg'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

heat_2d_dg: Running heat_2d_dg: Calling 'make input': heat_2d_dg: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp && mpiexec -n 2 ../../bin/fluidity -l heat_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/vbparallel' rm -rf .msh .halo .vtu .pvtu .log .stat blob? \ matrixdump matrixdump.info rm -rf flredecomp gmsh -2 -bin square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/vb_parallel' vb_parallel: Running vb_parallel: Calling 'make input': Error: vb_parallel.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/Stokes_square_convection_1e4_p1p1parallel' rm -f square-structured-linear.msh rm -f square-structured-linear?.msh square-structured-linear_?.halo rm -f stokes-1e4-p1p1-parallel?*.pvtu stokes-1e4-p1p1-parallel?.vtu rm -f stokes-1e4-p1p1-parallel.detectors.dat stokes-1e4-p1p1-parallel.detectors stokes-1e4-p1p1-parallel.stat tmpf rm -f fluidity.err-? fluidity.log-? rm -f matrixdump matrixdump.info rm -f stokes-1e4-p1p1-parallel_?checkpoint.flml rm -f stokes-1e4-p1p1-parallel?checkpoint?.msh stokes-1e4-p1p1-parallel_?checkpoint?.halo rm -f stokes-1e4-p1p1-parallel_?_?checkpoint.pvtu stokes-1e4-p1p1-parallel?_?checkpoint.vtu rm -f stokes-1e4-p1p1-parallel?checkpoint.msh rm -f stokes-1e4-p1p1-parallel?_checkpoint.vtu rm -rf flredecomp .h5part rm -f adaptedmesh?.vtu boundingbox?_?.vtu finalmetric?.vtu gmon.out gradationmetric?.vtu interpolation_metricfinal?.vtu interpolation_metrichessian?_?.vtu interpolation_metricmerge?_?.vtu interpolation_metricmetric?_?.vtu metricinput?_?.vtu rm -rf stokes-1e4-p1p1-parallel_? cp src/square-structured-linear.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/Stokes_square_convection_1e4_p1p1_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

Stokes_square_convection_1e4_p1p1_parallel: Running Stokes_square_convection_1e4_p1p1_parallel: Calling 'make input': Stokes_square_convection_1e4_p1p1_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p1p1-parallel Stokes-square-convection-1e4-p1p1-parallel_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p1p1-parallel_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_vectorstensors' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp particleattributes? *~ particleattributes?? gmsh -2 -bin square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_vectors_tensors' particle_vectors_tensors: Running particle_vectors_tensors: Calling 'make input': Error: particle_vectors_tensors.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/photosynthetic_radiation' rm -f .halo .face .ele .edge .node .msh .poly .pvtu .vtu .s .d.1 .stat \ matrixdump matrixdump.info rm -rf photosyntheticradiation? flredecomp cp src/column.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/photosynthetic_radiation' PARMETIS ERROR tpwgts is NULL. ERROR Error message: Libsam has produced an empty partition for your problem. Please consider reconfiguring with Zoltan

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

photosynthetic_radiation: Running photosynthetic_radiation: Calling 'make input': photosynthetic_radiation: mpiexec -n 2 flredecomp -i 1 -o 2 photosynthetic_radiation photosynthetic_radiation_flredecomp && mpiexec -n 2 fluidity photosynthetic_radiation_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/detectors_parallel_adaptivity' rm -f .ele .edge .face .node .halo .pvtu .vtu .detectors.h5part .particles. .stat rm -f gmsh.log gmsh_err.log rm -f matrixdump matrixdump.info rm -f fluidity.err- fluidity.log- rm -rf detectors_[0-4] rm -rf flredecomp cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/detectors_parallel_adaptivity'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

detectors_parallel_adaptivity: Running detectors_parallel_adaptivity: Calling 'make input': detectors_parallel_adaptivity: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l detectors detectors_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l detectors_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/heat_2d_dgip' rm -fr .ele .edge .node .poly .halo .vtu .pvtu fluidity. .s .d.1 *.stat heat[01] \ matrixdump matrixdump.info rm -rf flredecomp cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/heat_2d_dg_ip'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

heat_2d_dg_ip: Running heat_2d_dg_ip: Calling 'make input': heat_2d_dg_ip: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp && mpiexec -n 2 ../../bin/fluidity -l heat_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/particle_attributearray' rm -rf .msh .halo .vtu .pvtu .log .err *.stat blob[012] .particles. flredecomp particleattributes? *~ particleattributes?? gmsh -2 -bin square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:3: default] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/particle_attribute_array' particle_attribute_array: Running particle_attribute_array: Calling 'make input': Error: particle_attribute_array.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/bc-smoothing' rm -f .log .err smoothed_bcs_parallel.flml rm -rf out .msh *.halo rm -rf matrixdump matrixdump.info gmsh -3 -o cube.msh src/cube.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/bc-smoothing' bc-smoothing: Running bc-smoothing: Calling 'make input': Error: bc-smoothing.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/biology_6_component_parallel'

serial

rm -f .ele .edge .face .msh .node .poly .vtu .s .d.1 .stat .detectors rm -f matrix rm -f fluidity.

