Workloadmanager selective

[agrass15268]

Description

Goal: to improve the selection of workload-managers (WM) as discussed in PR #59.

Instead of simply choosing a file according to its prefix, the settings for workload-managers have been outsourced to two new files in /bin/, slurm-preamble.sh and SGE-preamble.sh.

These are still selected according to their prefixes and contain the instructions for workload managers. Their content is simply prepended to the copied simulation.sh and simulation_charmm.sh files.

To that end, a new private function (_write_workload_preamble) was added to state.py.

This is not exactly the same solution as in PR #59, as that would have still required 8 files (due to needing charmm/openmm separation or argument switches).

This should be easily extendable to new WMs (requiring modification of the possible WMs in utils.py and a *-preamble.sh file) and MD engines (requiring a call to _write_workload_preamble after the submit file has been copied.)

All references to the old system were removed from state.py.

Todos

Notable points that this PR has either accomplished or will accomplish.

• [x] Reduced number of files necessary from 8 to 6
• [x] Local changes to the preamble file are applied across all simulations and do not require an edit to each file
• [x] Only one version of the simulation scripts to maintain

Status

Test builds of both slurm and SGE deliver the expected results on my side. I'd like to request @JohannesKarwou to run the full suite or whatever he deems necessary to ensure compatibility.

[JohannesKarwou]

@agrass15268 for me it does not work, it seems if one wants to calculate rsfe with slurm one gets the preamble of slurm but the rest of SGE

[agrass15268]

@agrass15268 for me it does not work, it seems if one wants to calculate rsfe with slurm one gets the preamble of slurm but the rest of SGE

I'm somewhat confused - that is the intended behaviour? Or rather, what do you mean with "the rest of SGE" - besides the preamble, the files are identical (and SGE-simulation-rsfe.sh no longer exists, so cannot be included).

The only thing i could think of is that the /build/ folder still contains the old files - could you try deleting it, running python setup.py install again and see if the problem persists?

[JohannesKarwou]

@agrass15268 for me it does not work, it seems if one wants to calculate rsfe with slurm one gets the preamble of slurm but the rest of SGE

I'm somewhat confused - that is the intended behaviour? Or rather, what do you mean with "the rest of SGE" - besides the preamble, the files are identical (and SGE-simulation-rsfe.sh no longer exists, so cannot be included).

The only thing i could think of is that the /build/ folder still contains the old files - could you try deleting it, running python setup.py install again and see if the problem persists?

Ok sorry your right, I had an internal problem :) Everything works fine

[agrass15268]

Ok, so since this is resolved and tests are all positive now- @JohannesKarwou apparently cannot merge this despite the review, and I obviously don't have any rights whatsoever. So if you would be so kind as to merge @wiederm? Regarding the merge conflict - that file can simply be deleted, it no longer exists.

[wiederm]

thanks! I resolved the conflict and merged!