Pointer errors running simulations

[joseph-tharayil]

Hi all,

I'm trying to run a neurodamus simulation on SCITAS (EPFL's cluster). Installation seems to work correctly, but when I try to launch a simulation, I'm getting an invalid pointer error. The launch script, simulation and circuit config files, and the traceback are attached. Does anyone know what this could indicate?

Thanks,
Joe

circuit_config.json
simulation_config.json
slurm-29975213.txt
launch.sh.txt

[WeinaJi]

Hello @joseph-tharayil ,

I see the trace from the slurm log

jst370:2806509] [ 8] /home/tharayil/neurodamus-env-3.10/lib/python3.10/site-packages/libsonata/_libsonata.cpython-310-x86_64-linux-gnu.so(_ZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEEC1EPKcS6_RKSt6localeNSt15regex_constants18syntax_option_typeE+0x758)[0x7f787b700c08]

It seems to be the dual ABI issue as we saw before in BlueBrain/libsonata#273 . I would recommend installing libsonata and neuron both from wheel or both from source.

For SCITAS, I remember there is the container built for neurodamus. Can you use that directly?

cc @JCGoran @jamesgking, we can also discuss it on Thursday.

[WeinaJi]

Hi @joseph-tharayil ,
https://github.com/BlueBrain/spacktainers?tab=readme-ov-file#running-with-apptainer
Please see the instruction on how to run Neurodamus on Jed from SCITAS. Currently you can use max. 12 nodes there because of an issue on mpi libary on SCITAS, @JCGoran can give you more information.

[joseph-tharayil]

Hi @WeinaJi,
I was able to get it running with the instructions in the link above.
Thank you!