[gmx-users] Parallel run on a Quad Core

[Chitrita Dutta Roy]

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

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.

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> 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>> 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
>>
>>
>>        _______________________________________________
>>        gmx-users mailing list    gmx-users at gromacs.org
>>        <mailto:gmx-users at gromacs.org>
>>        http://www.gromacs.org/mailman/listinfo/gmx-users
>>        Please search the archive at http://www.gromacs.org/search
>>        before posting!
>>        Please don't post (un)subscribe requests to the list. Use the
>>        www interface or send it to gmx-users-request at gromacs.org
>>        <mailto:gmx-users-request at gromacs.org>.
>>        Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>>    --    _________________
>>    HAPAX LEGOMENA
>>
>>    _______________________________________________
>>    gmx-users mailing list    gmx-users at gromacs.org
>>    <mailto:gmx-users at gromacs.org>
>>    http://www.gromacs.org/mailman/listinfo/gmx-users
>>    Please search the archive at http://www.gromacs.org/search before
>>    posting!
>>    Please don't post (un)subscribe requests to the list. Use the
>>    www interface or send it to gmx-users-request at gromacs.org
>>    <mailto:gmx-users-request at gromacs.org>.
>>    Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081221/76b4bf4e/attachment.html>