parallel

rm -rf biology_conservationparallel rm -rf .halo \ matrixdump matrixdump.info rm -rf flredecomp ../../bin/create_aligned_mesh box 50 50 -- -50 10 10 10 Warning: Failed to import vtk module Warning: Failed to import vtk module Warning: Failed to import vtktools module Warning: Failed to import vtk module make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/biology_6_component_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

biology_6_component_parallel: Running biology_6_component_parallel: Calling 'make input': biology_6_component_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l biology_conservation_parallel biology_conservation_parallel_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l biology_conservation_parallel_flredecomp.flml; ../../bin/fluidity -v2 -l biology_conservation.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/extrude_adapt3dparallel' rm -fr .msh .halo .vtu .pvtu rm -rf fluidity. .stat rm -rf matrixdump matrixdump.info rm -rf flredecomp checkpoint rm -rf box* gmsh -2 src/square.geo -o square.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/extrude_adapt3d_parallel' extrude_adapt3d_parallel: Running extrude_adapt3d_parallel: Calling 'make input': Error: extrude_adapt3d_parallel.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/5material-droplet-parallel' rm -rf .halo .stat .vtu .pvtu .node .ele .edge .log-0 .err-0 checkpoint .convergence rm -f .err-? .log-? rm -rf 5material-droplet? 5material-droplet?? \ matrixdump matrixdump.info rm -rf flredecomp* cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/5material-droplet-parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

5material-droplet-parallel: Running 5material-droplet-parallel: Calling 'make input': 5material-droplet-parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l 5material-droplet 5material-droplet_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l 5material-droplet_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/diffusion_2d_p0parallel' rm -fr .ele .edge .node .poly .halo .vtu .pvtu fluidity. .s .d.1 *.stat heat[0-9] \ matrixdump matrixdump.info rm -rf flredecomp* cp src/square.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/diffusion_2d_p0_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

diffusion_2d_p0_parallel: Running diffusion_2d_p0_parallel: Calling 'make input': diffusion_2d_p0_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l heat heat_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l heat_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/Stokes_square_convection_1e4_p2p1parallel' rm -f square-structured-linear.msh rm -f square-structured-linear?.msh square-structured-linear_?.halo rm -f stokes-1e4-p2p1-parallel?*.pvtu stokes-1e4-p2p1-parallel?.vtu rm -f stokes-1e4-p2p1-parallel.detectors stokes-1e4-p2p1-parallel.stat tmpf rm -f fluidity.err-? fluidity.log-? rm -f matrixdump matrixdump.info rm -f stokes-1e4-p2p1-parallel_?checkpoint.flml rm -f stokes-1e4-p2p1-parallel?checkpoint?.msh stokes-1e4-p2p1-parallel_?checkpoint?.halo rm -f stokes-1e4-p2p1-parallel_?_?checkpoint.pvtu stokes-1e4-p2p1-parallel?_?checkpoint.vtu rm -f stokes-1e4-p2p1-parallel?checkpoint.msh rm -f stokes-1e4-p2p1-parallel?checkpoint.vtu rm -f -R stokes-1e4-p2p1-parallel rm stokes-1e4-p2p1-parallel.dat rm -rf flredecomp rm -f adaptedmesh?.vtu boundingbox?_?.vtu finalmetric?.vtu gmon.out gradationmetric?.vtu interpolation_metricfinal?.vtu interpolation_metrichessian?_?.vtu interpolation_metricmerge?_?.vtu interpolation_metricmetric?_?.vtu metricinput?_?*.vtu cp src/square-structured-linear.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/Stokes_square_convection_1e4_p2p1_parallel'

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 16.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

