CompileError: command '/usr/bin/gcc' failed with exit code 1 about stan HOT 6 CLOSED

PyStan 2.0 was last updated ~4 years ago and hasn't been officially supported since May of 2021. Are you able to use cmdstanpy or pystan3 ?

from stan.

Unfortunately, the code I am running explicitly states you need to use pystan 2.0

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GCC failing due to no space left on device sounds like the code needlessly recompiles the model on every loop iteration.
The traceback suggests it happens on line 250 of ~/BHDMS/code/metric_HMDS.py:

hmds_m = stan.StanModel(model_code=HMDS_code, verbose=False)

You could try and move that line to global scope (e.g. next to where HMDS_code is defined) so the model gets compiled only once and hmds_m can be reused.

from stan.

Sorry, move what line to glocal scope?

from stan.

The line with stan.StanModel(model_code=...), line 250 in file metric_HMDS.py

Alternatively change that line, i.e.

hmds_m = stan.StanModel(model_code=HMDS_code, verbose=False)

to

global hmds_m
if hmds_m is None:
    hmds_m = stan.StanModel(model_code=HMDS_code, verbose=False)

and add to the start of the same file:

hmds_m = None

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Further discussion of this is probably better on the Stan Forums

from stan.