> > Message: 5 > Date: Sun, 31 Jan 2010 00:34:22 +0530 > From: Chandan Choudhury <[email protected]> > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with > mpicc > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > 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 "[email protected]" > | #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 <[email protected]> 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 <[email protected] > >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 "[email protected]" > >> | #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
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