Re: [gmx-users] MPI ERROR while installing GMX4.0.7
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
Re: [gmx-users] MPI ERROR while installing GMX4.0.7
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.
ban...@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 naz...@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@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 r...@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
[gmx-users] MPI ERROR while installing GMX4.0.7
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@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 r...@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@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 r...@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-loopsconftest.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,
