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psyplot / psy-view

An ncview-like GUI with psyplot
https://psyplot.github.io/psy-view
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psy-view segmentation fault on DWD NEC #51

Closed csteger closed 3 years ago

csteger commented 3 years ago

Hallo Philipp,

hier das Ticket für mein Problem auf unserer Maschine. Ich habe versucht psy-view bei uns auf der NEC zu installieren. Unter einem generischen user habe ich zunächst miniconda installiert. Danach habe ich wie hier (https://psyplot.readthedocs.io/projects/psy-view/en/latest/installing.html) beschrieben psy-view mit conda create -n psyplot -c conda-forge --override-channels psy-view installiert. Das ging alles soweit ohne Probleme.

Wenn ich dann aber die Umgebung aktiviere (conda activate psyplot) und versuche das GUI mit psy-view zu starten, bekomme ich einen segmentation fault.

Hier der output der Kommandozeile:

Output Konsole Installation: ``` icon-ku@rcnl101:~> conda create -n psyplot -c conda-forge --override-channels psy-view Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /hpc/uhome/icon-ku/miniconda3/envs/psyplot added / updated specs: - psy-view The following packages will be downloaded: package | build ---------------------------|----------------- cffi-1.14.5 | py39he32792d_0 227 KB conda-forge docrep-0.3.2 | pyh44b312d_0 19 KB conda-forge openssl-1.1.1j | h7f98852_0 2.1 MB conda-forge pygments-2.8.0 | pyhd8ed1ab_0 736 KB conda-forge pyzmq-22.0.3 | py39hea8fd45_0 530 KB conda-forge sphinx-3.5.1 | pyhd8ed1ab_0 1.5 MB conda-forge ------------------------------------------------------------ Total: 5.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu alabaster conda-forge/noarch::alabaster-0.7.12-py_0 babel conda-forge/noarch::babel-2.9.0-pyhd3deb0d_0 backcall conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0 backports conda-forge/noarch::backports-1.0-py_2 backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0 brotlipy conda-forge/linux-64::brotlipy-0.7.0-py39h3811e60_1001 bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 c-ares conda-forge/linux-64::c-ares-1.17.1-h36c2ea0_0 ca-certificates conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0 cartopy conda-forge/linux-64::cartopy-0.18.0-py39h3b23250_12 certifi conda-forge/linux-64::certifi-2020.12.5-py39hf3d152e_1 cffi conda-forge/linux-64::cffi-1.14.5-py39he32792d_0 cftime conda-forge/linux-64::cftime-1.4.1-py39hce5d2b2_0 chardet conda-forge/linux-64::chardet-4.0.0-py39hf3d152e_1 colorama conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0 cryptography conda-forge/linux-64::cryptography-3.4.4-py39h95dcef6_0 curl conda-forge/linux-64::curl-7.71.1-he644dc0_8 cycler conda-forge/noarch::cycler-0.10.0-py_2 dbus conda-forge/linux-64::dbus-1.13.6-hfdff14a_1 decorator conda-forge/noarch::decorator-4.4.2-py_0 docrep conda-forge/noarch::docrep-0.3.2-pyh44b312d_0 docutils conda-forge/linux-64::docutils-0.16-py39hf3d152e_3 expat conda-forge/linux-64::expat-2.2.10-h9c3ff4c_0 fasteners conda-forge/noarch::fasteners-0.14.1-py_3 fontconfig conda-forge/linux-64::fontconfig-2.13.1-hba837de_1004 freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1 funcargparse conda-forge/noarch::funcargparse-0.2.3-pyh9f0ad1d_0 geos conda-forge/linux-64::geos-3.9.1-h9c3ff4c_0 gettext conda-forge/linux-64::gettext-0.19.8.1-h0b5b191_1005 glib conda-forge/linux-64::glib-2.66.7-h9c3ff4c_0 glib-tools conda-forge/linux-64::glib-tools-2.66.7-h9c3ff4c_0 gst-plugins-base conda-forge/linux-64::gst-plugins-base-1.14.5-h0935bb2_2 gstreamer conda-forge/linux-64::gstreamer-1.18.3-h3560a44_0 hdf4 conda-forge/linux-64::hdf4-4.2.13-h10796ff_1004 hdf5 conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114 icu conda-forge/linux-64::icu-68.1-h58526e2_0 idna conda-forge/noarch::idna-2.10-pyh9f0ad1d_0 imagesize conda-forge/noarch::imagesize-1.2.0-py_0 ipykernel conda-forge/linux-64::ipykernel-5.4.2-py39hef51801_0 ipython conda-forge/linux-64::ipython-7.20.0-py39hef51801_2 ipython_genutils conda-forge/noarch::ipython_genutils-0.2.0-py_1 jedi conda-forge/linux-64::jedi-0.18.0-py39hf3d152e_2 jinja2 conda-forge/noarch::jinja2-2.11.3-pyh44b312d_0 jpeg conda-forge/linux-64::jpeg-9d-h36c2ea0_0 jupyter_client conda-forge/noarch::jupyter_client-6.1.11-pyhd8ed1ab_1 jupyter_core conda-forge/linux-64::jupyter_core-4.7.1-py39hf3d152e_0 