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mpi4py and hdf5 need to be fix for ASE runs #117

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bearecinos opened this issue Apr 3, 2023 · 1 comment
Open

mpi4py and hdf5 need to be fix for ASE runs #117

bearecinos opened this issue Apr 3, 2023 · 1 comment
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@bearecinos
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bug dependencies issues or warnings from dependencies

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@bearecinos
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bearecinos commented Apr 3, 2023 •
edited
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@jrmaddison @dngoldberg

I created a working environment on shin & bow, that runs the inversion for the ASE tomls. The problem is with one of these two libraries.

mpi4py and or hdf5

From the start, so from the environment.yml file, we need to fix h5py=3.6.0 and mpi4py=3.1.1. I can't pin the problem to a specific library and both have open issues now related to openmpi, memory, etc.

see: https://github.com/mpi4py/mpi4py/issues
and: https://github.com/HDFGroup/hdf5/issues

We just need to wait and see as for us these dependencies are broken ... for the time being if you want to create an environment on shin @dngoldberg you need to use the following environment.yml.

name: fenics_ice_trial
channels:
  - conda-forge
dependencies:
  - python=3.8
  - fenics=2019.1.0
  - fenics-dijitso
  - fenics-dolfin
  - fenics-ffc
  - fenics-fiat
  - fenics-libdolfin
  - fenics-ufl
  - matplotlib
  - numpy
  - ipython
  - scipy
  - seaborn
  - h5py=3.6.0
  - conda-build
  - mpi4py=3.1.1
  - toml
  - gitpython
  - "meshio[all]"
  - pytest
  - pytest-benchmark
  - pytest-mpi
  - pytest-dependency
  - pytest-order
  - cytoolz

You can just copy that to a new yml file and do:

via conda:
conda env create --file new_environment.yml

via mamba:
mamba env create --file new_environment.yml

After that Install fenics_ice and tlm_adjoint manually via pip. See instructions here.

There is no point of changing this on the fenics_ice repository instructions or install.sh as everything works except for very large areas thus very large arrays e.g. Amundsen basin. This issue is to do with mpi4py and hdf5 having problems handling those large arrays. An output of the error is detailed in this other issue #116 .
@bearecinos bearecinos added bug dependencies issues or warnings from dependencies labels Apr 3, 2023
@bearecinos bearecinos self-assigned this Apr 3, 2023
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bearecinos commented Apr 3, 2023 •
edited
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I thought I post the actual problem below for clarity ...
This messages either shows up when writing variables to the hdf5 format as in here or during the the actual solving of the inversion, at that stage is very hard to know which line of the code is giving me the error. Could be when it tries to write the inversion output.

