I tried the same thing on another installation (ubuntu, with apt and pip install) and got the same error message. How can I test whether this is not an installation issue? There is no error if I comment the "neuron_synapse_pair" entry.

Thanks

On Fri, Mar 7, 2025 at 9:41 AM Pablo Alejandro <pabloabur@gmail.com> wrote:
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 (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 (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>_______________________________________________
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--
Pablo Alejandro


--
Pablo Alejandro