kiwisolver conda-forge/linux-64::kiwisolver-1.3.1-py39h1a9c180_1 krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0 lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2 libblas conda-forge/linux-64::libblas-3.9.0-8_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-8_openblas libclang conda-forge/linux-64::libclang-11.0.1-default_ha53f305_1 libcurl conda-forge/linux-64::libcurl-7.71.1-hcdd3856_8 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-h516909a_1 libevent conda-forge/linux-64::libevent-2.1.10-hcdb4288_3 libffi conda-forge/linux-64::libffi-3.3-h58526e2_2 libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18 libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_18 libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-hff62375_18 libglib conda-forge/linux-64::libglib-2.66.7-h1f3bc88_0 libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18 libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0 liblapack conda-forge/linux-64::liblapack-3.9.0-8_openblas libllvm11 conda-forge/linux-64::libllvm11-11.0.1-hf817b99_0 libnetcdf conda-forge/linux-64::libnetcdf-4.7.4-nompi_h56d31a8_107 libnghttp2 conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0 libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1 libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2 libpq conda-forge/linux-64::libpq-12.3-h255efa7_3 libsodium conda-forge/linux-64::libsodium-1.0.18-h36c2ea0_1 libssh2 conda-forge/linux-64::libssh2-1.9.0-hab1572f_5 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18 libtiff conda-forge/linux-64::libtiff-4.2.0-hdc55705_0 libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000 libwebp-base conda-forge/linux-64::libwebp-base-1.2.0-h7f98852_0 libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1003 libxkbcommon conda-forge/linux-64::libxkbcommon-1.0.3-he3ba5ed_0 libxml2 conda-forge/linux-64::libxml2-2.9.10-h72842e0_3 lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0 markupsafe conda-forge/linux-64::markupsafe-1.1.1-py39h3811e60_3 matplotlib-base conda-forge/linux-64::matplotlib-base-3.3.4-py39h2fa2bec_0 monotonic conda-forge/noarch::monotonic-1.5-py_0 mysql-common conda-forge/linux-64::mysql-common-8.0.22-ha770c72_3 mysql-libs conda-forge/linux-64::mysql-libs-8.0.22-h935591d_3 ncurses conda-forge/linux-64::ncurses-6.2-h58526e2_4 netcdf4 conda-forge/linux-64::netcdf4-1.5.6-nompi_py39h36800e2_100 nspr conda-forge/linux-64::nspr-4.29-h9c3ff4c_1 nss conda-forge/linux-64::nss-3.61-hb5efdd6_0 numpy conda-forge/linux-64::numpy-1.20.1-py39hdbf815f_0 olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1 openssl conda-forge/linux-64::openssl-1.1.1j-h7f98852_0 packaging conda-forge/noarch::packaging-20.9-pyh44b312d_0 pandas conda-forge/linux-64::pandas-1.2.2-py39hde0f152_0 parso conda-forge/noarch::parso-0.8.1-pyhd8ed1ab_0 pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 pexpect conda-forge/noarch::pexpect-4.8.0-pyh9f0ad1d_2 pickleshare conda-forge/noarch::pickleshare-0.7.5-py_1003 pillow conda-forge/linux-64::pillow-8.1.0-py39hf95b381_2 pip conda-forge/noarch::pip-21.0.1-pyhd8ed1ab_0 proj conda-forge/linux-64::proj-7.2.0-h277dcde_2 prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.16-pyha770c72_0 psy-maps conda-forge/linux-64::psy-maps-1.3.2-py39hf3d152e_0 psy-simple conda-forge/linux-64::psy-simple-1.3.1-py39hf3d152e_0 psy-view conda-forge/linux-64::psy-view-0.1.0-py39hf3d152e_0 psyplot conda-forge/linux-64::psyplot-1.3.1-py39hf3d152e_0 psyplot-gui conda-forge/linux-64::psyplot-gui-1.3.0-py39hde42818_1 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 ptyprocess conda-forge/noarch::ptyprocess-0.7.0-pyhd3deb0d_0 pycparser conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2 pygments conda-forge/noarch::pygments-2.8.0-pyhd8ed1ab_0 pyopenssl conda-forge/noarch::pyopenssl-20.0.1-pyhd8ed1ab_0 pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 pyqt conda-forge/linux-64::pyqt-5.12.3-py39hf3d152e_7 pyqt-impl conda-forge/linux-64::pyqt-impl-5.12.3-py39h0fcd23e_7 pyqt5-sip conda-forge/linux-64::pyqt5-sip-4.19.18-py39he80948d_7 pyqtchart conda-forge/linux-64::pyqtchart-5.12-py39h0fcd23e_7 pyqtwebengine conda-forge/linux-64::pyqtwebengine-5.12.1-py39h0fcd23e_7 pyshp conda-forge/noarch::pyshp-2.1.3-pyh44b312d_0 pysocks conda-forge/linux-64::pysocks-1.7.1-py39hf3d152e_3 python