*** buffer overflow detected ***: terminated
[bow:04213] *** Process received signal ***
[bow:04213] Signal: Aborted (6)
[bow:04213] Signal code:  (-6)
[bow:04216] *** Process received signal ***
[bow:04216] Signal: Aborted (6)
[bow:04216] Signal code:  (-6)
[bow:04213] [ 0] [bow:04209] *** Process received signal ***
[bow:04209] Signal: Aborted (6)
[bow:04209] Signal code:  (-6)
/lib64/libpthread.so.0(+0xf630)[0x7fcef26ea630]
[bow:04213] [ 1] [bow:04216] [ 0] /lib64/libc.so.6(gsignal+0x37)[0x7fcef1a323d7]
[bow:04213] [ 2] /lib64/libpthread.so.0(+0xf630)[0x7ff0f1df4630]
[bow:04216] [ 1] /lib64/libc.so.6(abort+0x148)[0x7fcef1a33ac8]
[bow:04213] [ 3] /lib64/libc.so.6(gsignal+0x37)[0x7ff0f113c3d7]
[bow:04216] [ 2] /lib64/libc.so.6(+0x78f67)[0x7fcef1a74f67]
[bow:04213] [ 4] /lib64/libc.so.6(abort+0x148)[0x7ff0f113dac8]
[bow:04216] [ 3] [bow:04209] [ 0] /lib64/libc.so.6(__fortify_fail+0x37)[0x7fcef1b14697]
[bow:04213] [ 5] /lib64/libpthread.so.0(+0xf630)[0x7fe2ad017630]
[bow:04209] [ 1] /lib64/libc.so.6(+0x78f67)[0x7ff0f117ef67]
[bow:04216] [ 4] /lib64/libc.so.6(+0x116812)[0x7fcef1b12812]
[bow:04213] [ 6] /lib64/libc.so.6(gsignal+0x37)[0x7fe2ac35f3d7]
[bow:04209] [ 2] /lib64/libc.so.6(+0x115d1b)[0x7fcef1b11d1b]
[bow:04213] [ 7] /lib64/libc.so.6(__fortify_fail+0x37)[0x7ff0f121e697]
[bow:04216] [ 5] /lib64/libc.so.6(abort+0x148)[0x7fe2ac360ac8]
[bow:04209] [ 3] /lib64/libc.so.6(_IO_default_xsputn+0xe1)[0x7fcef1a79031]
[bow:04213] [ 8] /lib64/libc.so.6(+0x116812)[0x7ff0f121c812]
[bow:04216] [ 6] /lib64/libc.so.6(+0x78f67)[0x7fe2ac3a1f67]
[bow:04209] [ 4] /lib64/libc.so.6(+0x115d1b)[0x7ff0f121bd1b]
[bow:04216] [ 7] /lib64/libc.so.6(_IO_vfprintf+0x23b9)[0x7fcef1a46a09]
[bow:04213] [ 9] /lib64/libc.so.6(__fortify_fail+0x37)[0x7fe2ac441697]
[bow:04209] [ 5] /lib64/libc.so.6(__vsprintf_chk+0x88)[0x7fcef1b11da8]
[bow:04213] [10] /lib64/libc.so.6(_IO_default_xsputn+0xe1)[0x7ff0f1183031]
[bow:04216] [ 8] /lib64/libc.so.6(+0x116812)[0x7fe2ac43f812]
[bow:04209] [ 6] /lib64/libc.so.6(_IO_vfprintf+0x23b9)[0x7ff0f1150a09]
[bow:04216] [ 9] /lib64/libc.so.6(__sprintf_chk+0x7d)[0x7fcef1b11cfd]
[bow:04213] [11] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_sharedfp_lockedfile.so(mca_sharedfp_lockedfile_component_file_query+0x6b)[0x7fcec556a17b]
[bow:04213] [12] /lib64/libc.so.6(+0x115d1b)[0x7fe2ac43ed1b]
[bow:04209] [ 7] [bow:04219] *** Process received signal ***
[bow:04219] Signal: Aborted (6)
[bow:04219] Signal code:  (-6)
/lib64/libc.so.6(__vsprintf_chk+0x88)[0x7ff0f121bda8]
[bow:04216] [10] /lib64/libc.so.6(_IO_default_xsputn+0xe1)[0x7fe2ac3a6031]
[bow:04209] [ 8] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_sharedfp_base_file_select+0x16b)[0x7fcee948055b]
[bow:04213] [13] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/../libmca_common_ompio.so.41(mca_common_ompio_file_open+0x2eb)[0x7fcec560579b]
[bow:04213] [14] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_io_ompio.so(mca_io_ompio_file_open+0x20)[0x7fcec5613880]
[bow:04213] [15] /lib64/libc.so.6(__sprintf_chk+0x7d)[0x7ff0f121bcfd]
[bow:04216] [11] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_sharedfp_lockedfile.so(mca_sharedfp_lockedfile_component_file_query+0x6b)[0x7ff0c4c7317b]
[bow:04216] [12] /lib64/libc.so.6(_IO_vfprintf+0x23b9)[0x7fe2ac373a09]
[bow:04209] [ 9] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_io_base_file_select+0x259)[0x7fcee9470789]
[bow:04213] [16] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(ompi_file_open+0x194)[0x7fcee9401114]
[bow:04213] [17] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_sharedfp_base_file_select+0x16b)[0x7ff0e8b8a55b]
[bow:04216] [13] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/../libmca_common_ompio.so.41(mca_common_ompio_file_open+0x2eb)[0x7ff0c4d0e79b]
[bow:04216] [14] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_io_ompio.so(mca_io_ompio_file_open+0x20)[0x7ff0c4d1c880]
[bow:04216] [15] /lib64/libc.so.6(__vsprintf_chk+0x88)[0x7fe2ac43eda8]
[bow:04209] [10] /lib64/libc.so.6(__sprintf_chk+0x7d)[0x7fe2ac43ecfd]
[bow:04209] [11] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_sharedfp_lockedfile.so(mca_sharedfp_lockedfile_component_file_query+0x6b)[0x7fe27fe9617b]
