[gmx-users] error: Cannot compile and link MPI code with mpicc
Chandan Choudhury
iitdckc at gmail.com
Mon Feb 1 08:01:32 CET 2010
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.tech at gmail.com>wrote:
>
>
>> 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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