Can't install petsc4py in Ubuntu

Issue #143 closed
Mujahed Patil created an issue

Hello,

I need to use open framework openMDAO for my project in Ubuntu. Which needs mpi4py and petsc4py, I have installed mpi4py using pip command $ pip install mpi4py.

But I am not able to install petsc4py using command $ pip install petsc petsc4py. It gives error as follows:

(base) mujahed@Lenovo-G50-80:~$ pip install petsc petsc4py
Collecting petsc
  Using cached petsc-3.13.4.tar.gz (14.9 MB)
Collecting petsc4py
  Using cached petsc4py-3.13.0.tar.gz (1.9 MB)
    ERROR: Command errored out with exit status 1:
     command: /home/mujahed/anaconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-bwcqa2gd/petsc4py/setup.py'"'"'; __file__='"'"'/tmp/pip-install-bwcqa2gd/petsc4py/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-kjttgt6a
         cwd: /tmp/pip-install-bwcqa2gd/petsc4py/
    Complete output (52 lines):
    running egg_info
    creating /tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info
    writing /tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info/PKG-INFO
    writing dependency_links to /tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info/dependency_links.txt
    writing requirements to /tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info/requires.txt
    writing top-level names to /tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info/top_level.txt
    writing manifest file '/tmp/pip-pip-egg-info-kjttgt6a/petsc4py.egg-info/SOURCES.txt'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-bwcqa2gd/petsc4py/setup.py", line 270, in <module>
        main()
      File "/tmp/pip-install-bwcqa2gd/petsc4py/setup.py", line 267, in main
        run_setup()
      File "/tmp/pip-install-bwcqa2gd/petsc4py/setup.py", line 119, in run_setup
        setup(packages     = ['petsc4py',
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 165, in setup
        return distutils.core.setup(**attrs)
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 297, in run
        self.find_sources()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 304, in find_sources
        mm.run()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 535, in run
        self.add_defaults()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/egg_info.py", line 571, in add_defaults
        sdist.add_defaults(self)
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/command/sdist.py", line 226, in add_defaults
        self._add_defaults_python()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/sdist.py", line 135, in _add_defaults_python
        build_py = self.get_finalized_command('build_py')
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/cmd.py", line 299, in get_finalized_command
        cmd_obj.ensure_finalized()
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/cmd.py", line 107, in ensure_finalized
        self.finalize_options()
      File "/home/mujahed/anaconda3/lib/python3.8/site-packages/setuptools/command/build_py.py", line 39, in finalize_options
        orig.build_py.finalize_options(self)
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/command/build_py.py", line 43, in finalize_options
        self.set_undefined_options('build',
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/cmd.py", line 287, in set_undefined_options
        src_cmd_obj.ensure_finalized()
      File "/home/mujahed/anaconda3/lib/python3.8/distutils/cmd.py", line 107, in ensure_finalized
        self.finalize_options()
      File "/tmp/pip-install-bwcqa2gd/petsc4py/conf/baseconf.py", line 398, in finalize_options
        self.petsc_dir  = config.get_petsc_dir(self.petsc_dir)
      File "/tmp/pip-install-bwcqa2gd/petsc4py/conf/baseconf.py", line 336, in get_petsc_dir
        petsc_dir = petsc.get_petsc_dir()
    AttributeError: module 'petsc' has no attribute 'get_petsc_dir'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I don’t have computer science background and this is the first time I am dealing with something like mpi.

I have Ubuntu 20.04.1 LTS and I am using Anaconda3 as well.

Can anyone please help ?

Comments (11)

  1. Lisandro Dalcin

    Get PETSc (which is not a Python package) installed by pip is not so easy. I recommend running pip uninstall petsc; pip install petsc; pip install petsc4py;. However, you should really install PETSc yourself wherever you want, set the PETSC_DIR environment variable, then pip install petsc4py

    Or maybe you should look at using Anaconda Python and packages from the conda-forge channel, they provide petsc and petsc4py ready to be used.

  2. Lisandro Dalcin

    If you are using Anaconda, then create a new environment, then try

    conda install -c conda-forge petsc4py

  3. Mujahed Patil reporter

    Thank you very much, Lisandro for replying. I much appreciate it. And I am very glad to say that it worked. I installed petsc4py successfully by creating new environment using anaconda.

