Greetings,
ase test fails on an openmpi error, where openmpi is module library.
Any help please ?
[email protected]:~/work/projects/open-collection/theoretical_chemistry/software/ase/buildup_on_servers/jinr_ru/vmXY_hydra/ase-tests/.ase info
platform Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.17
python-3.10.13 /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/Python/v3.10.13/bin/python3.10
ase-3.23.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/ase
numpy-1.26.4 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/numpy
scipy-1.12.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/scipy
matplotlib-3.8.3 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/matplotlib
spglib-2.5.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/spglib
ase_ext-20.9.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/ase_ext
flask-3.0.3 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/flask
psycopg2-2.9.9 (dt dec pq3 ext lo64) /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/psycopg2
pyamg-5.2.1 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/pyamg
[email protected]:~/work/projects/open-collection/theoretical_chemistry/software/ase/buildup_on_servers/jinr_ru/vmXY_hydra/ase-tests/.module list
Currently Loaded Modulefiles:
1) BASE/1.0 2) Python/v3.10.13 3) GVR/v1.0-1 4) openmpi/v1.8.8-1
[email protected]:~/work/projects/open-collection/theoretical_chemistry/software/ase/buildup_on_servers/jinr_ru/vmXY_hydra/ase-tests/.ase test -j0
About to run pytest with these parameters:
=========================================================================== test session starts ===========================================================================
platform linux -- Python 3.10.13, pytest-8.3.3, pluggy-1.5.0
Libraries
=========
ase-3.23.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/ase
numpy-1.26.4 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/numpy
scipy-1.12.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/scipy
matplotlib-3.8.3 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/matplotlib
spglib-2.5.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/spglib
ase_ext-20.9.0 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/ase_ext
flask-3.0.3 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/flask
psycopg2-2.9.9 (dt dec pq3 ext lo64) /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/psycopg2
pyamg-5.2.1 /lustre/home/user/m/milias/.local/lib/python3.10/site-packages/pyamg
Calculators
===========
Config: No configuration file specified
Datafiles: ase-datafiles package not installed
[ ] abinit not installed: 'abinit'
[ ] ace cfg=<ase.config.Config object at 0x7fec3c1e9a50>
[ ] aims not installed: 'aims'
[ ] amber cfg=<ase.config.Config object at 0x7fec3c1e9a50>
[vm01.hydra.local:26519] mca: base: component_find: unable to open /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_mmap: /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_shmem_base_framework (ignored)
[vm01.hydra.local:26519] mca: base: component_find: unable to open /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_posix: /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_framework (ignored)
[vm01.hydra.local:26519] mca: base: component_find: unable to open /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_sysv: /cvmfs/hybrilit.jinr.ru/sw/slc7_x86-64/openmpi/v1.8.8-1/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_shmem_base_framework (ignored)
--------------------------------------------------------------------------
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
opal_shmem_base_select failed
--> Returned value -1 instead of OPAL_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
opal_init failed
--> Returned value Error (-1) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** 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)
[vm01.hydra.local:26519] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
[email protected]:~/work/projects/open-collection/theoretical_chemistry/software/ase/buildup_on_servers/jinr_ru/vmXY_hydra/ase-tests/.