Hi,
> sun...@chem.iitb.ac.in wrote: >> Dear Open-mpi users, >> >> I installed openmpi-1.4.1 in my user area and then set the path for >> openmpi in the .bashrc file as follow. However, am still getting >> following >> error message whenever am starting the parallel molecular dynamics >> simulation using GROMACS. So every time am starting the MD job, I need >> to >> source the .bashrc file again. >> >> Earlier in some other machine I did the same thing and was not getting >> any >> problem. >> >> Could you guys suggest what would be the problem? >> >> > Have you set OPAL_PREFIX to /home/sunitap/soft/openmpi? How to set OPAL_PREFIX? During the installation of openmpi, I ran configure with --prefix=/home/sunitap/soft/openmpi Did you mean this? > > If you do a ldd on mdrun_mpi does libmpi.so.0 come up not found? I got libmpi.so.0 not found. The output I got is ========= ldd `which mdrun_mpi` libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00000039e1800000) libnsl.so.1 => /lib64/libnsl.so.1 (0x00000039dd600000) libm.so.6 => /lib64/libm.so.6 (0x00000039d5e00000) libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000039d9600000) libICE.so.6 => /usr/lib64/libICE.so.6 (0x00000039da600000) libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039d7200000) libmpi.so.0 => not found libopen-rte.so.0 => not found libopen-pal.so.0 => not found libdl.so.2 => /lib64/libdl.so.2 (0x00000039d6200000) libutil.so.1 => /lib64/libutil.so.1 (0x00000039e4a00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039d6600000) libc.so.6 => /lib64/libc.so.6 (0x00000039d5a00000) libz.so.1 => /usr/lib64/libz.so.1 (0x00000039d6a00000) libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000039d6e00000) libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000039d7600000) /lib64/ld-linux-x86-64.so.2 (0x00000039d5600000) ========= > If so and there truly is a libmpi.so.0 in /home/sunitap/soft/openmpi/lib > you may want to make sure the bitness of libmpi.so.0 and mdrun_mpi are > the same by > doing a file command on both. > ---------------------------- The file command on both gives following output. file ~/soft/gromacs/bin/mdrun_mpi /home/sunitap/soft/gromacs/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 2.6.9, not stripped file /home/sunitap/soft/openmpi/lib/libmpi.so.0 /home/sunitap/soft/openmpi/lib/libmpi.so.0: symbolic link to `libmpi.so.0.0.1' ---------------------------- Thanks. Sunita > --td >> ============.bashrc============ >> #path for openmpi >> export PATH=$PATH:/home/sunitap/soft/openmpi/bin >> export CFLAGS="-I/home/sunitap/soft/openmpi/include" >> export LDFLAGS="-L/home/sunitap/soft/openmpi/lib" >> export LD_LIBRARY_PATH=/home/sunitap/soft/openmpi/lib:$LD_LIBRARY_PATH >> >> ============== error message ============== >> mdrun_mpi: error while loading shared libraries: libmpi.so.0: cannot >> open >> shared object file: No such file or directory >> >> ============================================ >> >> Thanks for any help. >> Best regards, >> Sunita >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > > > -- > Oracle > Terry D. Dontje | Principal Software Engineer > Developer Tools Engineering | +1.650.633.7054 > Oracle * - Performance Technologies* > 95 Network Drive, Burlington, MA 01803 > Email terry.don...@oracle.com <mailto:terry.don...@oracle.com> > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users