    But there is another error that occured during testing of openMDAO by running the command $ testflo openmdao -n 1. Following error occured:

    (omdenvironment) mujahed@Lenovo-G50-80:~$ testflo openmdao -n 1
    .............................................................................SSS......../home/mujahed/anaconda3/envs/omdenvironment/lib/python3.8/site-packages/openmdao/core/group.py:1113: UserWarning:Group (sub): Attempted to connect from 'tgt.x' to 'cmp.x', but 'tgt.x' is an input. All connections must be from an output to an input.
    .......................................(mpi) /home/mujahed/anaconda3/envs/omdenvironment/lib/python3.8/site-packages/openmdao/utils/tests/test_find_citations.py:TestFindCitePar.test_find_cite_petsc ... FAIL (00:00:0.00, 0 MB)
    *** An error occurred in MPI_Init_thread
    *** on a NULL communicator
    *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
    ***    and potentially your MPI job)
    [Lenovo-G50-80:04984] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
    *** An error occurred in MPI_Init_thread
    *** on a NULL communicator
    *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
    ***    and potentially your MPI job)
    [Lenovo-G50-80:04983] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
    

    Above error message is repeating.

    I am using openmpi 4.0.4, mpi 1.0, mpi4py 3.0.3, petsc 3.13.4 and petsc4py 3.13.0

    Can you please help me with this?

    Thanks again.

  4. Lisandro Dalcin

    This probably means that somehow you build some packages with Open MPI, and some others with MPICH. Are you using MPI as installed with conda? Or better, can you paste the exact sequence of commands you used to create your environment, including the installation of openmdao? openmdao should be built with the same MPI as thhe other packages, that means you have to use openmpi from conda-forge, and that you may need to conda install openmpi-mpicc to get the MPI compiler wrappers.

  5. Mujahed Patil reporter

    Initially I installed openmpi but not in the environment of openmdao.

    I uninstalled it by command $ sudo apt-get purge openmpi-common

    Following are the commands from terminal :

    1. conda create --name omdenvironment
    2. conda activate omdenvironment
    3. conda install -c conda-forge petsc4py
    4. conda install -c conda-forge openmdao[all]
    5. pip install openmdao[test]
    6. conda install -c anaconda mpi4py
    7. testflo openmdao -n 1

    Also I have installed some packages using anaconda-navigator:environments

    Like blas, matplotlib etc.

    Finally, I ran command conda install openmpi-mpicc but it doesn’t work. It is giving same error as above.

    I am attaching the list of packages in my openmdao environment:

