Hi Pooja, Thank you for your guidance. I removed the comments but I got a different error message: [INFO] [2025.3.7 9:35:8 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it. For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T -- Copyright (C) 2004 The NEST Initiative
Version: 3.8.0 Built: Mar 5 2025 14:24:10
This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details.
Problems or suggestions? Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl' [INFO] [2025.3.7 9:35:9 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it. For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T -- Copyright (C) 2004 The NEST Initiative
Version: 3.8.0 Built: Mar 5 2025 14:24:10
This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for details.
Problems or suggestions? Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver [18,stdp_synapse_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit! [36,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit! [40,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit! [1741300508.992276] [xcs-node-01:414339:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued. [1741300508.992283] [xcs-node-01:414339:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory. Traceback (most recent call last): File "/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/test.py", line 58, in <module> NESTCodeGeneratorUtils.generate_code_for("iaf_psc_delta_neuron.nestml", File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator_utils.py", line 138, in generate_code_for generate_nest_target(input_path=input_fns, File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 291, in generate_nest_target generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level, File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 215, in generate_target return process() File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 514, in process generate_code(code_generator, models) File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 459, in generate_code code_generators.generate_code(models) File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 288, in generate_code self.generate_synapses(synapses) File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/code_generator.py", line 174, in generate_synapses self.generate_synapse_code(synapse) File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 271, in generate_synapse_code super().generate_synapse_code(synapse) File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/code_generator.py", line 225, in generate_synapse_code template_namespace=self._get_synapse_model_namespace(synapse), File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 575, in _get_synapse_model_namespace assert len(namespace["pre_ports"]) <= 1, "Synapses only support one spiking input port" AssertionError: Synapses only support one spiking input port
On Thu, Mar 6, 2025 at 7:01 PM Babu, Pooja p.babu@fz-juelich.de wrote:
Hi Pablo,
Thank you for writing in!
The following lines in the script “test.py” are commented:
codegen_opts={#"neuron_synapse_pairs”: # [{"neuron": "iaf_psc_delta_neuron”, # "synapse": "stdp_synapse"}], … }
Could you uncomment them and run the script again?
Regards, Pooja
On 6. Mar 2025, at 05:53, Pablo Alejandro pabloabur@gmail.com wrote:
Hi everyone,
I am currently working with nest/nestml that was installed with EasyBuild https://docs.easybuild.io/ (i.e. a tool to manage software in HPC systems). Nest was installed with OpenMPI support (see nest_easybuild.eb attached) and it seems to be working fine. Nestml is failing when I try the stdp tutorial https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html (see error log slurm-782.out and test.py script attached). I also attached the installation steps for nestml (nestml_easybuild.eb) and the slurm script (run_job_simple.sh) to this email.
Could someone please assist me with further debugging this? This looks like an installation problem, but I get no errors if I'm using no synapse models.
Thanks
-- Pablo Alejandro <run_job_simple.sh><nestml_easybuild.eb><test.py><nest_easybuild.eb> <slurm-782.out>_______________________________________________ NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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