conda-forge/linux-64::python-3.9.1-hffdb5ce_5_cpython python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 python_abi conda-forge/linux-64::python_abi-3.9-1_cp39 pytz conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0 pyyaml conda-forge/linux-64::pyyaml-5.4.1-py39h3811e60_0 pyzmq conda-forge/linux-64::pyzmq-22.0.3-py39hea8fd45_0 qt conda-forge/linux-64::qt-5.12.9-h9d6b050_2 qtconsole conda-forge/noarch::qtconsole-5.0.2-pyhd8ed1ab_0 qtpy conda-forge/noarch::qtpy-1.9.0-py_0 readline conda-forge/linux-64::readline-8.0-he28a2e2_2 requests conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0 scipy conda-forge/linux-64::scipy-1.6.0-py39hee8e79c_0 setuptools conda-forge/linux-64::setuptools-49.6.0-py39hf3d152e_3 shapely conda-forge/linux-64::shapely-1.7.1-py39ha61afbd_4 six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0 snowballstemmer conda-forge/noarch::snowballstemmer-2.1.0-pyhd8ed1ab_0 sphinx conda-forge/noarch::sphinx-3.5.1-pyhd8ed1ab_0 sphinx_rtd_theme conda-forge/noarch::sphinx_rtd_theme-0.5.1-pyhd3deb0d_0 sphinxcontrib-app~ conda-forge/noarch::sphinxcontrib-applehelp-1.0.2-py_0 sphinxcontrib-dev~ conda-forge/noarch::sphinxcontrib-devhelp-1.0.2-py_0 sphinxcontrib-htm~ conda-forge/noarch::sphinxcontrib-htmlhelp-1.0.3-py_0 sphinxcontrib-jsm~ conda-forge/noarch::sphinxcontrib-jsmath-1.0.1-py_0 sphinxcontrib-qth~ conda-forge/noarch::sphinxcontrib-qthelp-1.0.3-py_0 sphinxcontrib-ser~ conda-forge/noarch::sphinxcontrib-serializinghtml-1.1.4-py_0 sqlite conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0 tk conda-forge/linux-64::tk-8.6.10-h21135ba_1 tornado conda-forge/linux-64::tornado-6.1-py39h3811e60_1 traitlets conda-forge/noarch::traitlets-5.0.5-py_0 tzdata conda-forge/noarch::tzdata-2021a-he74cb21_0 urllib3 conda-forge/noarch::urllib3-1.26.3-pyhd8ed1ab_0 wcwidth conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_2 wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0 xarray conda-forge/noarch::xarray-0.16.2-pyhd8ed1ab_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0 xz conda-forge/linux-64::xz-5.2.5-h516909a_1 yaml conda-forge/linux-64::yaml-0.2.5-h516909a_0 zeromq conda-forge/linux-64::zeromq-4.3.4-h9c3ff4c_0 zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010 zstd conda-forge/linux-64::zstd-1.4.8-ha95c52a_1 Proceed ([y]/n)? y Downloading and Extracting Packages pygments-2.8.0 | 736 KB | #################################################################### | 100% sphinx-3.5.1 | 1.5 MB | #################################################################### | 100% docrep-0.3.2 | 19 KB | #################################################################### | 100% pyzmq-22.0.3 | 530 KB | #################################################################### | 100% cffi-1.14.5 | 227 KB | #################################################################### | 100% openssl-1.1.1j | 2.1 MB | #################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate psyplot # # To deactivate an active environment, use # # $ conda deactivate ```
Output conda list (unter env. Psyplot) ``` ############################################ (psyplot) icon-ku@rcnl101:~> conda list # packages in environment at /hpc/uhome/icon-ku/miniconda3/envs/psyplot: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge alabaster 0.7.12 py_0 conda-forge babel 2.9.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge brotlipy 0.7.0 py39h3811e60_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h36c2ea0_0 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cartopy 0.18.0 py39h3b23250_12 conda-forge certifi 2020.12.5 py39hf3d152e_1 conda-forge cffi 1.14.5 py39he32792d_0 conda-forge cftime 1.4.1 py39hce5d2b2_0 conda-forge chardet 4.0.0 py39hf3d152e_1 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge cryptography 3.4.4 py39h95dcef6_0 conda-forge curl 7.71.1 he644dc0_8 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 hfdff14a_1 conda-forge decorator 4.4.2 py_0 conda-forge docrep 0.3.2 pyh44b312d_0 conda-forge docutils 0.16 py39hf3d152e_3 conda-forge expat 2.2.10 h9c3ff4c_0 conda-forge fasteners 0.14.1 py_3 conda-forge fontconfig 2.13.1 hba837de_1004 conda-forge freetype 2.10.4 h0708190_1 conda-forge funcargparse 0.2.3 pyh9f0ad1d_0 conda-forge geos 3.9.1 h9c3ff4c_0 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge glib 2.66.7 h9c3ff4c_0 conda-forge glib-tools 2.66.7 