[gmx-users] Re: Gromacs and Condor

[Martina Bertsch, PhD]

Dear Amadeu,

In order to setup environment for condor, you need to create two files: a submission description file and a shell script (sets up environment for your job, e.g., gmx). See the example below for details.
   
   Commands to use:
   Submit job: "condor_submit your_submission_description_file_name".
   Check job status: "condor_q" or "condor_status"
   Remove job: "condor_rm your_job_id " (you can get your job id from "condor_q" command.
        
   A few notes: 
    1. Make sure shell script is executable (e.g. chmod u+x mdrun-script.tcsh).
    2. Always login on the primary node and submit your job. You don't need to login to internal nodes any more. Condor will find an empty CPU for you automatically.
    3. The maximum number of jobs that can run concurrently is usually equal to the number of total CPUs in the cluster. If more jobs are submitted, they will stay in the queue and wait until the other jobs finish.
    4. The policy is first come, first served.
    5. In the submission description file, all you need to modify are the first three lines. They are your shell script file name, error log and regular log.
    6. It is better to first test and debug your shell script as you normally do. Then submit the job using condor. Otherwise, you might spend more troubleshooting time under the context of condor.  
    7. For more information visit http://www.cs.wisc.edu/condor/

The following example is for user martina with home directory
/home5/martina.

EXAMPLE: 

Submission description file name for gromacs: mdrun.submit

executable=mdrun-script.tcsh 
error=mdrun.err
log=mdrun.log
getenv=True
universe=vanilla
notification=never
queue 

Shell script file name: mdrun-script.tcsh

#!/bin/tcsh
prepare gromacs-3.1.4
cd /home5/martina/testjob-condor/mdrun 
mdrun -nice 0 -v -s eq.tpr -f eq.trr -c MT1_mlt_posteq.gro -e eq.edr -g eq.log 

Command to submit this job: condor_submit mdrun.submit

Regards,
Martina Bertsch, Ph.D.

Amadeu K. Sum wrote:

>Dear Martina,
>
>I have come across your recent posting in the Gromacs
>mailing list about the usage of Gromacs with the Condor
>queueing system, however, I have not found any replies
>to your inquiry. I was wondering whether you have
>managed to get Gromacs to work with Condor. I am a
>postdoc at the University of Wisconsin, and we
>extensively use Condor and are starting to use Gromacs
>for our research too. I have tried to compile Gromacs
>with Condor, but I have not gotten it to work. If you
>don't mind, I would appreciate any experience you might
>have with Gromacs and Condor.
>
>Thanks in advance for your help and I apologize for the
>unsolicited message.
>
>Best regards,
>
>		Amadeu Sum
>
>-----------------------------------------------------
> Postdoctoral Fellow - de Pablo Group
> Univ. Wisconsin - Chemical & Biological Engineering
> 1415 Engineering Drive - Madison, WI 53706
> Phone: (608) 265-4926
>
>
>