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conda-forge / fenics-feedstock

A conda-smithy repository for fenics.
BSD 3-Clause "New" or "Revised" License
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RuntimeWarning: mpi4py.MPI.Prequest size changed #141

Closed johannesring closed 3 years ago

johannesring commented 3 years ago

Issue:

When running the python version of the Poisson demo, I see a lot of warnings like this:

  if MPI.size(mpi_comm) == 1:
/home/johannr/miniconda3/envs/fenics-test2/lib/python3.9/site-packages/dolfin/jit/jit.py:46: RuntimeWarning: mpi4py.MPI.Prequest size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject


Environment (conda list):

``` $ conda list # packages in environment at /home/johannr/miniconda3/envs/fenics-test2: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge binutils_linux-64 2.36 hf3e587d_1 conda-forge boost-cpp 1.74.0 h312852a_4 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.2 h7f98852_0 conda-forge ca-certificates 2021.5.30 ha878542_0 conda-forge certifi 2021.5.30 py39hf3d152e_0 conda-forge cmake 3.21.2 h8897547_0 conda-forge cycler 0.10.0 py_2 conda-forge dbus 1.13.6 h48d8840_2 conda-forge eigen 3.3.9 h4bd325d_1 conda-forge expat 2.4.1 h9c3ff4c_0 conda-forge fenics 2019.1.0 py39hf3d152e_21 conda-forge fenics-dijitso 2019.1.0 py39hf3d152e_21 conda-forge fenics-dolfin 2019.1.0 py39hc6fefde_21 conda-forge fenics-ffc 2019.1.0 py39hf3d152e_21 conda-forge fenics-fiat 2019.1.0 py39hf3d152e_21 conda-forge fenics-libdolfin 2019.1.0 h5ba192a_21 conda-forge fenics-ufl 2019.1.0 py39hf3d152e_21 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge freetype 2.10.4 h0708190_1 conda-forge gcc_impl_linux-64 9.4.0 h03d3576_8 conda-forge gcc_linux-64 9.4.0 h391b98a_1 conda-forge gettext 0.19.8.1 h73d1719_1006 conda-forge glib 2.68.4 h9c3ff4c_1 conda-forge glib-tools 2.68.4 h9c3ff4c_1 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gmpy2 2.1.0b5 py39h78fa15d_0 conda-forge gst-plugins-base 1.18.5 hf529b03_0 conda-forge gstreamer 1.18.5 h76c114f_0 conda-forge gxx_impl_linux-64 9.4.0 h03d3576_8 conda-forge gxx_linux-64 9.4.0 h0316aca_1 conda-forge hdf5 1.10.6 mpi_mpich_h996c276_1014 conda-forge hypre 2.18.2 hc98498a_1 conda-forge icu 68.1 h58526e2_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jpeg 9d h36c2ea0_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_14 conda-forge kiwisolver 1.3.2 py39h1a9c180_0 conda-forge krb5 1.19.2 hcc1bbae_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge lerc 2.2.1 h9c3ff4c_0 conda-forge libblas 3.9.0 11_linux64_openblas conda-forge libcblas 3.9.0 11_linux64_openblas conda-forge libclang 11.1.0 default_ha53f305_1 conda-forge libcurl 7.79.0 h2574ce0_0 conda-forge libdeflate 1.7 h7f98852_5 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 3.4.2 h9c3ff4c_1 conda-forge libgcc-devel_linux-64 9.4.0 hd854feb_8 conda-forge libgcc-ng 11.2.0 h1d223b6_8 conda-forge libgfortran-ng 11.2.0 h69a702a_8 conda-forge libgfortran5 11.2.0 h5c6108e_8 conda-forge libglib 2.68.4 h174f98d_1 conda-forge libgomp 11.2.0 h1d223b6_8 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 11_linux64_openblas conda-forge libllvm11 11.1.0 hf817b99_2 conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.17 pthreads_h8fe5266_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libpq 13.3 hd57d9b9_0 conda-forge libsanitizer 9.4.0 h79bfe98_8 conda-forge libssh2 1.10.0 ha56f1ee_0 conda-forge libstdcxx-devel_linux-64 