comments inline.. 2010/8/14 Mark Abraham <[email protected]>: > 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) > Mark -Manik > > ----- Original Message ----- > From: Manik Mayur <[email protected]> > Date: Saturday, August 14, 2010 15:14 > Subject: [gmx-users] Parallel mdrun not working on gentoo linux > To: Discussion list for GROMACS users <[email protected]> > >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
