Thanks. I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc file, and could compile the mpi version of gromacs. The next thing is I got the error on executing mdrun_mpi -h Following is the output. Kindly help.
corsica:/usr/local/gromacs/bin # mdrun_mpi -h [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182 -------------------------------------------------------------------------- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_rml_base_select failed --> Returned value -13 instead of ORTE_SUCCESS -------------------------------------------------------------------------- -------------------------------------------------------------------------- It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): ompi_mpi_init: orte_init_stage1 failed --> Returned "Not found" (-13) instead of "Success" (0) -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** before MPI was initialized *** MPI_ERRORS_ARE_FATAL (goodbye) [corsica:17130] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed! -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 1, 2010 at 10:50 AM, Sarath Kumar <bskumar.t...@gmail.com>wrote: > > >> Message: 5 >> Date: Sun, 31 Jan 2010 00:34:22 +0530 >> From: Chandan Choudhury <iitd...@gmail.com> >> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with >> mpicc >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: >> <4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Ronald !! >> Thanks for your reply. >> I recompiled the openmpi. But while executing ./configure --enable-mpi in >> gromacs4.0.7 the following error is shown in config.log file. >> >> configure:4536: checking for mpicc >> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc >> configure:4563: result: mpicc >> configure:4577: checking whether the MPI cc command works >> configure:4601: mpicc -o conftest -g -O2 conftest.c >&5 >> conftest.c:15:17: error: mpi.h: No such file or directory >> configure:4607: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "gromacs" >> | #define PACKAGE_TARNAME "gromacs" >> | #define PACKAGE_VERSION "4.0.7" >> | #define PACKAGE_STRING "gromacs 4.0.7" >> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org" >> | #define PACKAGE "gromacs" >> | #define VERSION "4.0.7" >> | #define GMX_SOFTWARE_SQRT >> | #define GMX_QMMM_GAUSSIAN >> | #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010" >> | #define BUILD_USER "r...@corsica" >> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686" >> | /* end confdefs.h. */ >> | #include <mpi.h> >> | int >> | main () >> | { >> | int argc; char **argv; MPI_Init(&argc,&argv); >> | ; >> | return 0; >> | } >> configure:4619: error: Cannot compile and link MPI code with mpicc >> >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz <rol...@utk.edu> wrote: >> >> > Hi, >> > >> > your MPI installation has to be brogen. mpicc always has to be able to >> find >> > libmpi. Please reinstall mpi correctly. >> > >> > Roland >> > >> > On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury <iitd...@gmail.com >> >wrote: >> > >> >> Hi gmx users !! >> >> >> >> On compiling GMX paralley, following error was encountered. How can I >> >> tackle this. >> >> Kindly help. >> >> >> >> >> >> checking for mpicc... mpicc >> >> checking whether the MPI cc command works... configure: error: Cannot >> >> compile and link MPI code with mpicc >> >> >> >> The config.log file reads >> >> >> >> configure:4536: checking for mpicc >> >> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc >> >> configure:4563: result: mpicc >> >> configure:4577: checking whether the MPI cc command works >> >> configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/ >> >> conftest.c >&5 >> >> /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: >> >> cannot find -lmpi >> >> collect2: ld returned 1 exit status >> >> configure:4607: $? = 1 >> >> configure: failed program was: >> >> | /* confdefs.h. */ >> >> | #define PACKAGE_NAME "gromacs" >> >> | #define PACKAGE_TARNAME "gromacs" >> >> #define PACKAGE_VERSION "4.0.7" >> >> | #define PACKAGE_STRING "gromacs 4.0.7" >> >> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org" >> >> | #define PACKAGE "gromacs" >> >> | #define VERSION "4.0.7" >> >> | #define GMX_SOFTWARE_SQRT >> >> | #define GMX_QMMM_GAUSSIAN >> >> | #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010" >> >> | #define BUILD_USER "r...@shiraz" >> >> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686" >> >> | /* end confdefs.h. */ >> >> | #include <mpi.h> >> >> | int >> >> | main () >> >> | { >> >> | int argc; char **argv; MPI_Init(&argc,&argv); >> >> | ; >> >> | return 0; >> >> | } >> >> configure:4619: error: Cannot compile and link MPI code with mpicc >> >> >> >> >> >> Chandan >> >> >> >> -- >> >> Chandan kumar Choudhury >> >> NCL, Pune >> >> INDIA >> >> >> >> -- >> >> ****************************************** >> > > Hi. > If u r using RHL or Fedora series.. > > Try this before reinstalling openmpi. > > Its better to update the Compilers before installing MPI. > > I did this in Fedora 10.i386. > > yum install -y *gcc* > > yum install -y *c++* > > Then install open-mpi > as ./configure, make, make install. > If u still have the same problem > > error: Cannot compile and link MPI code with mpicc. > > Then remove the open-mpi installed folder. > > then do yum install -y *open-mpi* > > And then try installing gromacs with MPI. > > Actually, the first option worked for me. > Also i prefer lam-mpi is the best. > > > > -- > B. Sarath Kumar, B.tech. > Anna University, Chennai > > -- > 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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