Hi, thanks for your prompt reply.
So, I tried running some tests again on 3 different machines, here are the specs:
- Python 3.9.6, pystan 3.1.1 (installed via conda), gcc 9.3.0. I got the following error message:
Traceback (most recent call last):
File "/home/mardian/bayesian_inference/IntermediaryModel.py", line 466, in <module>
fit = posterior.sample(num_chains=6, num_warmup=5000, num_samples=5000)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 84, in sample
return self.hmc_nuts_diag_e_adapt(num_chains=num_chains, **kwargs)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 103, in hmc_nuts_diag_e_adapt
return self._create_fit(function=function, num_chains=num_chains, **kwargs)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 306, in _create_fit
return asyncio.run(go())
File "/home/mardian/anaconda3/envs/env/lib/python3.9/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
return future.result()
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 231, in go
raise RuntimeError(message)
RuntimeError: Exception during call to services function: `BrokenProcessPool('A process in the process pool was terminated abruptly while the future was running or pending.')`, traceback: `[' File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/httpstan/services_stub.py", line 159, in call\n future.result()\n', ' File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/httpstan/services_stub.py", line 159, in call\n future.result()\n']`
- Python 3.8.5, pystan 3.2.0 (installed via conda), gcc 9.3.0, I got the following error message:
Traceback (most recent call last):
File "IntermediaryModel.py", line 466, in <module>
fit = posterior.sample(num_chains=6, num_warmup=5000, num_samples=5000)
File "/home/mardian/miniconda3/envs/env/lib/python3.8/site-packages/stan/model.py", line 84, in sample
return self.hmc_nuts_diag_e_adapt(num_chains=num_chains, **kwargs)
File "/home/mardian/miniconda3/envs/env/lib/python3.8/site-packages/stan/model.py", line 103, in hmc_nuts_diag_e_adapt
return self._create_fit(function=function, num_chains=num_chains, **kwargs)
File "/home/mardian/miniconda3/envs/env/lib/python3.8/site-packages/stan/model.py", line 306, in _create_fit
return asyncio.run(go())
File "/home/mardian/miniconda3/envs/env/lib/python3.8/asyncio/runners.py", line 43, in run
return loop.run_until_complete(main)
File "/home/mardian/miniconda3/envs/env/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
return future.result()
File "/home/mardian/miniconda3/envs/env/lib/python3.8/site-packages/stan/model.py", line 231, in go
raise RuntimeError(message)
RuntimeError: Exception during call to services function: `IndexError("Exception: array[uni, ...] index: accessing element out of range. index 3 out of range; expecting index to be between 1 and 2 (in '/tmp/httpstan_5sk13x19/model_l7scj23i.stan', line 69, column 8 to column 33)")`, traceback: `[' File "/home/mardian/miniconda3/envs/env/lib/python3.8/site-packages/httpstan/services_stub.py", line 159, in call\n future.result()\n']`
- Python 3.9.6, pystan 3.2.0 (installed via conda), gcc 9.3.0, here are the error message:
Traceback (most recent call last):
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/aiohttp/web_protocol.py", line 422, in _handle_request
resp = await self._request_handler(request)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/aiohttp/web_app.py", line 499, in _handle
resp = await handler(request)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/httpstan/views.py", line 103, in handle_create_model
_, stanc_warnings = httpstan.compile.compile(program_code, stan_model_name)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/httpstan/compile.py", line 24, in compile
with importlib.resources.path(__package__, "stanc") as stanc_binary:
File "/home/mardian/anaconda3/envs/env/lib/python3.9/contextlib.py", line 117, in __enter__
return next(self.gen)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/importlib/resources.py", line 175, in _path_from_reader
opener_reader = reader.open_resource(norm_resource)
File "<frozen importlib._bootstrap_external>", line 1055, in open_resource
FileNotFoundError: [Errno 2] No such file or directory: '/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/httpstan/stanc'
Traceback (most recent call last):
File "/home/mardian/bayesian_inference/IntermediaryModel.py", line 465, in <module>
posterior = stan.build(model, data=data)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 512, in build
return asyncio.run(go())
File "/home/mardian/anaconda3/envs/env/lib/python3.9/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
return future.result()
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/model.py", line 479, in go
match = re.search(r"""ValueError\(['"](.*)['"]\)""", resp.json()["message"])
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/stan/common.py", line 24, in json
return simdjson.loads(self.content)
File "/home/mardian/anaconda3/envs/env/lib/python3.9/site-packages/simdjson/__init__.py", line 52, in loads
return parser.parse(s, True)
File "simdjson/csimdjson.pyx", line 455, in csimdjson.Parser.parse
ValueError: The JSON document has an improper structure: missing or superfluous commas, braces, missing keys, etc.
I do not understand why I got 3 different errors for the same script that I run on different machines. I also recompile the model (clean the cache, as suggested), but still got these errors. How can I fix these?
Thanks