[gmx-users] Parallel run on a Quad Core

[Chitrita Dutta Roy]

Sorry for the first step i used manual extraction as that was a bzip
package.

On Sun, Dec 21, 2008 at 10:05 PM, Chitrita Dutta Roy
<chitrita.md at gmail.com>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
>
> 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
>>>
>>>
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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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