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virtualcell / vcell

Virtual Cell Framework
http://vcell.org/
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smaller biosimulators container and server solvers #569

Closed jcschaff closed 1 year ago

jcschaff commented 2 years ago

Background

addressing the following:

  1. needed to add 'validate-batch' CLI command to biosimulators_vcell docker image for use on server/slurm (to validate 1000+ public models in HPC cluster).
  2. existing biosimulators_vcell docker image was very large (>2.5GB) causing deployment problems.
  3. biosimulators_vcell used standalone linux solvers (localsolvers/linux64) rather that solvers used by server in vcell-solvers image.

  1. added 'validate-batch' to docker_run.sh
  2. added JRE/Python3 to vcell-solvers base image and de-deplicated large python dependencies (for venv and global packages).
  3. now uses the new ghcr.io/virtualcell/vcell-solvers:v0.0.41 as a base image (to get solvers, java, and python).
jcschaff commented 1 year ago

container was refactored since then.