I’m trying to run NEST on Jureca, but I get an error:
Traceback (most recent call last): File "/p/project/jinm60/users/wybo1/Code/NEAST_models/BBP/tests/run_all_tests.py", line 2, in <module> import nest.lib.hl_api_exceptions as nestexceptions File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/__init__.py", line 64, in <module> from .ll_api_kernel_attributes import KernelAttribute # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api_kernel_attributes.py", line 22, in <module> from .ll_api import spp, sps, sr, stack_checker File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api.py", line 53, in <module> from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: libltdl.so.7: cannot open shared object file: No such file or directory
Apparently it doesn’t find pynestkernel.so (I think?). However, this file is definitely there.
wybo1@jrlogin09 ~/.../site-packages/nest> pwd /p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest wybo1@jrlogin09 ~/.../site-packages/nest> ls __init__.py __pycache__ lib ll_api.py ll_api_kernel_attributes.py logic math pynest-init.sli pynestkernel.so random raster_plot.py server spatial spatial_distributions versionchecker.py visualization.py voltage_trace.py
The problem also only manifests itself while running from a SLURM script.
I followed the install instruction here: https://nest-simulator.readthedocs.io/en/stable/installation/noenv_install.h...
And source the nest_vars.sh file according to the instructions: `source /p/home/jusers/wybo1/jureca/nest/nest-install/bin/nest_vars.sh`
Also, `make installcheck` passes successfully (both from the login node and from a slurm script).
Cheers, Willem
---------------------- Dr. Willem Wybo Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15http://www.fz-juelich.de/pgi/PGI-15 ----------------------
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Hi Willem,
For Jureca I've found that the cluster module system can provide most of the required base NEST dependencies, my slurm scripts use something along the lines of:
`module load Stages/2023 GCCcore/.11.3.0 GCC/11.3.0 CMake/3.23.1 OpenMPI/4.1.4 Python/3.10.4 PyYAML/6.0 SciPy-bundle/2022.05 matplotlib/3.5.2 mpi4py/3.1.4 GSL/2.7 Boost/1.79.0 Autotools/20220317 IPython/8.5.0` or the upgraded versions for 2024 (https://apps.fz-juelich.de/jsc/llview/jureca_modules/)
In case you are using an apptainer image to run you may have to export a few paths explicitly because the cluster will automatically mount /p/software, which can override project specific paths.
Kind regards Catherine
On 08.02.24 12:57, Willem Wybo wrote: I’m trying to run NEST on Jureca, but I get an error:
Traceback (most recent call last): File "/p/project/jinm60/users/wybo1/Code/NEAST_models/BBP/tests/run_all_tests.py", line 2, in <module> import nest.lib.hl_api_exceptions as nestexceptions File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/__init__.py", line 64, in <module> from .ll_api_kernel_attributes import KernelAttribute # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api_kernel_attributes.py", line 22, in <module> from .ll_api import spp, sps, sr, stack_checker File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api.py", line 53, in <module> from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: libltdl.so.7: cannot open shared object file: No such file or directory
Apparently it doesn’t find pynestkernel.so (I think?). However, this file is definitely there.
wybo1@jrlogin09 ~/.../site-packages/nest> pwd /p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest wybo1@jrlogin09 ~/.../site-packages/nest> ls __init__.py __pycache__ lib ll_api.py ll_api_kernel_attributes.py logic math pynest-init.sli pynestkernel.so random raster_plot.py server spatial spatial_distributions versionchecker.py visualization.py voltage_trace.py
The problem also only manifests itself while running from a SLURM script.
I followed the install instruction here: https://nest-simulator.readthedocs.io/en/stable/installation/noenv_install.h...
And source the nest_vars.sh file according to the instructions: `source /p/home/jusers/wybo1/jureca/nest/nest-install/bin/nest_vars.sh`
Also, `make installcheck` passes successfully (both from the login node and from a slurm script).
Cheers, Willem
---------------------- Dr. Willem Wybo Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15http://www.fz-juelich.de/pgi/PGI-15 ----------------------
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Hi Catherine,
Thanks for the heads up. Loading auto tools indeed solved the issue.
Cheers, Willem
---------------------- Dr. Willem Wybo Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15http://www.fz-juelich.de/pgi/PGI-15 ----------------------
On 8. Feb 2024, at 13:59, Catherine Mia <c.schoefmann@fz-juelich.demailto:c.schoefmann@fz-juelich.de> wrote:
Hi Willem,
For Jureca I've found that the cluster module system can provide most of the required base NEST dependencies, my slurm scripts use something along the lines of:
`module load Stages/2023 GCCcore/.11.3.0 GCC/11.3.0 CMake/3.23.1 OpenMPI/4.1.4 Python/3.10.4 PyYAML/6.0 SciPy-bundle/2022.05 matplotlib/3.5.2 mpi4py/3.1.4 GSL/2.7 Boost/1.79.0 Autotools/20220317 IPython/8.5.0` or the upgraded versions for 2024 (https://apps.fz-juelich.de/jsc/llview/jureca_modules/)
In case you are using an apptainer image to run you may have to export a few paths explicitly because the cluster will automatically mount /p/software, which can override project specific paths.
Kind regards Catherine
On 08.02.24 12:57, Willem Wybo wrote: I’m trying to run NEST on Jureca, but I get an error:
Traceback (most recent call last): File "/p/project/jinm60/users/wybo1/Code/NEAST_models/BBP/tests/run_all_tests.py", line 2, in <module> import nest.lib.hl_api_exceptions as nestexceptions File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/__init__.py", line 64, in <module> from .ll_api_kernel_attributes import KernelAttribute # noqa ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api_kernel_attributes.py", line 22, in <module> from .ll_api import spp, sps, sr, stack_checker File "/p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest/ll_api.py", line 53, in <module> from . import pynestkernel as kernel # noqa pylint: disable=no-name-in-module ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ImportError: libltdl.so.7: cannot open shared object file: No such file or directory
Apparently it doesn’t find pynestkernel.so (I think?). However, this file is definitely there.
wybo1@jrlogin09 ~/.../site-packages/nest> pwd /p/home/jusers/wybo1/jureca/nest/nest-install/lib64/python3.11/site-packages/nest wybo1@jrlogin09 ~/.../site-packages/nest> ls __init__.py __pycache__ lib ll_api.py ll_api_kernel_attributes.py logic math pynest-init.sli pynestkernel.so random raster_plot.py server spatial spatial_distributions versionchecker.py visualization.py voltage_trace.py
The problem also only manifests itself while running from a SLURM script.
I followed the install instruction here: https://nest-simulator.readthedocs.io/en/stable/installation/noenv_install.h...
And source the nest_vars.sh file according to the instructions: `source /p/home/jusers/wybo1/jureca/nest/nest-install/bin/nest_vars.sh`
Also, `make installcheck` passes successfully (both from the login node and from a slurm script).
Cheers, Willem
---------------------- Dr. Willem Wybo Peter Grünberg Institute 15 - Neuromorphic Software Ecosystems Forschungszentrum Jülich www.fz-juelich.de/pgi/PGI-15http://www.fz-juelich.de/pgi/PGI-15 ----------------------
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
_______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
-
Catherine Mia -
Willem Wybo