[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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