Issue loading gromacs module on Stampede/Lonestar using BigJob

[Vivek Balasubramanian]

Hi all,

I am trying to load the gromacs module on Stampede/Lonestar and run simple experiments. The module does not seem to get loaded while submitting a compute job (which loads the module) but works fine when I do it using a saga-job.

I used the following two test scripts for the same.

Saga script : https://bitbucket.org/vivek-balasubramanian/test/src/b210eebfb6e2d090ca4130218f51c9efcbda7ed7/gromacs_saga_remote.py?at=master
BigJob script : https://bitbucket.org/vivek-balasubramanian/test/src/b210eebfb6e2d090ca4130218f51c9efcbda7ed7/gromacs_bigjob_remote.py?at=master


I get the following error when I run the BigJob script :-
-----------------------------------------------------------------------------------------
Lmod has detected the following error: Did not find: gromacs

Try: "module spider gromacs"
-----------------------------------------------------------------------------------------

"module spider gromacs" does not work either.


I was hoping someone could give me an idea as to why this would happen or if there is anything that I might be missing.


Thank you for your time.
Vivek

[Melissa Romanus]

Vivek,

Can you strike out the redis password in your code when it is available from a public facing repository please?

Also, how many times did you try this test with BigJob, because I can't replicate your problem. If you only ran the BigJob script once, you could have ended up on a defunct compute node that had issues with loading the modules. You should try multiple compute nodes (multiple runs) if this happens again (we've come across this before). If you're able to identify the node that gives you trouble, you can contact TACC about the issue so they can fix it. 

My error from your script is a gromacs error. See below.

(python)login4$ vim stderr.txt


       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
         Copyright (c) 2001-2012,2013, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
       modify it under the terms of the GNU Lesser General Public License
        as published by the Free Software Foundation; either version 2.1
             of the License, or (at your option) any later version.

                               :-)  pdb2gmx  (-:


-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.3
Source code file: /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.3/src/gmxlib/statutil.c, line: 364

Fatal error:
Expected a string argument for option -ff

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"What's the point, yo, what's the spread?" (Red Hot Chili Peppers)

Hope that helps.

-Melissa

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[Vivek Balasubramanian]

Hi Melissa,

Striked out the redis pwd.

I ran it multiple times. I was facing the same problem on Futuregrid as well, I was able to fix it by setting up the module path in the bashrc. I tried the same by setting up the module path in Stampede using

export LMOD_DEFAULT_MODULEPATH=/opt/apps/xsede/modulefiles:/opt/apps/modulefiles:/opt/modulefiles

This was similar to a problem(fixed by setting up this path) faced by another bigjob-user in this group. I think I am facing this problem because the environment variables are not being carried over to non-interactive shells, so the fix should be by setting up the module path. Possible ? Suggestions ?

Any other path that might need to be added to this variable ?

Thank you for your time.
Vivek

[Melissa Romanus]

Yeah, this is a common issue we used to have on Lonestar, but hadn't run into it on Stampede before. It's interesting...