h9c3ff4c_0 conda-forge gst-plugins-base 1.14.5 h0935bb2_2 conda-forge gstreamer 1.18.3 h3560a44_0 conda-forge hdf4 4.2.13 h10796ff_1004 conda-forge hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge icu 68.1 h58526e2_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge imagesize 1.2.0 py_0 conda-forge ipykernel 5.4.2 py39hef51801_0 conda-forge ipython 7.20.0 py39hef51801_2 conda-forge ipython_genutils 0.2.0 py_1 conda-forge jedi 0.18.0 py39hf3d152e_2 conda-forge jinja2 2.11.3 pyh44b312d_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge jupyter_client 6.1.11 pyhd8ed1ab_1 conda-forge jupyter_core 4.7.1 py39hf3d152e_0 conda-forge kiwisolver 1.3.1 py39h1a9c180_1 conda-forge krb5 1.17.2 h926e7f8_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge libblas 3.9.0 8_openblas conda-forge libcblas 3.9.0 8_openblas conda-forge libclang 11.0.1 default_ha53f305_1 conda-forge libcurl 7.71.1 hcdd3856_8 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 hcdb4288_3 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_18 conda-forge libgfortran-ng 9.3.0 hff62375_18 conda-forge libgfortran5 9.3.0 hff62375_18 conda-forge libglib 2.66.7 h1f3bc88_0 conda-forge libgomp 9.3.0 h2828fa1_18 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 8_openblas conda-forge libllvm11 11.0.1 hf817b99_0 conda-forge libnetcdf 4.7.4 nompi_h56d31a8_107 conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libopenblas 0.3.12 pthreads_h4812303_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 12.3 h255efa7_3 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.3.0 h6de172a_18 conda-forge libtiff 4.2.0 hdc55705_0 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.0 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.10 h72842e0_3 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 1.1.1 py39h3811e60_3 conda-forge matplotlib-base 3.3.4 py39h2fa2bec_0 conda-forge monotonic 1.5 py_0 conda-forge mysql-common 8.0.22 ha770c72_3 conda-forge mysql-libs 8.0.22 h935591d_3 conda-forge ncurses 6.2 h58526e2_4 conda-forge netcdf4 1.5.6 nompi_py39h36800e2_100 conda-forge nspr 4.29 h9c3ff4c_1 conda-forge nss 3.61 hb5efdd6_0 conda-forge numpy 1.20.1 py39hdbf815f_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openssl 1.1.1j h7f98852_0 conda-forge packaging 20.9 pyh44b312d_0 conda-forge pandas 1.2.2 py39hde0f152_0 conda-forge parso 0.8.1 pyhd8ed1ab_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.1.0 py39hf95b381_2 conda-forge pip 21.0.1 pyhd8ed1ab_0 conda-forge proj 7.2.0 h277dcde_2 conda-forge prompt-toolkit 3.0.16 pyha770c72_0 conda-forge psy-maps 1.3.2 py39hf3d152e_0 conda-forge psy-simple 1.3.1 py39hf3d152e_0 conda-forge psy-view 0.1.0 py39hf3d152e_0 conda-forge psyplot 1.3.1 py39hf3d152e_0 conda-forge psyplot-gui 1.3.0 py39hde42818_1 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.8.0 pyhd8ed1ab_0 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.12.3 py39hf3d152e_7 conda-forge pyqt-impl 5.12.3 py39h0fcd23e_7 conda-forge pyqt5-sip 4.19.18 py39he80948d_7 conda-forge pyqtchart 5.12 py39h0fcd23e_7 conda-forge pyqtwebengine 5.12.1 py39h0fcd23e_7 conda-forge pyshp 2.1.3 pyh44b312d_0 conda-forge pysocks 1.7.1 py39hf3d152e_3 conda-forge python 3.9.1 hffdb5ce_5_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.9 1_cp39 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py39h3811e60_0 conda-forge pyzmq 22.0.3 py39hea8fd45_0 conda-forge qt 5.12.9 h9d6b050_2 conda-forge qtconsole 5.0.2 pyhd8ed1ab_0 conda-forge qtpy 1.9.0 py_0 conda-forge readline 8.0 he28a2e2_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge scipy 1.6.0 py39hee8e79c_0 conda-forge setuptools 49.6.0 py39hf3d152e_3 conda-forge shapely 1.7.1 py39ha61afbd_4 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge snowballstemmer 2.1.0 pyhd8ed1ab_0 conda-forge sphinx 3.5.1 pyhd8ed1ab_0 conda-forge sphinx_rtd_theme 0.5.1 pyhd3deb0d_0 conda-forge sphinxcontrib-applehelp 1.0.2 py_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge sqlite 3.34.0 h74cdb3f_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py39h3811e60_1 conda-forge traitlets 5.0.5 py_0 conda-forge tzdata 2021a he74cb21_0 conda-forge urllib3 1.26.3 pyhd8ed1ab_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge xarray 0.16.2 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.8 ha95c52a_1 conda-forge ```
Chilipp commented 3 years ago