    (omdenvironment) mujahed@Lenovo-G50-80:~$ conda list
    # packages in environment at /home/mujahed/anaconda3/envs/omdenvironment:
    #
    # Name                    Version                   Build  Channel
    _libgcc_mutex             0.1                 conda_forge    conda-forge
    _openmp_mutex             4.5                       1_gnu    conda-forge
    alabaster                 0.7.12                   pypi_0    pypi
    appdirs                   1.4.4                    pypi_0    pypi
    argon2-cffi               20.1.0           py38h7b6447c_1  
    attrs                     19.3.0                     py_0  
    babel                     2.8.0                    pypi_0    pypi
    backcall                  0.2.0                      py_0  
    blas                      1.0                    openblas  
    bleach                    3.1.5                      py_0  
    brotlipy                  0.7.0           py38h1e0a361_1000    conda-forge
    ca-certificates           2020.6.20            hecda079_0    conda-forge
    certifi                   2020.6.20        py38h32f6830_0    conda-forge
    cffi                      1.14.1           py38he30daa8_0  
    chardet                   3.0.4           py38h32f6830_1006    conda-forge
    coverage                  4.5.4            py38h516909a_0    conda-forge
    cryptography              3.0              py38h766eaa4_0    conda-forge
    cycler                    0.10.0                   py38_0  
    dbus                      1.13.16              hb2f20db_0  
    decorator                 4.4.2                      py_0  
    defusedxml                0.6.0                      py_0  
    docutils                  0.16                     pypi_0    pypi
    entrypoints               0.3                      py38_0  
    expat                     2.2.9                he6710b0_2  
    fontconfig                2.13.0               h9420a91_0  
    freetype                  2.10.2               h5ab3b9f_0  
    glib                      2.65.0               h3eb4bd4_0  
    gst-plugins-base          1.14.0               hbbd80ab_1  
    gstreamer                 1.14.0               hb31296c_0  
    hdf5                      1.10.6          nompi_h3c11f04_101    conda-forge
    hypre                     2.18.2               h3c37bf7_1    conda-forge
    icu                       58.2                 he6710b0_3  
    idna                      2.10               pyh9f0ad1d_0    conda-forge
    imagesize                 1.2.0                    pypi_0    pypi
    importlib-metadata        1.7.0                    py38_0  
    importlib_metadata        1.7.0                         0  
    ipykernel                 5.3.4            py38h5ca1d4c_0  
    ipython                   7.16.1           py38h5ca1d4c_0  
    ipython_genutils          0.2.0                    py38_0  
    jedi                      0.17.0                   py38_0  
    jinja2                    2.11.2                     py_0  
    jpeg                      9b                   h024ee3a_2  
    jsonschema                3.2.0                    py38_0  
    jupyter_client            6.1.6                      py_0  
    jupyter_core              4.6.3                    py38_0  
    kiwisolver                1.2.0            py38hfd86e86_0  
    lcms2                     2.11                 h396b838_0  
    ld_impl_linux-64          2.34                 hc38a660_9    conda-forge
    libblas                   3.8.0               17_openblas    conda-forge
    libcblas                  3.8.0               17_openblas    conda-forge
    libffi                    3.3                  he6710b0_2  
    libgcc-ng                 9.3.0               h24d8f2e_16    conda-forge
    libgfortran-ng            7.5.0               hdf63c60_16    conda-forge
    libgomp                   9.3.0               h24d8f2e_16    conda-forge
    liblapack                 3.8.0               17_openblas    conda-forge
    libopenblas               0.3.10               h5a2b251_0  
    libopenblas-static        0.3.10                        0  
    libpng                    1.6.37               hbc83047_0  
    libsodium                 1.0.18               h7b6447c_0  
    libstdcxx-ng              9.3.0               hdf63c60_16    conda-forge
    libtiff                   4.1.0                h2733197_1  
    libuuid                   1.0.3                h1bed415_2  
    libxcb                    1.14                 h7b6447c_0  
    libxml2                   2.9.10               he19cac6_1  
    lz4-c                     1.9.2                he6710b0_1  
    markupsafe                1.1.1            py38h7b6447c_0  
    matplotlib                3.3.1                         0  
    matplotlib-base           3.3.1            py38h817c723_0  
    metis                     5.1.0             he1b5a44_1005    conda-forge
    mistune                   0.8.4           py38h7b6447c_1000  
    mpi                       1.0                     openmpi    conda-forge
    mpi4py                    3.0.3            py38hd0bea5a_0    anaconda
    mumps-include             5.2.1                         8    conda-forge
    mumps-mpi                 5.2.1                h7e80380_8    conda-forge
    my-caserecorder999        -                        pypi_0    pypi
    my-implicitcomponent999   -                        pypi_0    pypi
    nbconvert                 5.6.1                    py38_0  
    nbformat                  5.0.7                      py_0  
    ncurses                   6.2                  he1b5a44_1    conda-forge
    networkx                  2.5                        py_0    conda-forge
