On 8. Feb 2024, at 13:59, Catherine Mia <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.html#noenv

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

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