Hey @csteger ! Danke für die Nachricht! Bekommst du nur die Nachricht Segmentation Fault? Oder gibt es da noch mehr?

csteger commented 3 years ago

Hi @Chilipp,

nur Segmentation fault. Sehr humorlos.

Hier ist der Kommandozeilen-Output:

icon-ku@rcnl100: conda activate psyplot
/hpc/uhome/icon-ku /hpc/uhome/icon-ku/miniconda3/envs/psyplot/etc/conda/activate.d/glib_activate.sh
/hpc/uhome/icon-ku /hpc/uhome/icon-ku/miniconda3/envs/psyplot/etc/conda/activate.d/proj4-activate.sh
(psyplot) icon-ku@rcnl100: psy-view
Segmentation fault
Chilipp commented 3 years ago

moin @csteger. Ich vermute, dass ein paar Library Paths gesetzt sind und deshalb nicht die conda-Libraries genutzt werden. conda activate psyplot && conda info -a würde da mehr Aufschluss geben. Kannst du das bitte kurz hier posten?

psy-view an sich ist ja einfacher python code und auf Clustern ist es eigentlich besser, die System-Libraries zu verwenden anstelle von Conda. Alternativ zu conda kannst du also probieren, ob ihr die folgenden Dependencies auf eurem Cluster vielleicht schon installiert habt:

  1. numpy
  2. pandas
  3. PyQt5
  4. cartopy
  5. scipy
  6. matplotlib
  7. dask
  8. toolz
  9. python>=3.7

Du kannst das testen indem du dir den Output von folgendem Befehl anschaust: pip freeze (dafür darf conda aber nicht im PATH sein, also conda --help sollte fehlschlagen).

Auf unserem Cluster am HZG z.B. konnte ich psy-view via 

    module load applications/python/3.8
    pip3 install psy-view dask toolz PyQt5==5.12.* pyqtwebengine==5.12.* --user

installieren.

csteger commented 3 years ago

@Chilipp Hier ist der output von conda info -a Das andere probiere ich mal aus. Danke.