    nomkl                     3.0                           0  
    notebook                  6.1.1                    py38_0  
    numpy                     1.19.1           py38hbc27379_2    conda-forge
    numpydoc                  1.1.0                    pypi_0    pypi
    olefile                   0.46                       py_0  
    openblas                  0.3.10                        0  
    openblas-devel            0.3.10                        0  
    openmdao                  3.2.1                      py_0    conda-forge
    openmpi                   4.0.4                hdf1f1ad_0    conda-forge
    openssl                   1.1.1g               h516909a_1    conda-forge
    packaging                 20.4                       py_0  
    pandoc                    2.10.1                        0  
    pandocfilters             1.4.2                    py38_1  
    parameterized             0.7.4                    pypi_0    pypi
    parmetis                  4.0.3             hc401efc_1005    conda-forge
    parso                     0.8.0                      py_0  
    pcre                      8.44                 he6710b0_0  
    petsc                     3.13.4               h2041a36_0    conda-forge
    petsc4py                  3.13.0           py38h745227e_3    conda-forge
    pexpect                   4.8.0                    py38_0  
    pickleshare               0.7.5                 py38_1000  
    pillow                    7.2.0            py38hb39fc2d_0  
    pip                       20.2.2                     py_0    conda-forge
    prometheus_client         0.8.0                      py_0  
    prompt-toolkit            3.0.5                      py_0  
    ptscotch                  6.0.9                h9271a0d_1    conda-forge
    ptyprocess                0.6.0                    py38_0  
    pycodestyle               2.6.0                    pypi_0    pypi
    pycparser                 2.20                       py_2  
    pydocstyle                2.0.0                    pypi_0    pypi
    pydoe2                    1.3.0                      py_0    conda-forge
    pyee                      7.0.2                    pypi_0    pypi
    pygments                  2.6.1                      py_0  
    pyopenssl                 19.1.0                     py_1    conda-forge
    pyparsing                 2.4.7                      py_0  
    pyppeteer2                0.2.2                    pypi_0    pypi
    pyqt                      5.9.2            py38h05f1152_4  
    pyrsistent                0.16.0           py38h7b6447c_0  
    pysocks                   1.7.1            py38h32f6830_1    conda-forge
    python                    3.8.5                hcff3b4d_0  
    python-dateutil           2.8.1                      py_0  
    python_abi                3.8                      1_cp38    conda-forge
    pytz                      2020.1                   pypi_0    pypi
    pyzmq                     19.0.1           py38he6710b0_1  
    qt                        5.9.7                h5867ecd_1  
    readline                  8.0                  he28a2e2_2    conda-forge
    requests                  2.24.0             pyh9f0ad1d_0    conda-forge
    scalapack                 2.0.2             hfc3855d_1008    conda-forge
    scipy                     1.5.2            py38h8c5af15_0    conda-forge
    scotch                    6.0.9                h0eec0ba_1    conda-forge
    send2trash                1.5.0                    py38_0  
    setuptools                49.6.0           py38h32f6830_0    conda-forge
    sip                       4.19.13          py38he6710b0_0  
    six                       1.15.0                     py_0  
    snowballstemmer           2.0.0                    pypi_0    pypi
    sphinx                    3.2.1                    pypi_0    pypi
    sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
    sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
    sphinxcontrib-htmlhelp    1.0.3                    pypi_0    pypi
    sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
    sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
    sphinxcontrib-serializinghtml 1.1.4                    pypi_0    pypi
    sqlite                    3.33.0               h4cf870e_0    conda-forge
    suitesparse               5.6.0                h717dc36_0    conda-forge
    superlu                   5.2.1             hfe2efc7_1207    conda-forge
    tbb                       2020.1               hc9558a2_0    conda-forge
    terminado                 0.8.3                    py38_0  
    testflo                   1.4.2                      py_0    conda-forge
    testpath                  0.4.4                      py_0  
    tk                        8.6.10               hed695b0_0    conda-forge
    tornado                   6.0.4            py38h7b6447c_1  
    tqdm                      4.48.2                   pypi_0    pypi
    traitlets                 4.3.3                    py38_0  
    urllib3                   1.25.10                    py_0    conda-forge
    wcwidth                   0.2.5                      py_0  
    webencodings              0.5.1                    py38_1  
    websockets                8.1                      pypi_0    pypi
    wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
    xz                        5.2.5                h516909a_1    conda-forge
    zeromq                    4.3.2                he6710b0_2  
    zipp                      3.1.0                      py_0  
    zlib                      1.2.11            h516909a_1007    conda-forge
    zstd                      1.4.5                h9ceee32_0  
    

