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...@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 <jalem...@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.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 >>> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@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-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> >>> -- _________________ >>> HAPAX LEGOMENA >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@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-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@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-requ...@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@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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