[gmx-users] Parallel run on a Quad Core
Justin A. Lemkul
jalemkul at vt.edu
Sun Dec 21 17:45:09 CET 2008
Chitrita Dutta Roy wrote:
> tar -zxvf openmpi-1.2.8.tar.bz2
> cd openmpi-1.2.8
> ./configure
> make
> make install
>
> i had my fftw library installed.
>
> untarred gromacs went to its directory..
> ./configure --enable-mpi --program_suffix="_mpi"
> make
> make install
>
> grompp -f pr2.mdp -c em.gro -r em.gro -p scr8.top -n em.ndx -o pr.tpr
> mpirun -np 4 /usr/local/gromacs/bin/mdrun -v -s pr.tpr -deffnm pr
>
Well, that can't be right; all of your programs should have the _mpi suffix, if
you followed the steps above.
What you've done isn't entirely necessary, although I don't know if it will have
any adverse effects. Follow the exact instructions posted here, they are given
line-by-line and are perfectly clear:
http://www.gromacs.org/content/view/20/34/
> i tried like these besides i also tried with mdrun_mpi but the same
> occured rather showed more time requirement to complete.And i would also
> liked to know one thing if i want to do a fresh install removing the
> earlier one.How would i remove the earlier one.As i tried doing it from
> yum remove and rpm -e but all went in vain although they can show that
> these things are installed.
>
Just remove the Gromacs directory and try again, as long as any previous
attempts haven't installed in other locations (i.e., /usr/local/bin, etc.)
-Justin
> Thanks again for your help.Plz instruct me to get one complete set of
> steps to succefully install the Gromacs with mpi and to utilize the
> power of four cores.
>
>
> On Sun, Dec 21, 2008 at 9:52 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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.mayur at gmail.com <mailto:manik.mayur at gmail.com>
> <mailto:manik.mayur at gmail.com <mailto:manik.mayur at gmail.com>>>
> wrote:
>
> On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy
> <chitrita.md <http://chitrita.md>
> <http://chitrita.md>@gmail.com <http://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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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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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