I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated .
________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wed, May 25, 2011 7:16:44 PM Subject: Re: [gmx-users] query regarding replica exchange On 26/05/2011 8:50 AM, Joshua L. Phillips wrote: > You will need a file formatted like the following: > > node0 slots=4 max_slots=4 > node1 slots=4 max_slots=4 > ... > node9 slots=4 max_slots=4 > > You will then need to use the -hostfile option to supply the filename to > either mpiexec or mpirun (not mdrun). Indeed. Details will vary with the nature of the MPI installation - but it's an MPI issue, not a GROMACS issue. The only relevant detail is that you wish every pair of cores assigned to a replica to be on the same machine. The above approach will generally achieve that. Mark > -- Josh > > On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote: >> Hi, >> >> >> I am planning to run replica exchange simulation using gromacs >> 4.0.7 . I have read the manual about REMD. Only thing I wanted to know >> is that how I can specify the name of host-machines where I am >> planning to run the simulations. >> >> >> I have 10 different quad-core computers each intra-connected with the >> other each running OPENMPI. I want to run 20 replica each using 2 >> cores in parallel. >> >> >> So, I was wondering whether I have to create any file containing the >> names of those machines . If so, can someone give an example of format >> of the file which contain those names ? Finally, what keyword I should >> use in mdrun to specify that file for running replica exchange. >> >> >> Also, I am not using any PBS for submitting jobs. >> >> >> Sanku >> >> >> >> >> >> >> >> >> -- >> gmx-users mailing list gmx-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 mailing list gmx-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
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