[gmx-users] MPI ERROR while installing GMX4.0.7
Nuno Azoia
nazoia at det.uminho.pt
Fri Jan 15 12:34:10 CET 2010
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
> --
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