conda info -a ``` (psyplot) icon-ku@rcnl100:~> conda info -a active environment : psyplot active env location : /hpc/uhome/icon-ku/miniconda3/envs/psyplot shell level : 1 user config file : /hpc/uhome/icon-ku/.condarc populated config files : /hpc/uhome/icon-ku/.condarc conda version : 4.9.2 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : __glibc=2.17=0 __unix=0=0 __archspec=1=x86_64 base environment : /hpc/uhome/icon-ku/miniconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /hpc/uhome/icon-ku/miniconda3/pkgs /hpc/uhome/icon-ku/.conda/pkgs envs directories : /hpc/uhome/icon-ku/miniconda3/envs /hpc/uhome/icon-ku/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Linux/3.10.0-1062.18.1.el7.x86_64 rhel/7.7 glibc/2.17 UID:GID : 16917:16015 netrc file : None offline mode : False # conda environments: # base /hpc/uhome/icon-ku/miniconda3 psyplot * /hpc/uhome/icon-ku/miniconda3/envs/psyplot sys.version: 3.8.5 (default, Sep 4 2020, 07:30:14) ... sys.prefix: /hpc/uhome/icon-ku/miniconda3 sys.executable: /hpc/uhome/icon-ku/miniconda3/bin/python conda location: /hpc/uhome/icon-ku/miniconda3/lib/python3.8/site-packages/conda conda-build: None conda-env: /hpc/uhome/icon-ku/miniconda3/bin/conda-env user site dirs: CIO_TEST: CLASSPATH: /hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/lib/mpi.jar:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/daal/lib/daal.jar CONDA_DEFAULT_ENV: psyplot CONDA_EXE: /hpc/uhome/icon-ku/miniconda3/bin/conda CONDA_PREFIX: /hpc/uhome/icon-ku/miniconda3/envs/psyplot CONDA_PROMPT_MODIFIER: (psyplot) CONDA_PYTHON_EXE: /hpc/uhome/icon-ku/miniconda3/bin/python CONDA_ROOT: /hpc/uhome/icon-ku/miniconda3 CONDA_SHLVL: 1 CPATH: /hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/ipp/include:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mkl/include:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/pstl/include:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/pstl/stdlib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/tbb/include:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/daal/include CPLUS_INCLUDE_PATH: /hpc/sw/netcdf4/4.7.3/x86/intel/include:/hpc/sw/hdf5/1.10.5/x86/intel/include CURL_CA_BUNDLE: C_INCLUDE_PATH: /hpc/sw/netcdf4/4.7.3/x86/intel/include:/hpc/sw/hdf5/1.10.5/x86/intel/include ECFS_SYS_PATH: /usr/local/ecfs/prodn FI_PROVIDER_PATH: /hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/libfabric/lib/prov FPATH: /usr/share/Modules/sbin.ksh INCLUDE_PATH: /hpc/sw/netcdf4/4.7.3/x86/intel/include:/hpc/sw/hdf5/1.10.5/x86/intel/include INFOPATH: /hpc/sw/intel/documentation_2020/en/debugger/gdb-ia/info/ LD_LIBRARY_PATH: /hpc/sw/libdwd//1.1.7/x86/intel/lib:/hpc/sw/eccodes//2.14.1/x86/intel/lib:/hpc/sw/netcdf4/4.7.3/x86/intel/lib:/hpc/sw/hdf5/1.10.5/x86/intel/lib:/hpc/sw/aec//1.0.3/x86/intel/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/libfabric/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/lib/release:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/ipp/lib/intel64:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/compiler/lib/intel64_lin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/tbb/lib/intel64/gcc4.8:/hpc/sw/intel/debugger_2020/python/intel64/lib:/hpc/sw/intel/debugger_2020/libipt/intel64/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/daal/lib/intel64_lin:/hpc/sw/gnu/mpfr/4.0.2/lib:/hpc/sw/gnu/mpc/1.1.0/lib:/hpc/sw/gnu/gmp/6.1.0/lib:/hpc/sw/gnu/gcc/9.1.0/lib64:/hpc/sw/gnu/gcc/9.1.0/lib:/e/uhome/kfroehli/bin/NCL/lib