[bow:04209] [12] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_io_base_file_select+0x259)[0x7ff0e8b7a789]
[bow:04216] [16] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(MPI_File_open+0x129)[0x7fcee9427c89]
[bow:04213] [18] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_sharedfp_base_file_select+0x16b)[0x7fe2a3dad55b]
[bow:04209] [13] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/../libmca_common_ompio.so.41(mca_common_ompio_file_open+0x2eb)[0x7fe27ff2c79b]
[bow:04209] [14] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(ompi_file_open+0x194)[0x7ff0e8b0b114]
[bow:04216] [17] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_io_ompio.so(mca_io_ompio_file_open+0x20)[0x7fe27ff3a880]
[bow:04209] [15] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x338298)[0x7fcee9072298]
[bow:04213] [19] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(MPI_File_open+0x129)[0x7ff0e8b31c89]
[bow:04216] [18] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_io_base_file_select+0x259)[0x7fe2a3d9d789]
[bow:04209] [16] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(ompi_file_open+0x194)[0x7fe2a3d2e114]
[bow:04209] [17] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5FD_open+0x15e)[0x7fcee8e5e1be]
[bow:04213] [20] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x338298)[0x7ff0e877c298]
[bow:04216] [19] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(MPI_File_open+0x129)[0x7fe2a3d54c89]
[bow:04209] [18] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5F_open+0x4d5)[0x7fcee8e4c7a5]
[bow:04213] [21] [bow:04219] [ 0] /lib64/libpthread.so.0(+0xf630)[0x7f5992243630]
[bow:04219] [ 1] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5FD_open+0x15e)[0x7ff0e85681be]
[bow:04216] [20] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x338298)[0x7fe2a399f298]
[bow:04209] [19] /lib64/libc.so.6(gsignal+0x37)[0x7f599158b3d7]
[bow:04219] [ 2] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL__native_file_create+0x17)[0x7fcee903b817]
[bow:04213] [22] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5F_open+0x4d5)[0x7ff0e85567a5]
[bow:04216] [21] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5FD_open+0x15e)[0x7fe2a378b1be]
[bow:04209] [20] /lib64/libc.so.6(abort+0x148)[0x7f599158cac8]
[bow:04219] [ 3] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x2e73e2)[0x7fcee90213e2]
[bow:04213] [23] /lib64/libc.so.6(+0x78f67)[0x7f59915cdf67]
[bow:04219] [ 4] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL__native_file_create+0x17)[0x7ff0e8745817]
[bow:04216] [22] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5F_open+0x4d5)[0x7fe2a37797a5]
[bow:04209] [21] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL_file_create+0xbf)[0x7fcee90296bf]
[bow:04213] [24] /lib64/libc.so.6(__fortify_fail+0x37)[0x7f599166d697]
[bow:04219] [ 5] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x2e73e2)[0x7ff0e872b3e2]
[bow:04216] [23] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL__native_file_create+0x17)[0x7fe2a3968817]
[bow:04209] [22] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5Fcreate+0x163)[0x7fcee8e3c693]
[bow:04213] [25] /lib64/libc.so.6(+0x116812)[0x7f599166b812]
[bow:04219] [ 6] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL_file_create+0xbf)[0x7ff0e87336bf]
[bow:04216] [24] /lib64/libc.so.6(+0x115d1b)[0x7f599166ad1b]
[bow:04219] [ 7] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x2e73e2)[0x7fe2a394e3e2]
[bow:04209] [23] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5Fcreate+0x163)[0x7ff0e8546693]
[bow:04216] [25] /lib64/libc.so.6(_IO_default_xsputn+0xe1)[0x7f59915d2031]
[bow:04219] [ 8] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin13HDF5Interface9open_fileEP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_b+0x94)[0x7fceeadc61c4]
[bow:04213] [26] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL_file_create+0xbf)[0x7fe2a39566bf]
[bow:04209] [24] /lib64/libc.so.6(_IO_vfprintf+0x23b9)[0x7f599159fa09]
[bow:04219] [ 9] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5Fcreate+0x163)[0x7fe2a3769693]
[bow:04209] [25] /lib64/libc.so.6(__vsprintf_chk+0x88)[0x7f599166ada8]
[bow:04219] [10] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin8HDF5FileC2EP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_+0x1a7)[0x7fceead9acf7]
