Re: [OMPI users] problem with .bashrc stetting of openmpi
> Hello Sunitha, > If you have admin privileges on this system add library path to > /etc/ld.so.conf I don't have admin privileges. > > eg: echo "/home/sunitap/soft/openmpi/lib" >> /etc/ld.so.conf > > ldconfig > > Rangam > > From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of > sun...@chem.iitb.ac.in [sun...@chem.iitb.ac.in] > Sent: Monday, August 16, 2010 12:28 AM > To: Open MPI Users > Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi > > Hi, > >> hello Sunita, >> >> what linux distribution is this? > The linux distribution is Red Hat Enterprise Linux Server release 5.5 > (Tikanga) >> >> On Fri, Aug 13, 2010 at 1:57 AM, <sun...@chem.iitb.ac.in> wrote: >> > Thanks, > Sunita > >>> 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? >>> >>> .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 >>> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] problem with .bashrc stetting of openmpi
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 (0x0039e180) libnsl.so.1 => /lib64/libnsl.so.1 (0x0039dd60) libm.so.6 => /lib64/libm.so.6 (0x0039d5e0) libSM.so.6 => /usr/lib64/libSM.so.6 (0x0039d960) libICE.so.6 => /usr/lib64/libICE.so.6 (0x0039da60) libX11.so.6 => /usr/lib64/libX11.so.6 (0x0039d720) libmpi.so.0 => not found libopen-rte.so.0 => not found libopen-pal.so.0 => not found libdl.so.2 => /lib64/libdl.so.2 (0x0039d620) libutil.so.1 => /lib64/libutil.so.1 (0x0039e4a0) libpthread.so.0 => /lib64/libpthread.so.0 (0x0039d660) libc.so.6 => /lib64/libc.so.6 (0x0039d5a0) libz.so.1 => /usr/lib64/libz.so.1 (0x0039d6a0) libXau.so.6 => /usr/lib64/libXau.so.6 (0x0039d6e0) libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x0039d760) /lib64/ld-linux-x86-64.so.2 (0x0039d560) = > 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
Re: [OMPI users] problem with .bashrc stetting of openmpi
Hi, > hello Sunita, > > what linux distribution is this? The linux distribution is Red Hat Enterprise Linux Server release 5.5 (Tikanga) > > On Fri, Aug 13, 2010 at 1:57 AM, <sun...@chem.iitb.ac.in> wrote: > Thanks, Sunita >> 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? >> >> .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 >> > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] problem with .bashrc stetting of openmpi
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? .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
Re: [OMPI users] mpi.h file is missing in openmpi
Hi Reuti, Thank you so much. I installed openmpi locally from the source file. It has all header files in the include folder. I could install charmm without any problem. Best regards, Sunita > Hi, > > Am 25.03.2010 um 11:30 schrieb sun...@chem.iitb.ac.in: > >> Openmpi is installed in a Intel Xeon quad core 2.4Ghz machine loaded >> with >> Red Hat Enterprise Linux 5. The loaded openmpi version is 1.2.5. While >> trying to install CHARMM software, it asked for the path of mpi.h file >> and >> library files libmpi. I didn't find 'include' folder in the openmpi >> folder >> which contains all the header files like mpi.h. However, it contains >> 'bin', 'etc', 'lib' and 'share' sub-folders. > > maybe only the runtime package and not the developer package was > installed. Due to the ancient version you have, I would suggest to > download the actual source and install on your own with: > > $ ./configure --prefix=/home/patel/local/openmpi-1.4.1 > > and after a "make" and "make install" you can access the actual header and > library files. For CHARMM ist might be necessary to supply the path to the > include files with -I/home/patel/local/openmpi-1.4.1/include in CFLAGS and > the path to your libs in LDFLAGS -L/home/patel/local/openmpi-1.4.1/lib > (names maybe different in CHARMM though). > > As long as you built the dynamic version, it's necessary to supply a > runtime also an export > LD_LIBRARY_PATH=/home/patel/local/openmpi-1.4.1/lib:$LD_LIBRARY_PATH > > -- Reuti > >> >> It looks like that mpi.h file does not exist. Which version of openmpi >> has >> the mpi.h header file? >> >> Any help would be appreciated. >> >> Regards, >> Dr. Sunita Patel >> - >> Visiting Fellow >> Department of Chemical Sciences >> T.I.F.R., Homi Bhabha Road, Colaba >> Mumbai - 45 >> - >> >> >> >> >> >> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
