Re: [gmx-users] Re: Running Gromacs in Clusters
I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I've tried eliminating the node=X and got the error. I've tried use node=2 (or any number higher than 1) and it goes to the queue even if there is empty nodes. I'm almost trying to compile gromacs again but now with OpemMPI... -- Marcelo Depólo -- 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
Fwd: [gmx-users] Re: Running Gromacs in Clusters
On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com wrote: I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I would be very surprised if this is true. The nornal sequences of events during submission process is the following: 1) The system looks into your submission script and finds out the resource requirements. 2) If the requirements are met, the job gets R status and the remaining commands (which do not start with #PBS) are executed. 3) If there is a problem with the message parallel interface or the [scientific] code, the job dies with some MPI-specific error message, or with code-specific message, or usually both of them. What I see in your report, your error message comes from PBS, i.e. neither MPI nor gromacs are launched. -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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
[gmx-users] Re: Running Gromacs in Clusters
On Wed, Nov 7, 2012 at 11:48 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Wed, Nov 7, 2012 at 11:24 PM, Marcelo Depolo marcelodep...@gmail.com wrote: I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I would be very surprised if this is true. The nornal sequences of events during submission process is the following: 1) The system looks into your submission script and finds out the resource requirements. 2) If the requirements are met, the job gets R status and the remaining commands (which do not start with #PBS) are executed. 3) If there is a problem with the message parallel interface or the [scientific] code, the job dies with some MPI-specific error message, or with code-specific message, or usually both of them. What I see in your report, your error message comes from PBS, i.e. neither MPI nor gromacs are launched. Are you stating that other programs on your cluster run successfully on multiple nodes using the same (the #PBS part) submission script and only gromacs-jobs complain about lack of resources? I cannot believe... -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- 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
