Thanks for your help. ok i have gone through that and even the wiki dirty install.Ok i will go through those once more and will see if it works.Thanks once again.
On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul <jalem...@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 <jalem...@vt.edu<mailto: >> 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> >> <mailto: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> >> <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 >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto: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> >> <mailto: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> >> <mailto: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/searchbefore >> 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> >> <mailto: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 >> <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 >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> _______________________________________________ >> 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 >> >> >> > -- > ======================================== > > 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 >
_______________________________________________ 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