[gmx-users] error: Cannot compile and link MPI code with mpicc

[Sarath Kumar]

>
> Message: 5
> Date: Sun, 31 Jan 2010 00:34:22 +0530
> From: Chandan Choudhury <iitdckc at gmail.com>
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>        mpicc
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <4e22679c1001301104r5f1d725bjd5824e68cb3cb1a7 at 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 at 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 "root at 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 <roland at 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 <iitdckc at 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 at 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 "root at 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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