[gmx-users] Using Gromacs on Condor
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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using Gromacs on Condor
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... HTH 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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using Gromacs on Condor
On 4/27/2011 9:08 PM, 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. Condor is not a suitable platform for running molecular dynamics in parallel, unfortunately. Low-latency communication is required if the processors do not share the same piece of silicon, and nobody running Condor will have that. You can get some value from Condor if you have several simulations to run, by making it easy to run each one on a different machine. Starting and stopping simulations is not much of a problem, with checkpointing in GROMACS 4.x. 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!!! Sounds like you need to work with your supervisor to change expectations, or look around for some free time you can ask for... try big or new computing facilities, especially new ones with recently-installed under-utilized hardware. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