9.4.0 hd854feb_8 conda-forge libstdcxx-ng 11.2.0 he4da1e4_8 conda-forge libtiff 4.3.0 hf544144_1 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.42.0 h7f98852_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp-base 1.2.1 h7f98852_0 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge matplotlib 3.4.3 py39hf3d152e_0 conda-forge matplotlib-base 3.4.3 py39h2fa2bec_0 conda-forge metis 5.1.0 h58526e2_1006 conda-forge mpc 1.2.1 h9f54685_0 conda-forge mpfr 4.1.0 h9202a9a_1 conda-forge mpi 1.0 mpich conda-forge mpi4py 3.1.1 py39h6438238_0 conda-forge mpich 3.4.2 h846660c_100 conda-forge mpmath 1.2.1 pyhd8ed1ab_0 conda-forge mumps-include 5.2.1 ha770c72_10 conda-forge mumps-mpi 5.2.1 hd6b9cac_10 conda-forge mysql-common 8.0.25 ha770c72_2 conda-forge mysql-libs 8.0.25 hfa10184_2 conda-forge ncurses 6.2 h58526e2_4 conda-forge nspr 4.30 h9c3ff4c_0 conda-forge nss 3.69 hb5efdd6_0 conda-forge numpy 1.21.2 py39hdbf815f_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openssl 1.1.1l h7f98852_0 conda-forge parmetis 4.0.3 h2a9763c_1005 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge petsc 3.14.5 h60475ce_0 conda-forge petsc4py 3.14.1 py39h16c3f58_1 conda-forge pillow 8.3.2 py39ha612740_0 conda-forge pip 21.2.4 pyhd8ed1ab_0 conda-forge pkg-config 0.29.2 h36c2ea0_1008 conda-forge pkgconfig 1.5.5 py39hf3d152e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptscotch 6.0.9 h253636d_1 conda-forge pybind11 2.6.2 py39h1a9c180_0 conda-forge pybind11-global 2.6.2 py39h1a9c180_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 python 3.9.7 hb7a2778_1_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.9 2_cp39 conda-forge qt 5.12.9 hda022c4_4 conda-forge readline 8.1 h46c0cb4_0 conda-forge rhash 1.4.1 h7f98852_0 conda-forge scalapack 2.0.2 hf659fdc_1009 conda-forge scotch 6.0.9 h3858553_1 conda-forge setuptools 58.0.4 py39hf3d152e_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slepc 3.14.2 h44d3fa2_0 conda-forge slepc4py 3.14.0 py39h1e75aa9_1 conda-forge sqlite 3.36.0 h9cd32fc_1 conda-forge suitesparse 5.6.0 h717dc36_0 conda-forge superlu 5.2.2 h16cfea0_0 conda-forge superlu_dist 6.2.0 h25dcc4a_4 conda-forge sympy 1.8 py39hf3d152e_0 conda-forge sysroot_linux-64 2.12 he073ed8_14 conda-forge tbb 2020.2 h4bd325d_4 conda-forge tk 8.6.11 h27826a3_1 conda-forge tornado 6.1 py39h3811e60_1 conda-forge tzdata 2021a he74cb21_1 conda-forge wheel 0.37.0 pyhd8ed1ab_1 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 zlib 1.2.11 h516909a_1010 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : fenics-test2 active env location : /home/johannr/miniconda3/envs/fenics-test2 shell level : 1 user config file : /home/johannr/.condarc populated config files : /home/johannr/.condarc conda version : 4.10.0 conda-build version : not installed python version : 3.9.1.final.0 virtual packages : __linux=5.11.0=0 __glibc=2.33=0 __unix=0=0 __archspec=1=x86_64 base environment : /home/johannr/miniconda3 (writable) conda av data dir : /home/johannr/miniconda3/etc/conda conda av metadata url : https://repo.anaconda.com/pkgs/main channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /home/johannr/miniconda3/pkgs /home/johannr/.conda/pkgs envs directories : /home/johannr/miniconda3/envs /home/johannr/.conda/envs platform : linux-64 user-agent : conda/4.10.0 requests/2.25.1 CPython/3.9.1 Linux/5.11.0-25-generic ubuntu/21.04 glibc/2.33 UID:GID : 1000:1000 netrc file : None offline mode : False ```