LD_RUN_PATH: /hpc/sw/gnu/gcc/9.1.0/lib64:/hpc/sw/gnu/gcc/9.1.0/lib LIBDWD_BUFRTABLE_PATH: /hpc/sw/libdwd//1.1.7/x86/intel/definitions/bufr/tabellen LIBDWD_BUFR_CONFIG_PATH: /hpc/sw/libdwd//1.1.7/x86/intel/definitions/bufr/config/wmo LIBRARY_PATH: /hpc/sw/libdwd//1.1.7/x86/intel/lib:/hpc/sw/eccodes//2.14.1/x86/intel/lib:/hpc/sw/netcdf4/4.7.3/x86/intel/lib:/hpc/sw/hdf5/1.10.5/x86/intel/lib:/hpc/sw/aec//1.0.3/x86/intel/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/libfabric/lib:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/ipp/lib/intel64:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/compiler/lib/intel64_lin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/tbb/lib/intel64/gcc4.8:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/daal/lib/intel64_lin MANPATH: /hpc/sw/libdwd//1.1.7/x86/intel/man:/hpc/sw/intel/man/common:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/man:/hpc/sw/intel/documentation_2020/en/debugger/gdb-ia/man/:/hpc/sw/gnu/gcc/9.1.0/share/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man:/usr/local/ecfs/prodn/man:/opt/nec/nqsv/man:/usr/local/ecfs/prodn/man:/opt/nec/nqsv/man MODULEPATH: /etc/modulefiles:/hpc/sw/modulefiles/meta:/hpc/sw/modulefiles/nec/apps:/hpc/sw/modulefiles/dwd/apps:/hpc/sw/modulefiles/nec/x86:/hpc/sw/modulefiles/dwd/x86 NLSPATH: /hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/compiler/lib/intel64/locale/%l_%t/%N:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin/locale/%l_%t/%N:/hpc/sw/intel/debugger_2020/gdb/intel64/share/locale/%l_%t/%N PATH: /hpc/uhome/icon-ku/miniconda3/bin:/hpc/uhome/icon-ku/miniconda3/envs/psyplot/bin:/hpc/uhome/icon-ku/miniconda3/condabin:/e/uhome/kfroehli/bin/NCL/bin:/hpc/sw/cdo/1.9.8/x86/gnu/bin:/hpc/sw/nec/sbin:/hpc/sw/libdwd/1.1.7/x86/intel/bin:/hpc/sw/eccodes/2.14.1/x86/intel/bin:/hpc/sw/netcdf4/4.7.3/x86/intel/bin:/hpc/sw/hdf5/1.10.5/x86/intel/bin:/hpc/sw/aec/1.0.3/x86/intel/bin:/hpc/sw/skyClient/opt/dwd/skyClient-11.0.3-0.x86_64/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/bin/intel64:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/libfabric/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/bin:/hpc/sw/intel/debugger_2020/gdb/intel64/bin:/hpc/sw/gnu/gcc/9.1.0/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/nec/nqsv/bin:/opt/nec/nqsv/sbin:/opt/nec/nqsv/bin:/opt/nec/nqsv/sbin PKG_CONFIG_PATH: /hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mkl/bin/pkgconfig REQUESTS_CA_BUNDLE: SSL_CERT_FILE: SysPATH: /hpc/sw/nec/sbin:/hpc/sw/libdwd//1.1.7/x86/intel/bin:/hpc/sw/eccodes//2.14.1/x86/intel/bin:/hpc/sw/netcdf4/4.7.3/x86/intel/bin:/hpc/sw/hdf5/1.10.5/x86/intel/bin:/hpc/sw/aec//1.0.3/x86/intel/bin:/hpc/sw/skyClient/opt/dwd/skyClient-11.0.3-0.x86_64/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/bin/intel64:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/libfabric/bin:/hpc/sw/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64/bin:/hpc/sw/intel/debugger_2020/gdb/intel64/bin:/hpc/sw/gnu/gcc/9.1.0/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/nec/nqsv/bin:/opt/nec/nqsv/sbin:/opt/nec/nqsv/bin:/opt/nec/nqsv/sbin TMPPATH: /scratch ```
Chilipp commented 3 years ago

