[gmx-users] Parallel run on a Quad Core
Chitrita Dutta Roy
chitrita.md at gmail.com
Sun Dec 21 17:53:42 CET 2008
But one thing as i did make links so definitely there are links of those
executables in /usr/local/bin.How can i easily remove them..??
On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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