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 <[email protected]
<mailto:[email protected]>> wrote:
Message: 5
Date: Sun, 31 Jan 2010 00:34:22 +0530
From: Chandan Choudhury <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code
with
mpicc
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID:
<[email protected]
<mailto:[email protected]>>
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 "[email protected]
<mailto:[email protected]>"
| #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 "r...@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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>>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 "[email protected]
<mailto:[email protected]>"
>> | #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 "r...@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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