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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Feb 1 08:10:18 CET 2010


On 01/02/10 18:01, Chandan Choudhury wrote:
> 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

Have you set up your machine to run MPI jobs properly? Read the MPI 
library documentation and make a non-GROMACS test case work properly first.

Mark

> [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
> <mailto:bskumar.tech at gmail.com>> wrote:
>
>
>
>         Message: 5
>         Date: Sun, 31 Jan 2010 00:34:22 +0530
>         From: Chandan Choudhury <iitdckc at gmail.com
>         <mailto: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
>         <mailto:gmx-users at gromacs.org>>
>         Message-ID:
>         <4e22679c1001301104r5f1d725bjd5824e68cb3cb1a7 at mail.gmail.com
>         <mailto: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
>         <mailto: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
>         <mailto: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 <mailto: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
>         <mailto: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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