I am trying to run a Bayesian inference script on a high performance cluster with SUSE Linux Enterprise Server 15 SP2. Running this script from the command line with
python3 script.py works fine. But trying to run the script with a Slurm bash script throws the following error:
filelock._error.Timeout: The file lock '.1662466228.theano/compiledir_Linux-5.3-46_6.0.29-cray_ari_c-x86_64-with-glibc2.26-x86_64-3.9.12-64/.lock' could not be acquired.
I already included the following changes to the theano.config in the bash script:
theano-cache purge stamp=$(date +%s) export THEANO_FLAGS="base_compiledir=.$stamp.theano/,compile__timeout=24,compile__wait=20"
These are suggested solutions from Running multiple instances of Pymc3 scripts simultaneously causes error! · Issue #1463 · pymc-devs/pymc · GitHub and Running multiple instances of Pymc3 scripts simultaneously causes error! · Issue #1463 · pymc-devs/pymc · GitHub.
I use pymc3 version 3.11.2 and theano-pymc version 1.1.2.