    Can you please help me out?

    Thank you again for replying that quick.

  6. Lisandro Dalcin

    You should try to install all the packages from the conda-forge channel, so you should always do conda install -c conda-forge <package>. This is my recommendation:

    • Get rid of your environment and create a new fresh one
    • Configure the environment such that you always use the conda-forge channel first:
    conda config --add channels conda-forge
    conda config --set channel_priority strict
    conda config --set show_channel_urls true
    
    • Now , just to make things explicit, install your preferred MPI. I’m a MPICH user, and I always recommend it, but you are free to make your own choice and live with the consequences. If you issue the command below, you should see a confirmation that the package comes from the conda-forge channel.
    conda install mpich
    
    • Now install mp4py and petsc4py. conda will install the proper builds that use MPICH. Again, check that both packages come from the conda-forge channel. This is somethig you were doing wrong last time, you were installing mpi4py from the default anaconda channel, don’t!!
    conda install mpi4py petsc4py
    
    • Finally, install OpenMDAO. I see that they have a conda-forge package.
    conda install openmdao
    

    Alterntatively, you could install OpenMDAO with pipif really needed. But you should always prefer the conda package if available.

  7. Mujahed Patil reporter

    I followed all the above steps as you explained. It stopped giving error about mpi. Now the test is giving another error as follows:

    (omdenv) mujahed@Lenovo-G50-80:~$ testflo openmdao -n 1
    .............................................................................SSS......../home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/core/group.py:1113: UserWarning:Group (sub): Attempted to connect from 'tgt.x' to 'cmp.x', but 'tgt.x' is an input. All connections must be from an output to an input.
    .........................................................................................................SSS.SSSS......................................................................................................................................................................................................................................S.............................................................................................S.................................S........................................................................S.SS.......................................S.............................................................................................................................................................S....................................................SSS..........SSSSSSSSSSS..S....................................................................................................................................S............................................................................................................................................................................S..................................................................S........(mpi) /home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/core/tests/test_prob_remote2.py:ProbRemote4TestCase.test_prob_split_comm ... FAIL (00:00:0.01, 381 MB)
    Traceback (most recent call last):
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/testflo/test.py", line 425, in _try_call
        func()
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/core/tests/test_prob_remote2.py", line 307, in test_prob_split_comm
        prob.driver = om.pyOptSparseDriver()
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/drivers/pyoptsparse_driver.py", line 138, in __init__
        raise RuntimeError('pyOptSparseDriver is not available, pyOptsparse is not installed.')
    RuntimeError: pyOptSparseDriver is not available, pyOptsparse is not installed.
    
    (mpi) /home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/core/tests/test_prob_remote2.py:ProbRemoteTestCase.test_get_remote ... FAIL (00:00:0.01, 195 MB)
    Traceback (most recent call last):
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/testflo/test.py", line 425, in _try_call
        func()
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/site-packages/openmdao/core/tests/test_prob_remote2.py", line 200, in test_get_remote
        prob.get_val('par.c2.x', get_remote=False)
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/unittest/case.py", line 227, in __exit__
        self._raiseFailure("{} not raised".format(exc_name))
      File "/home/mujahed/anaconda3/envs/omdenv/lib/python3.8/unittest/case.py", line 164, in _raiseFailure
        raise self.test_case.failureException(msg)
    AssertionError: RuntimeError not raised
    
    ...SSS..................................S............S.....X......................................................................................................................................................................................SS.SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS......
       Normal return from subroutine COBYLA
    
       NFVALS =   56   F =-1.080000E+02    MAXCV = 0.000000E+00
       X = 3.500001E+00  -3.500001E+00
    .................................................
       Normal return from subroutine COBYLA
    
       NFVALS =  124   F =-2.733333E+01    MAXCV = 0.000000E+00
       X = 6.666667E+00  -7.333332E+00
    .........................................................................................................................................................................................................................................................................................................................................................................S.....................................................................................................................S...........................................
       Normal return from subroutine COBYLA
    
       NFVALS =   54   F =-2.700000E+01    MAXCV = 0.000000E+00
       X = 6.999999E+00  -6.999999E+00
    .............................................SSS..............................................................................................................S...........................................................................................................................................................................................................................................................................................................................................................
    
