Sequence module requires an Evaluation request before a Build3DStructure request.

[gitoliver]

In $GEMSHOME/tests/008.test.multi-conformer-builds.sh if you comment out the Evaluation test and let 008.1.sub-test.bash run, the min-gas.pdb is never produced. I suspect that two jobs are trying to run in the same folder as I see:

-rw-r--r-- 1 oliver oliver    0 Jan 24 10:30 slurm_Glycan-afa73698--3.out
-rw-r--r-- 1 oliver oliver    0 Jan 24 10:30 slurm_Glycan-afa73698--3.err
-rw-r--r-- 1 oliver oliver    0 Jan 24 10:30 slurm_Glycan-afa73698--2.out
-rw-r--r-- 1 oliver oliver    0 Jan 24 10:30 slurm_Glycan-afa73698--2.err

And the double entries here:

-fd0770e8c60f/New_Builds/e6c2e2e8-758b-58b8-b5ff-d138da38dd22$ cat build-status.log
[INFO] - Wed Jan 24 04:30:38 EST 2024 - Status log opened.
[INFO] - Wed Jan 24 04:30:38 EST 2024 - This job is running in a Slurm cluster.
[INFO] - Wed Jan 24 04:30:38 EST 2024 - Sourcing of AMBERHOME[=/programs/amber]/amber.sh completed
[INFO] - Wed Jan 24 04:30:38 EST 2024 - Sourcing of AMBERHOME[=/programs/amber]/amber.sh completed
[INFO] - Wed Jan 24 04:30:38 EST 2024 - Gas-phase tleap processing completed
[INFO] - Wed Jan 24 04:30:39 EST 2024 - Gas-phase tleap processing completed
[INFO] - Wed Jan 24 04:30:39 EST 2024 - Gas-phase minimization completed
[ERROR] - Wed Jan 24 04:30:39 EST 2024 - Post-gas-phase cpptraj processing failed with code 1
[INFO] - Wed Jan 24 04:30:39 EST 2024 - Gas-phase minimization completed
[ERROR] - Wed Jan 24 04:30:39 EST 2024 - Post-gas-phase cpptraj processing failed with code 1

This is based on the latest bug-fixes in gems-test. There was likely logic that stopped this somewhere in there that got by-passed when resolving the other issues.

The website always does an Evaluation first, it's just API users that will trigger this bug. Unfortunately it poisens the well so any subsequent requests, Evaluate or Build3DStructure, bork.

Options:

• I go back in a fix it.
• We update our docs to tell API users to always do an Evaluate. If they only want the default structure, that is enough. If they want a specific conformer, they need to do an Evaluate first anyway.

[Lachele]

When I made GLYCAM Delgator Docker , I added the capability for builds without evaluations, but it only applies to non-website builds. To activate that feature, just don't set any environment variables that tell GEMS that it's in a website context.

Arguably, the website needs the evaluation pass because of how it works, so we can't get rid of the eval. But we should bake the evaluation into GEMS as an implied service if a build is requested without an evaluation. We could also make GEMS smarter about evaluations and builds in general. I made a fancy design for this sort of thing, lol.

Not that we have anyone available to do any of these things right now.