8 Feb
2024
8 Feb
'24
1:59 p.m.
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.…
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-15<http://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.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto: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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------