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GLYCAM-Web / website

A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.
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MDaaS: on test.glycam.org the nstlim for each of the steps is too small. #153

Closed gitoliver closed 8 months ago

gitoliver commented 8 months ago

Tool: MDaaS

Build any structure on test.glycam.org that's bigger than 2 residues (to avoid the GPU issue). It will finish very quickly and you can see in the Downloads folder that it isn't running the steps for long enough:

Bug Description: oliver@frankus:~/Downloads/MD_Simulation_73e2e632-5005-45ea-9db2-611421a93aa3_All$ grep nstlim *.in 02.relax.in: nstlim = 2, 06.relax.in: nstlim = 2, 07.relax.in: nstlim = 2, 08.relax.in: nstlim = 2, 09.relax.in: nstlim = 2, 10.produ.in: nstlim = 2, Each of these need to be much higher now to get a realistic simulation. They are great default values for testing in the dev env, but should change when we deploy to the websites.

gitoliver commented 8 months ago

From Grayson, here is the relevant code: https://github.com/GLYCAM-Web/MD_Utils/blame/md-test/scripts/Run_Multi-Part_Simulation.bash#L288

gitoliver commented 8 months ago

https://github.com/GLYCAM-Web/gems/blob/57905a37abacec9caf9d1bddd4fcb3f001348c20/gemsModules/mmservice/mdaas/tasks/set_up_run_md_directory.py#L62 This is the logic that copies the Local_Run_Parameters.bash.example to to Local_Run_Parameters.bash (which toggles the MDUtilsTestRunWorkflow='Yes'). This could be desired behaviour on test.glycam.org, or we need to update that logic and not have this file be copied. Fyi: https://github.com/GLYCAM-Web/MD_Utils/blob/md-test/protocols/RoeProtocol/Local_Run_Parameters.bash.example

gitoliver commented 8 months ago

Fixed by Grayson.