    The following tests failed:
    test_prob_remote2.py:ProbRemote4TestCase.test_prob_split_comm
    test_prob_remote2.py:ProbRemoteTestCase.test_get_remote
    
    
    Passed:  2574
    Failed:  2
    Skipped: 106
    
    
    Ran 2682 tests using 1 processes
    Wall clock time:   00:22:48.28
    

    First I installed openMDAO using conda install openmdao and conda install testflo but it was giving the error as above so I uninstalled it. Then I tried using pip install openmdao[all] and pip install openmdao[test] but the error was the same.

    Following are the packages installed in the environment:

    (omdenv) mujahed@Lenovo-G50-80:~$ conda list
    # packages in environment at /home/mujahed/anaconda3/envs/omdenv:
    #
    # Name                    Version                   Build  Channel
    _libgcc_mutex             0.1                 conda_forge    conda-forge
    _openmp_mutex             4.5                       1_gnu    conda-forge
    alabaster                 0.7.12                   pypi_0    pypi
    appdirs                   1.4.4                    pypi_0    pypi
    babel                     2.8.0                    pypi_0    pypi
    baron                     0.9                      pypi_0    pypi
    bokeh                     2.2.0                    pypi_0    pypi
    ca-certificates           2020.6.20            hecda079_0    conda-forge
    certifi                   2020.6.20        py38h32f6830_0    conda-forge
    chardet                   3.0.4                    pypi_0    pypi
    colorama                  0.4.3                    pypi_0    pypi
    coverage                  4.5.4                    pypi_0    pypi
    cycler                    0.10.0                   pypi_0    pypi
    decorator                 4.4.2                    pypi_0    pypi
    docutils                  0.16                     pypi_0    pypi
    hdf5                      1.10.6          nompi_h3c11f04_101    conda-forge
    hypre                     2.18.2               hc98498a_1    conda-forge
    idna                      2.10                     pypi_0    pypi
    imagesize                 1.2.0                    pypi_0    pypi
    jinja2                    2.11.2                   pypi_0    pypi
    kiwisolver                1.2.0                    pypi_0    pypi
    ld_impl_linux-64          2.34                 hc38a660_9    conda-forge
    libblas                   3.8.0               17_openblas    conda-forge
    libcblas                  3.8.0               17_openblas    conda-forge
    libffi                    3.2.1             he1b5a44_1007    conda-forge
    libgcc-ng                 9.3.0               h24d8f2e_16    conda-forge
    libgfortran-ng            7.5.0               hdf63c60_16    conda-forge
    libgomp                   9.3.0               h24d8f2e_16    conda-forge
    liblapack                 3.8.0               17_openblas    conda-forge
    libopenblas               0.3.10          pthreads_hb3c22a3_4    conda-forge
    libstdcxx-ng              9.3.0               hdf63c60_16    conda-forge
    markupsafe                1.1.1                    pypi_0    pypi
    matplotlib                3.3.1                    pypi_0    pypi
    metis                     5.1.0             he1b5a44_1005    conda-forge
    mock                      4.0.2                    pypi_0    pypi
    mpi                       1.0                       mpich    conda-forge
    mpi4py                    3.0.3            py38h4a80816_1    conda-forge
    mpich                     3.3.2                hc856adb_0    conda-forge
    mumps-include             5.2.1                         8    conda-forge
    mumps-mpi                 5.2.1                h1f24c91_8    conda-forge
    ncurses                   6.2                  he1b5a44_1    conda-forge
    networkx                  2.5                      pypi_0    pypi
    numpy                     1.19.1           py38hbc27379_2    conda-forge
    numpydoc                  1.1.0                    pypi_0    pypi
    openmdao                  3.2.1                    pypi_0    pypi
    openssl                   1.1.1g               h516909a_1    conda-forge
    packaging                 20.4                     pypi_0    pypi
    parameterized             0.7.4                    pypi_0    pypi
    parmetis                  4.0.3             h9f7b9cf_1005    conda-forge
    petsc                     3.13.4               h82b89f7_0    conda-forge
    petsc4py                  3.13.0           py38h8c4a8b4_3    conda-forge
    pillow                    7.2.0                    pypi_0    pypi
    pip                       20.2.2                     py_0    conda-forge
    ptscotch                  6.0.9                h294ddb0_1    conda-forge
    pycodestyle               2.6.0                    pypi_0    pypi
    pydocstyle                2.0.0                    pypi_0    pypi
    pydoe2                    1.3.0                    pypi_0    pypi
    pyee                      7.0.2                    pypi_0    pypi
    pygments                  2.6.1                    pypi_0    pypi
    pyparsing                 2.4.7                    pypi_0    pypi
    pyppeteer2                0.2.2                    pypi_0    pypi
    python                    3.8.5           h1103e12_5_cpython    conda-forge
    python-dateutil           2.8.1                    pypi_0    pypi
    python_abi                3.8                      1_cp38    conda-forge
    pytz                      2020.1                   pypi_0    pypi
    pyyaml                    5.3.1                    pypi_0    pypi
    readline                  8.0                  he28a2e2_2    conda-forge
    redbaron                  0.9.2                    pypi_0    pypi
    requests                  2.24.0                   pypi_0    pypi
    rply                      0.7.7                    pypi_0    pypi
    scalapack                 2.0.2             hfacbc1e_1008    conda-forge
    scipy                     1.5.2                    pypi_0    pypi
    scotch                    6.0.9                h0eec0ba_1    conda-forge
    setuptools                49.6.0           py38h32f6830_0    conda-forge
    six                       1.15.0                   pypi_0    pypi
    snowballstemmer           2.0.0                    pypi_0    pypi
    sphinx                    3.2.1                    pypi_0    pypi
    sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
    sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
    sphinxcontrib-htmlhelp    1.0.3                    pypi_0    pypi
    sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
    sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
    sphinxcontrib-serializinghtml 1.1.4                    pypi_0    pypi
    sqlite                    3.33.0               h4cf870e_0    conda-forge
    suitesparse               5.6.0                h717dc36_0    conda-forge
    superlu                   5.2.1             hfe2efc7_1207    conda-forge
    superlu_dist              6.2.0                h5e15a89_2    conda-forge
    tbb                       2020.1               hc9558a2_0    conda-forge
    testflo                   1.4.2                    pypi_0    pypi
    tk                        8.6.10               hed695b0_0    conda-forge
    tornado                   6.0.4                    pypi_0    pypi
    tqdm                      4.48.2                   pypi_0    pypi
    typing-extensions         3.7.4.3                  pypi_0    pypi
    urllib3                   1.25.10                  pypi_0    pypi
    websockets                8.1                      pypi_0    pypi
    wheel                     0.35.1             pyh9f0ad1d_0    conda-forge
    xz                        5.2.5                h516909a_1    conda-forge
    zlib                      1.2.11            h516909a_1007    conda-forge
    

