[gmx-users] MPI ERROR while installing GMX4.0.7
Chandan Choudhury
iitdckc at gmail.com
Fri Jan 15 19:19:38 CET 2010
Dear Nuno
thanks for your helpful suggestion. It worked successful.
But the following command mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb doesnt seem to run parallely. I have mentiond the output below.
....................
bansal at corsica:~/CKC/L2PJR> mpirun -np 2 mdrun_mpi_d -v -s em_1.tpr -c
em_1.pdb
[corsica:17339] [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
--------------------------------------------------------------------------
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_system_init.c at line 42
[corsica:17339] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init.c at line 52
--------------------------------------------------------------------------
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jan 15, 2010 at 5:04 PM, Nuno Azoia <nazoia at det.uminho.pt> wrote:
> Hello!
>
> I had the same problem, and for me the solution was to set up the
> openmpi/lib directory. The compiler is not able to find it alone.
>
> I'm using bash, so for me the solution was:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/directory/openmpi/lib
>
> of course you have to change "/your/directory" with the correct path in
> your system.
>
> I hope this will help.
>
> Nuno Azoia
>
> On Fri, 2010-01-15 at 12:30 +0530, Chandan Choudhury wrote:
> > Hello gmx-users !!
> >
> > I am trying to install gromacs 4.0.7 double precision with mpi. I
> > downloaded openmpi-1.4. and installed it.
> > Then executed
> > ./configure --enable-mpi --program-suffix=_mpi_d
> > --prefix=/usr/local/gromacs407_double_mpi --enable-double
> >
> > It showed checking for mpicc...
> > mpicc
> > checking whether the MPI cc command works...
> > yes
> > checking for catamount...
> > no
> > checking how to run the C preprocessor... mpicc
> > -E
> > checking whether mpicc accepts -O3...
> > yes
> > checking whether mpicc accepts -funroll-all-loops...
> > yes
> > checking whether mpicc accepts -O3 -fomit-frame-pointer
> > -finline-functions -Wall -Wno-unused -funroll-all-loops...
> > yes
> > checking for grep that handles long lines and
> > -e... /usr/bin/grep
> > checking for egrep... /usr/bin/grep
> > -E
> > checking for ANSI C header files...
> > no
> > checking for sys/types.h...
> > yes
> > checking for sys/stat.h...
> > yes
> > checking for stdlib.h...
> > yes
> > checking for string.h...
> > yes
> > checking for memory.h...
> > yes
> > checking for strings.h...
> > yes
> > checking for inttypes.h...
> > yes
> > checking for stdint.h...
> > yes
> > checking for unistd.h...
> > yes
> > checking whether byte ordering is bigendian...
> > no
> > checking for int...
> > yes
> > checking size of int... configure: error: cannot compute sizeof
> > (int)
> > See `config.log' for more details.
> >
> > The part of the config.log reads as:
> >
> > --configure:4577: checking whether the MPI cc command works
> > configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
> > configure:4607: $? = 0
> > configure:4613: result: yes
> > configure:4636: checking for catamount
> > configure:4664: mpicc -c -g -O2 conftest.c >&5
> > conftest.c:20:2: error: #error not catamount
> > configure:4670: $? = 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_DOUBLE
> > | #define GMX_SOFTWARE_SQRT
> > | #define GMX_QMMM_GAUSSIAN
> > | #define BUILD_TIME "Sun Jan 17 01:26:27 EST 2010"
> > | #define BUILD_USER "root at corsica"
> > | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> > | #define GMX_MPI
> > | /* end confdefs.h. */
> > |
> > | #if defined __QK_USER__
> > | #else
> > | #error not catamount
> > | #endif
> > |
> > | int
> > | main ()
> > | {
> > |
> > | ;
> > | return 0;
> > | }
> > configure:4706: result: no
> > configure:5590: checking how to run the C preprocessor
> > configure:5630: mpicc -E conftest.c
> > configure:5636: $? = 0
> > configure:5667: mpicc -E conftest.c
> > conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
> > |
> > | int
> > | main ()
> > | {
> > |
> > | ;
> > | return 0;
> > | }
> > configure:4706: result: no
> > configure:5590: checking how to run the C preprocessor
> > configure:5630: mpicc -E conftest.c
> > configure:5636: $? = 0
> > configure:5667: mpicc -E conftest.c
> > conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
> > configure:5673: $? = 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_DOUBLE
> > | #define GMX_SOFTWARE_SQRT
> > | #define GMX_QMMM_GAUSSIAN
> > | #define BUILD_TIME "Sun Jan 17 01:26:27 EST 2010"
> > | #define BUILD_USER "root at corsica"
> > | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> > | #define GMX_MPI
> > | #define F77_OR_C_FUNC(name,NAME) name
> > | #define F77_OR_C_FUNC_(name,NAME) name
> > | /* end confdefs.h. */
> > | #include <ac_nonexistent.h>
> > configure:5706: result: mpicc -E
> > configure:5735: mpicc -E conftest.c
> > configure:5741: $? = 0
> > configure:5772: mpicc -E conftest.c
> > conftest.c:19:28: error: ac_nonexistent.h: No such file or directory
> >
> ..............................................................................................
> >
> ..............................................................................................
> > configure:6203: checking whether mpicc accepts -O3
> > configure:6221: result: yes
> > configure:6501: checking whether mpicc accepts -funroll-all-loops
> > configure:6519: result: yes
> > configure:6558: checking whether mpicc accepts -O3
> > -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> > -funroll-all-loops
> > configure:6576: result: yes
> > configure:6668: checking for grep that handles long lines and -e
> > configure:6742: result: /usr/bin/grep
> > configure:6747: checking for egrep
> > configure:6825: result: /usr/bin/grep -E
> > configure:6830: checking for ANSI C header files
> > configure:6868: mpicc -c -O3 -fomit-frame-pointer -finline-functions
> > -Wall -Wno-unused -funroll-all-loops conftest.c >&5
> > configure:6874: $? = 0
> > configure:6973: mpicc -o conftest -O3 -fomit-frame-pointer
> > -finline-functions -Wall -Wno-unused -funroll-all-loops conftest.c
> > >&5
> > configure:6976: $? = 0
> > configure:6982: ./conftest
> > ./conftest: error while loading shared libraries: libmpi.so.0: cannot
> > open shared object file: No such file or directory
> > configure:6985: $? = 127
> > configure: program exited with status 127
> >
> > I also searched the gmx-users list, but cant understand it. Google
> > also didnt help me.
> >
> > Looking forward from you all.
> >
> > Chandan
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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