<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>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 .</div><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, May 25, 2011 7:16:44 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] query regarding replica exchange<br></font><br>
On 26/05/2011 8:50 AM, Joshua L. Phillips wrote:<br>> You will need a file formatted like the following:<br>><br>> node0 slots=4 max_slots=4<br>> node1 slots=4 max_slots=4<br>> ...<br>> node9 slots=4 max_slots=4<br>><br>> You will then need to use the -hostfile option to supply the filename to<br>> either mpiexec or mpirun (not mdrun).<br><br>Indeed. Details will vary with the nature of the MPI installation - but <br>it's an MPI issue, not a GROMACS issue. The only relevant detail is that <br>you wish every pair of cores assigned to a replica to be on the same <br>machine. The above approach will generally achieve that.<br><br>Mark<br><br>> -- Josh<br>><br>> On Wed, 2011-05-25 at 11:50 -0700, Sanku M wrote:<br>>> Hi,<br>>><br>>><br>>> I am planning to run replica exchange simulation using gromacs<br>>> 4.0.7 . I have read the manual about REMD. Only thing I wanted to
know<br>>> is that how I can specify the name of host-machines where I am<br>>> planning to run the simulations.<br>>><br>>><br>>> I have 10 different quad-core computers each intra-connected with the<br>>> other each running OPENMPI. I want to run 20 replica each using 2<br>>> cores in parallel.<br>>><br>>><br>>> So, I was wondering whether I have to create any file containing the<br>>> names of those machines . If so, can someone give an example of format<br>>> of the file which contain those names ? Finally, what keyword I should<br>>> use in mdrun to specify that file for running replica exchange.<br>>><br>>><br>>> Also, I am not using any PBS for submitting jobs.<br>>><br>>><br>>> Sanku<br>>><br>>><br>>><br>>><br>>><br>>><br>>><br>>><br>>> -- <br>>> gmx-users mailing list
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