----- Original Message ----- From: Manik Mayur <manik.ma...@gmail.com> Date: Monday, August 16, 2010 3:02 Subject: Re: [gmx-users] Parallel mdrun not working on gentoo linux To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> comments inline.. > > 2010/8/14 Mark Abraham <mark.abra...@anu.edu.au>: > > Did you build a parallel GROMACS? If so, how? Do MPI test > programs run? > > I used the following command.. > > ./configure --enable-mpi --disable-nice --with-fft=fftw3 -- > program-suffix=_mpi > make mdrun > make install-mdrun > > and yes, mpi test programs are running fine. > > further, $mdrun_mpi just results in a blinking cursor at newline > (earlier it displayed an array of info strings) That's weird. Sounds like a dynamic linking error. Is there another version of MPI installed? (Get rid of it.) Try enforcing static linking. Or, try these http://gentoo-portage.com/sci-chemistry/gromacs Mark > > ----- Original Message ----- > > From: Manik Mayur <manik.ma...@gmail.com> > > Date: Saturday, August 14, 2010 15:14 > > Subject: [gmx-users] Parallel mdrun not working on gentoo linux > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > >> Hi All, > >> > >> I am trying to build gromacs-4.0.7 on my gentoo box. My non- > parallel>> version of mdrun is working without any issues but > when I try to run > >> the parallel version of mdrun, it kind of hangs (even no help > info).>> Some details- > >> > >> 1) $uname -a > >> Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23 IST > 2010 i686 > >> Intel(R) Core(TM)2 Quad CPU Q8200 @ 2.33GHz GenuineIntel GNU/Linux > >> > >> 2) openmpi -version : 1.4.1 (through emerge) > >> > >> 3) $ ldd /usr/local/bin/mdrun_mpi > >> linux-gate.so.1 => (0xb77f6000) > >> libmd_mpi.so.5 => /usr/local/gromacs/lib/libmd_mpi.so.5 > (0xb76ee000)>> libgmx_mpi.so.5 => > /usr/local/gromacs/lib/libgmx_mpi.so.5>> (0xb7460000) > libxml2.so.2 => /usr/lib/libxml2.so.2 (0xb7321000) > >> libz.so.1 => /lib/libz.so.1 (0xb730d000) > >> libnsl.so.1 => /lib/libnsl.so.1 (0xb72f5000) > >> libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0xb71b2000) > >> libm.so.6 => /lib/libm.so.6 (0xb718d000) > >> libSM.so.6 => /usr/lib/libSM.so.6 (0xb7184000) > >> libuuid.so.1 => /lib/libuuid.so.1 (0xb717f000) > >> libICE.so.6 => /usr/lib/libICE.so.6 (0xb7166000) > >> libX11.so.6 => /usr/lib/libX11.so.6 (0xb7041000) > >> libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7025000) > >> libXau.so.6 => /usr/lib/libXau.so.6 (0xb7021000) > >> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb701b000) > >> libdl.so.2 => /lib/libdl.so.2 (0xb7017000) > >> libmpi.so.0 => /usr/lib/libmpi.so.0 (0xb6f84000) > >> libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0xb6f3d000) > >> libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0xb6ed2000) > >> libutil.so.1 => /lib/libutil.so.1 (0xb6ece000) > >> libpthread.so.0 => /lib/libpthread.so.0 (0xb6eb5000) > >> libc.so.6 => /lib/libc.so.6 (0xb6d6f000) > >> /lib/ld-linux.so.2 (0xb77f7000) > >> > >> Please somebody tell me what is the problem? > >> > >> Thanks, > >> > >> Manik Mayur > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.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://lists.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://lists.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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