[gmx-users] error: Cannot compile and link MPI code with mpicc
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sun Jan 31 17:27:59 CET 2010
Looks to me like you are not linking properly to the mpi libraries.
Please post your gromacs compilation commands in full. For example,
mine are posted below. Note also that some clusters make it more
difficult for you depending on their setup. I have used clusters in
which the simplest way to ensure access to all of the necessary MPI
libraries is to submit my compilation as a job to the MPI queue.
export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec
export GROMACS_LOCATION=/scratch/cneale/exe/intel/gromacs-4.0.5/exec
export CPPFLAGS="-I$FFTW_LOCATION/include
-I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/include
-I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/lib"
export LDFLAGS=-L$FFTW_LOCATION/lib
./configure --prefix=$GROMACS_LOCATION --without-motif-includes
--without-motif-libraries --without-x --without-xml --enable-mpi
--program-suffix="_openmpi" >output.configure.mpi 2>&1
make >output.make.mpi 2>&1
make install-mdrun >output.make_install.mpi 2>&1
-- original message --
On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury <iitdckc at
gmail.com>wrote:
> 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
>>>
>>> --
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>
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