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airavata-courses / TeamZenith

Team Zenith Repository for Spring 2016 I590 Class
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GROMACS submission for Milestone 3 #28

Closed marpierc closed 8 years ago

marpierc commented 8 years ago

To complete milestone 3, you need to support GROMACS submission. UI looks great.

a2l007 commented 8 years ago

Marlon, In addition to adding the required modules, we tried the exact steps as mentioned in: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Trestles/GROMACS/README but, the commands being used for gromacs: pdb2gmx and grompp are unavailable in Karst. As a result the job fails. Are you aware of any other configuration that needs to be done before Gromacs can be run?

marpierc commented 8 years ago

You need to load the modules: module load gromacs. See the list in the KB article on gromacs: https://kb.iu.edu/d/besc

From: ajinkya-dhamnaskar notifications@github.com<mailto:notifications@github.com> Reply-To: airavata-courses/TeamZenith reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, March 18, 2016 at 12:17 PM To: airavata-courses/TeamZenith TeamZenith@noreply.github.com<mailto:TeamZenith@noreply.github.com> Cc: marpierc marpierc@iu.edu<mailto:marpierc@iu.edu> Subject: Re: [TeamZenith] GROMACS submission for Milestone 3 (#28)

Marlon, In addition to adding the required modules, we tried the exact steps as mentioned in: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Trestles/GROMACS/README but, the commands being used for gromacs: pdb2gmx and grompp are unavailable in Karst. As a result the job fails. Are you aware of any other configuration that needs to be done before Gromacs can be run?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/airavata-courses/TeamZenith/issues/28#issuecomment-198432063

a2l007 commented 8 years ago

Hello Marlon, As described in my earlier update, I have already loaded the required modules, that are: openmpi/intel/1.6.3 and gromacs/intel/4.6.5

marpierc commented 8 years ago

OK I see a difference now: if I load module load openmpi/intel/1.6.3 and module load gromacs/intel/4.6.5, then the commands are not there.

But if I just use "module load gromacs", I see the following output: [marpierc@h3 ~]$ module load gromacs GROMACS molecular dynamics package version 4.6.5 loaded. [marpierc@h3 ~]$ /N/soft/rhel6/gromacs/intel/serial/4.6.5/bin/grompp [marpierc@h3 ~]$ which pdb2gmx /N/soft/rhel6/gromacs/intel/serial/4.6.5/bin/pdb2gmx

marpierc commented 8 years ago

This is the serial version of GROMACS but given the other issues, it's fine if this works.

a2l007 commented 8 years ago

We got GROMACS working and have pushed the required changes into Milestone-3 branch. Please review.

a2l007 commented 8 years ago

Closing the issue as Milestone3 has been graded.