Stokes_square_convection_1e4_p2p1_parallel: Running Stokes_square_convection_1e4_p2p1_parallel: Calling 'make input': Stokes_square_convection_1e4_p2p1_parallel: mpiexec -n 2 ../../bin/flredecomp -i 1 -o 2 -v -l Stokes-square-convection-1e4-p2p1-parallel Stokes-square-convection-1e4-p2p1-parallel_flredecomp && mpiexec -n 2 ../../bin/fluidity -v2 -l Stokes-square-convection-1e4-p2p1-parallel_flredecomp.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/examples/stokes_square_convection' **Cleaning the output from previous fluidity runs: rm -rf .pdf .png .stat .vtu checkpoint .log-0 .err-0 matrixdump mesh/.msh .edge .ele *.node **Generating structured meshes using gmsh in 2d: gmsh -2 -o square_24.msh mesh/square_24.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:5: preprocess] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/examples/stokes_square_convection' stokes_square_convection: Running stokes_square_convection: Calling 'make input': Error: stokes_square_convection.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/standing_wave-dg-adapt' rm -f standing_wave.stat rm -f .vtu .detectors .h5part rm -f fluidity.err-0 fluidity.log-0 rm -f .ele .face .node *.msh \ matrixdump matrixdump.info gmsh -3 -bin src/standing_wave.geo -o standing_wave.msh make[1]: gmsh: Command not found make[1]: *** [Makefile:4: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/standing_wave-dg-adapt' standing_wave-dg-adapt: Running standing_wave-dg-adapt: Calling 'make input': Error: standing_wave-dg-adapt.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/shocktube_1d_explicit' ../../bin/interval --region_ids=region_ids.py --dx=0.01 -- -1 2 tube make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/shocktube_1d_explicit' shocktube_1d_explicit: Running shocktube_1d_explicit: Calling 'make input': shocktube_1d_explicit: fluidity -v2 -l shocktube.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/spherical_mappings_2d' rm -rf .d. .stat .vtu .convergence checkpoint src/circle.msh fluidity.[le] \ matrixdump matrixdump.info gmsh -1 src/circle_shell.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/spherical_mappings_2d' spherical_mappings_2d: Running spherical_mappings_2d: Calling 'make input': Error: spherical_mappings_2d.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/mms_tracer_cv_adv_excludemass' rm -f .vtu .stat .log .node .ele .edge .msh checkpoint* \ matrixdump matrixdump.info cp src/MMS_A.msh . cp src/MMS_B.msh . cp src/MMS_C.msh . cp src/MMS_D.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/mms_tracer_cv_adv_excludemass'

• Steady state has been attained, exiting the timestep loop
• Steady state has been attained, exiting the timestep loop
• Steady state has been attained, exiting the timestep loop
• Steady state has been attained, exiting the timestep loop mms_tracer_cv_adv_excludemass: Running mms_tracer_cv_adv_excludemass: Calling 'make input': mms_tracer_cv_adv_excludemass: fluidity MMS_A_cv.flml > MMS_A.log; fluidity MMS_B_cv.flml > MMS_B.log; fluidity MMS_C_cv.flml > MMS_C.log; fluidity MMS_D_cv.flml > MMS_D.log

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/3material-twoblobs' rm -rf src/channel.msh .stat .vtu channel.node channel.ele channel.edge .log-0 .err-0 checkpoint .convergence *.png \ matrixdump matrixdump.info gmsh -2 src/channel.geo make[1]: gmsh: Command not found make[1]: *** [Makefile:2: input] Error 127 make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/3material-twoblobs' 3material-twoblobs: Running 3material-twoblobs: Calling 'make input': Error: 3material-twoblobs.xml raised an exception while running: Traceback (most recent call last):

File "/home/ian/fluidity/fluidity/tests/../bin/testharness", line 437, in threadrun runtime=test.run(dir)

File "/home/ian/fluidity/fluidity/python/fluidity/regressiontest.py", line 143, in run assert(ret == 0)

AssertionError

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/sem' rm -f .ele .edge .face .node .poly .vtu .s .d. .stat .s .log *.err \ matrixdump matrixdump.info cp src/box.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/sem' sem: Running sem: Calling 'make input': sem: fluidity -v3 sem.flml > sem.log 2>&1

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/annulus-diffusive' tar -xvjf src/annulus-structured-tanh-23x64.tar.bz2 annulus-structured-tanh-23x64.ele annulus-structured-tanh-23x64.face annulus-structured-tanh-23x64.node ../../bin/triangle2gmsh annulus-structured-tanh-23x64 Warning: Failed to import vtk module Warning: Failed to import vtk module Warning: Failed to import vtktools module Warning: Failed to import vtk module Reading .node file Reading .face file Reading .ele file make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/annulus-diffusive' make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/annulus-diffusive' rm -f annulus?*.pvtu annulus?.vtu rm -f annulus.detectors annulus.stat annulus.steady_state annulus.steady_state.dat tmpf rm -f fluidity.err-? fluidity.log-? rm -f matrixdump matrixdump.info rm -f annulus_?checkpoint.flml rm -f annulus?checkpoint?.ele annulus_?checkpoint?.face annulus_?checkpoint?.halo annulus_?checkpoint?.node rm -f annulus_?_?checkpoint.pvtu annulus?_?checkpoint.vtu rm -f annulus?checkpoint.ele annulus?checkpoint.face annulus?checkpoint.node rm -f annulus?_checkpoint.vtu rm -f adaptedmesh?.vtu boundingbox?_?.vtu finalmetric?.vtu gmon.out gradationmetric?.vtu interpolation_metricfinal?.vtu interpolation_metrichessian?_?.vtu interpolation_metricmerge?_?.vtu interpolation_metricmetric?_?.vtu metricinput?_?.vtu rm -f adapted_mesh.face adapted_mesh.ele adapted_mesh.node rm -f adaptedmesh?.face adaptedmesh?.ele adaptedmesh?.node rm -f adaptedstate?.pvtu adaptedstate?.vtu make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/annulus-diffusive' annulus-diffusive: Running annulus-diffusive: Calling 'make input': annulus-diffusive: make clean-run-debug; fluidity -v2 -l annulus.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/cube-1' rm -f cube-1 cube-10 .ele .face .node .vtu .s .d.1 .stat .log-0 *.err-0 \ matrixdump matrixdump.info cp src/cube-1.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/cube-1' cube-1: Running cube-1: Calling 'make input': cube-1: fluidity -v2 -l cube-1.flml

