[gmx-users] Using Gromacs on Condor

Peter C. Lai pcl at uab.edu
Wed Apr 27 13:46:46 CEST 2011

Work with your condor people to recompile gromacs against MPI on their system,
if that is not already the case.
It's probably helpful to specify +ParallelShutdownPolicy = "WAIT_FOR_ALL"
in the condor submission file...
See http://www.cs.wisc.edu/condor/manual/v7.6/2_9Parallel_Applications.html
Section 2.9.4...


On 2011-04-27 06:08:54AM -0500, Natalie Stephenson wrote:
> Hi,
> I was wondering if anyone new a way to run mdrun commands through a condor system.  I've been told by the people that run our system that unless I can split it into seperate threads then I would not be able to run it as a job, because it would just get stopped in the morning - which from what I've seen would just end my simulation and I would have to start again.
> Currently my simulations are taking around a month - which as I'm nearing the end of this project is getting quite frustrating as you can imagine.  Any ideas on how I can speed this without buying a new computer (which is an idea I've had veeto'd from my supervisor many many times!) would be much appreciated!!!
> Thanks
> Natalie

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |

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