ok @csteger, da sind tatsächlich einige Library Paths gesetzt, das ist das was ich vermutet habe. Ich vermute, das kann diese Probleme erklären. Deshalb ist es häufig besser, die System-Libraries auf Clustern zu benutzen anstelle von Conda.

Falls letzteres (also die System-Libraries) bei dir nicht funktioniert, probier mal, bevor du conda activate psyplot ausführst, die folgenden Environment variablen zurückzusetzen: C_INCLUDE_PATH, INCLUDE_PATH, LD_LIBRARY_PATH, LD_RUN_PATH, LIBRARY_PATH

also sowas wie

unset C_INCLUDE_PATH
unset INCLUDE_PATH
unset LD_LIBRARY_PATH
unset LD_RUN_PATH
unset LIBRARY_PATH
conda activate psyplot
psy-view
csteger commented 3 years ago

Hallo @Chilipp,

letztlich war es jetzt mit deinen Tipps ziemlich einfach:

  1. module load python/2021.1
  2. pip3 install psy-view dask toolz PyQt5==5.12. pyqtwebengine==5.12. --user
  3. ~.local/bin zu PATH Variable hinzufügen
  4. psy-view dateiname und das Bild ist da (auf dem Windowslaptop den ich derzeit im Homeoffice nutze musste Cygwin geöffent sein, sonst gab es eine Fehlermeldung und das Display konnte nicht geöffnet werden)

Ich habe mir psy-view bisher nur kurz angeschaut, aber das ist ein super tool für ICON Daten. Vielen Dank dafür und für die Hilfe bei der Installation.

Chilipp commented 3 years ago

gerne! freut mich, dass es geklappt hat =)