    I installed using $ pip install openmdao[all] only because conda install openmdao was giving error.

    Can you please help?

    Thank you again.

  8. Lisandro Dalcin

    So, you followed the steps, and you say MPI was giving errors, but you do not say what errors, and then you proceed to do something different, and you keep copying and pasting long listings. You are running the tests of OpenMDAO, and you get errors, and you keep asking about it, and I have nothing to do with OpenMDAO, how could I possible help? I cannot take responsibility for other packages using mpi4py. Does mpi4py work? Try running mpiexec -n 5 python -m mpi4py.bench helloworld . If that work, then mpi4py is working, and from there you should ask for help where the problems originate. At this point, you should look for help elsewhere, probably the OpenMDAO folks. This is unlikely an mpi4py issue, mpi4py is just a dependency of another software you are using.

  9. Lisandro Dalcin

    To see if petsc4py is working, you can clone the petsc4py repository, then execute python test/runtests.py. If that works, the petsc+petsc4py are also fine. From there, I cannot help with errors in OpenMDAO, you have to ask them about what’s going on. Maybe their tests are broken, or outdated, or you have a problem in your system, but they (OpenMDAO folks) should know better than I.

  10. Mujahed Patil reporter

    Thank you very much Lisandro, you have been great help for me on this issue. I ran above test successfully. As you said this is not the issue of mpi4py or petsc, it must be something else related to either tests or openMDAO.

    Thank you for understanding me and bearing with me for the whole time. Sorry for troubling you.

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