Chitrita Dutta Roy wrote:
I tried that way it basically creates 4 jobs and takes hold of 4 cpus
but the problem is that it shows to take more time than it would
normally without mpirun..and not only that a weird thing starts
happening.Once being progressed to some steps it retreats back again to
an older one and sometimes it just loops around in that fashion
calculating practically the same set of steps over and over again.
I somehow feel that the tpr file which is needed for the mdrun was not
built properly to run on 4 separate cores simultaneously.ANd that is why
maybe actually the 4 cores are running the same copy of the program and
so the same steps.And what i see is kinda race condition.I guess i
compiled it properly with mpi so..now i am helpless.
Thanks for your help.Waiting for some more.
Please post the following information:
1. The exact series of commands you gave when installing Gromacs.
2. The exact commands you are issuing to create your job (grompp and mdrun).
-Justin
On Sun, Dec 21, 2008 at 7:56 PM, Manik Mayur <manik.ma...@gmail.com
<mailto:manik.ma...@gmail.com>> wrote:
On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy <chitrita.md
<http://chitrita.md>@gmail.com <http://gmail.com>> wrote:
Thanks to all for helping me previously.
Now i am unable to arrange the .tpr file for position restraint
mdrun on a quad core as in version 4.0.2 grompp -np is not a
valid comand can anybody help me in building a tpr file for
parallel run on 4 cores of a quad core machine .I have installed
gromacs using Open MPI Library and my files are suffixed as _mpi.
try running: mpirun -np 4 mdrun_mpi options
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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