[bow:04213] [27] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x180e7a)[0x7fceeb281e7a]
[bow:04213] [28] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x95f1a)[0x7fceeb196f1a]
[bow:04213] [29] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin13HDF5Interface9open_fileEP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_b+0x94)[0x7ff0ea4d01c4]
[bow:04216] [26] /lib64/libc.so.6(__sprintf_chk+0x7d)[0x7f599166acfd]
[bow:04219] [11] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_sharedfp_lockedfile.so(mca_sharedfp_lockedfile_component_file_query+0x6b)[0x7f59650c117b]
[bow:04219] [12] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin13HDF5Interface9open_fileEP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_b+0x94)[0x7fe2a56f31c4]
[bow:04209] [26] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_sharedfp_base_file_select+0x16b)[0x7f5988fd955b]
[bow:04219] [13] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/../libmca_common_ompio.so.41(mca_common_ompio_file_open+0x2eb)[0x7f596515c79b]
[bow:04219] [14] python(PyCFunction_Call+0x52)[0x556dadede052]
[bow:04213] *** End of error message ***
/exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/openmpi/mca_io_ompio.so(mca_io_ompio_file_open+0x20)[0x7f596516a880]
[bow:04219] [15] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin8HDF5FileC2EP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_+0x1a7)[0x7ff0ea4a4cf7]
[bow:04216] [27] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x180e7a)[0x7ff0ea98be7a]
[bow:04216] [28] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x95f1a)[0x7ff0ea8a0f1a]
[bow:04216] [29] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(mca_io_base_file_select+0x259)[0x7f5988fc9789]
[bow:04219] [16] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin8HDF5FileC2EP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_+0x1a7)[0x7fe2a56c7cf7]
[bow:04209] [27] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x180e7a)[0x7fe2a5baee7a]
[bow:04209] [28] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x95f1a)[0x7fe2a5ac3f1a]
[bow:04209] [29] python(PyCFunction_Call+0x52)[0x5595b9bf1052]
[bow:04216] *** End of error message ***
/exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(ompi_file_open+0x194)[0x7f5988f5a114]
[bow:04219] [17] python(PyCFunction_Call+0x52)[0x55a39a3e0052]
[bow:04209] *** End of error message ***
/exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libmpi.so.40(MPI_File_open+0x129)[0x7f5988f80c89]
[bow:04219] [18] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x338298)[0x7f5988bcb298]
[bow:04219] [19] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5FD_open+0x15e)[0x7f59889b71be]
[bow:04219] [20] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5F_open+0x4d5)[0x7f59889a57a5]
[bow:04219] [21] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL__native_file_create+0x17)[0x7f5988b94817]
[bow:04219] [22] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(+0x2e73e2)[0x7f5988b7a3e2]
[bow:04219] [23] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5VL_file_create+0xbf)[0x7f5988b826bf]
[bow:04219] [24] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../.././libhdf5.so.200(H5Fcreate+0x163)[0x7f5988995693]
[bow:04219] [25] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin13HDF5Interface9open_fileEP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_b+0x94)[0x7f598a91f1c4]
[bow:04219] [26] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/../../../libdolfin.so.2019.1(_ZN6dolfin8HDF5FileC2EP19ompi_communicator_tNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_+0x1a7)[0x7f598a8f3cf7]
[bow:04219] [27] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x180e7a)[0x7f598addae7a]
[bow:04219] [28] /exports/csce/datastore/geos/users/brecinos/miniconda3/envs/fenics_ice/lib/python3.8/site-packages/dolfin/cpp.cpython-38-x86_64-linux-gnu.so(+0x95f1a)[0x7f598aceff1a]
[bow:04219] [29] python(PyCFunction_Call+0x52)[0x5585cf9aa052]
[bow:04219] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 0 on node bow exited on signal 6 (Aborted).
--------------------------------------------------------------------------

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