make[1]: Entering directory '/home/ian/fluidity/fluidity/tests/mms_tracer_cv_fesweby_adv_steady' rm -f .vtu .stat .log .node .ele .edge .msh checkpoint fluiditylog fluidityerr .steady_state \ matrixdump matrixdump.info cp src/MMS_A.msh . cp src/MMS_B.msh . cp src/MMS_C.msh . cp src/MMS_D.msh . make[1]: Leaving directory '/home/ian/fluidity/fluidity/tests/mms_tracer_cv_fesweby_adv_steady'

[iajzenszmi]

Here is a sloccount resources and budgeting listing for fluidity. (base) ian@ian-Aspire-One-753:~/fluidity/fluidity$ cd ~/fluidity (base) ian@ian-Aspire-One-753:~/fluidity$ sloccount ~/fluidity Creating filelist for fluidity Categorizing files. Finding a working MD5 command.... Found a working MD5 command. Warning: in fluidity, number of duplicates=3223 Computing results.

SLOC Directory SLOC-by-Language (Sorted) 433039 fluidity f90=167615,ansic=66517,cpp=58022,xml=39639,sh=39058, fortran=32185,python=29820,java=120,perl=63

Totals grouped by language (dominant language first): f90: 167615 (38.71%) ansic: 66517 (15.36%) cpp: 58022 (13.40%) xml: 39639 (9.15%) sh: 39058 (9.02%) fortran: 32185 (7.43%) python: 29820 (6.89%) java: 120 (0.03%) perl: 63 (0.01%)

Total Physical Source Lines of Code (SLOC) = 433,039 Development Effort Estimate, Person-Years (Person-Months) = 117.32 (1,407.88) (Basic COCOMO model, Person-Months = 2.4 * (KSLOC*1.05)) Schedule Estimate, Years (Months) = 3.28 (39.30) (Basic COCOMO model, Months = 2.5 (person-months**0.38)) Estimated Average Number of Developers (Effort/Schedule) = 35.82 Total Estimated Cost to Develop = $ 15,848,749 (average salary = $56,286/year, overhead = 2.40). SLOCCount, Copyright (C) 2001-2004 David A. Wheeler SLOCCount is Open Source Software/Free Software, licensed under the GNU GPL. SLOCCount comes with ABSOLUTELY NO WARRANTY, and you are welcome to redistribute it under certain conditions as specified by the GNU GPL license; see the documentation for details. Please credit this data as "generated using David A. Wheeler's 'SLOCCount'." (base) ian@ian-Aspire-One-753:~/fluidity$

[iajzenszmi]

If i had initially installed all the dependencies, this would never have been an issue.

[iajzenszmi]

Thank you.

[iajzenszmi]

Fluidity runs as follows. (base) ian@ian-Aspire-One-753:~/fluidity$ fluidity Revision: main:1ccc702b296ae4badb15fba1b76b4673d90b3757 Compile date: Dec 12 2021 05:15:59 OpenMP Support no Adaptivity support yes 2D adaptivity support no 3D MBA support no CGAL support no MPI support yes Double precision yes NetCDF support yes Signal handling support yes Stream I/O support yes PETSc support yes Hypre support yes ARPACK support no Python support yes Numpy support yes VTK support yes Zoltan support no Memory diagnostics no FEMDEM support no Hyperlight support no libsupermesh support no

Usage: fluidity [options ...] [simulation-file]

Options: -h, --help Help! Prints this message. -l, --log Create log file for each process (useful for non-interactive testing). -v , --verbose Verbose output to stdout, default level 0 -p, --profile Print profiling data at end of run This provides aggregated elapsed time for coarse-level computation (Turned on automatically if verbosity is at level 2 or above) -V, --version Version (base) ian@ian-Aspire-One-753:~/fluidity$