Hello Viktor,
Thank you for reporting this issue. I worked on the solution. It is difficult to use current and older releases with nest-server-mpi. From the logging I registered that the serialization issue is persistent. I think the issue is complex and requires multiple expert to solve it:
- NESTML -> Charl/ Pooja - NEST Server -> Sebastian - NEST Server MPI -> Sebastian (former Jochen) - NEST Docker -> Steffen / Sebastian
However I created a PR (https://github.com/nest/nest-docker/pull/260/files) in which `nest-server-mpi` is working with NEST master branch.
Be aware that the master branch is not stable and will be solid in next release (v3.9).
How to do: ``` wget https://raw.githubusercontent.com/nest/nest-docker/1b6ab9602c0feb6584f8180a5... docker-compose -f docker-comppse-dev.yml up nest-server-mpi ```
Please give a quick response whether it is working on your side. Thank you!
Best regards Sebastian
On 4/10/25 16:05, Viktor Vorobev wrote:
Hello, dear nest team!
I am trying to launch the experiment, using nest-server-mpi and NRP on the HPC. We also use a module generated by nestml. But I faced the issue, which I so far cannot solve myself... Probably you could help me.
We have a working experiment for the nest-server v3.7, which also works with v3.8.
I tried to launch nest-simulator in the container on the HPC, but I faced some mpi incompatibility issues, could not solve it fast and gave up for now. Then I installed nest-simulator 3.7 from source on the HPC. The simulation with nest-server also worked. After patching nest-server-mpi (serialization issue) I could launch it on the HPC and communicate with the API, but the experiment didn't work, and I switched to the local nest-simulator container for the test.
Locally, in the original nest/nest-simulator:3.7 and 3.8 containers, the nest-server-mpi is not starting. After the fixing the issue (with docopt and serialization) the nest-server-mpi is launching in nest/nest-simulator:dev container. But here is the problem, with this version the experiment is crashing even with nest-server, as well as with nest-server-mpi. And I cannot figure out the reason from the logs and git history...
I tried patching versions 3.7 and 3.8, then I can start nest-server-mpi, can use API, but the experiment itself doesn't work.
So, the summary:
The experiment works with nest-server 3.7 and 3.8, but doesn't work with the patched nest-server-mpi The experiment doesn't work with the nest-server with :dev container
What happens in the latest container with the nest-server:
nrp-nest-simulator | nrp-nest-simulator | Apr 03 16:11:15 SimulationManager::set_status [Info]: nrp-nest-simulator | Temporal resolution changed from 0.1 to 0.1 ms. nrp-nest-simulator | nrp-nest-simulator | Apr 03 16:11:15 Install [Info]: nrp-nest-simulator | loaded module controller_moduleAnd that's it, on the other side I get [json.exception.out_of_range.403] key 'data' not found
The nest script, which is executed at this moment is
nest.ResetKernel() nest.SetKernelStatus({"resolution": res}) nest.Install("controller_module") for i in range(njt): planner_p = nest.Create("tracking_neuron_nestml", n=N, params={"kp": plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": True, "traj": trj, "simulation_steps": len(trj)}) planner_n = nest.Create("tracking_neuron_nestml", n=N, params={"kp": plan_params["kp"], "base_rate": plan_params["base_rate"], "pos": False, "traj": trj, "simulation_steps": len(trj)})The same piece of code works in nest-server v3.7 and v3.8
What happens in the patched nest-server-mpi v 3.8 or 3.7, here it at least throws an exception
nrp-nest-simulator | ======================================== nrp-nest-simulator | nrp-nest-simulator | ==> MASTER 0/1743700791.3478301 (route_api_call): call=GetStatus, args=[[303]], kwargs={} nrp-nest-simulator | ==> MASTER 0/1743700791.3478405 (GetStatus): sending call bcast nrp-nest-simulator | ==> MASTER 0/1743700791.3478618 (GetStatus): sending data bcast, data=([[303]], {}) nrp-nest-simulator | ==> MASTER 0/1743700791.3480251 (GetStatus): local call, args=[NodeCollection(metadata=None, model=spike_recorder, size=1, first=303)], kwargs={} nrp-nest-simulator | ==> MASTER 0/1743700791.3480933 (GetStatus): waiting for response gather nrp-nest-simulator | ==> MASTER 0/1743700791.3484681 (GetStatus): received response gather, data=[({'element_type': 'recorder', 'events': {'senders': array([204]), 'times': array([13.5])}, 'frozen': False, 'global_id': 303, 'label': 'Brain stem pos', 'local': True, 'model': 'spike_recorder', 'model_id': 96, 'n_events': 1, 'node_uses_wfr': False, 'origin': 0.0, 'record_to': 'memory', 'start': 0.0, 'stop': 1.7976931348623157e+308, 'thread': 0, 'thread_local_id': 152, 'time_in_steps': False, 'vp': 0},), [{'element_type': 'recorder', 'events': {'senders': [], 'times': []}, 'frozen': False, 'global_id': 303, 'label': 'Brain stem pos', 'local': True, 'model': 'spike_recorder', 'model_id': 96, 'n_events': 0, 'node_uses_wfr': False, 'origin': 0.0, 'record_to': 'memory', 'start': 0.0, 'stop': 1.7976931348623157e+308, 'thread': 0, 'thread_local_id': 152, 'time_in_steps': False, 'vp': 1}]] nrp-nest-simulator | [2025-04-03 19:19:51,348] ERROR in app: Exception on /api/GetStatus [POST] nrp-nest-simulator | Traceback (most recent call last): nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/app.py", line 2070, in wsgi_app nrp-nest-simulator | response = self.full_dispatch_request() nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/app.py", line 1515, in full_dispatch_request nrp-nest-simulator | rv = self.handle_user_exception(e) nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask_cors/extension.py", line 165, in wrapped_function nrp-nest-simulator | return cors_after_request(app.make_response(f(*args, **kwargs))) nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/app.py", line 1513, in full_dispatch_request nrp-nest-simulator | rv = self.dispatch_request() nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/app.py", line 1499, in dispatch_request nrp-nest-simulator | return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) nrp-nest-simulator | File "/opt/nest/lib/python3.10/site-packages/nest/server/hl_api_server.py", line 317, in route_api_call nrp-nest-simulator | return jsonify(response) nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 348, in jsonify nrp-nest-simulator | f"{dumps(data, indent=indent, separators=separators)}\n", nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 129, in dumps nrp-nest-simulator | rv = _json.dumps(obj, **kwargs) nrp-nest-simulator | File "/usr/lib/python3.10/json/__init__.py", line 238, in dumps nrp-nest-simulator | **kw).encode(obj) nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line 199, in encode nrp-nest-simulator | chunks = self.iterencode(o, _one_shot=True) nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line 257, in iterencode nrp-nest-simulator | return _iterencode(o, 0) nrp-nest-simulator | File "/usr/lib/python3/dist-packages/flask/json/__init__.py", line 56, in default nrp-nest-simulator | return super().default(o) nrp-nest-simulator | File "/usr/lib/python3.10/json/encoder.py", line 179, in default nrp-nest-simulator | raise TypeError(f'Object of type {o.__class__.__name__} ' nrp-nest-simulator | TypeError: Object of type int64 is not JSON serializable nrp-nest-simulator | [2025-04-03 19:19:51,349] INFO in _internal: 172.18.0.3 - - [03/Apr/2025 19:19:51] "POST /api/GetStatus HTTP/1.1" 500 -Do you have any clues where I should dig? I would appreciate any help.
Best wishes, Viktor
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