[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...

Wed Aug 8 01:29:20 CEST 2012

On 8/08/2012 3:17 AM, rama david wrote:
> Hi Gromacs Friends,
>
> I am trying to install gromacs 4.5.4  in parallel operating system fedora 17
> I am using dell T 3500 precision , 6C.
>
> I downloaded openmppi-1.6
> Command line to install
>     ./configure --prefix=/usr/local
>   make all install
>
> For fftw 3.3.2 installation command line was .
>
> ./configure --enable-float
> make
> make install
>
> To Gromacs I wrote..
> ./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi
>
>
> System reply with
>    configure error : cannot compute sizeof ( off_t)...
>
> config .log show following error...It very big..I am pesting only a
> small part...
>
> Please tell me the reason for such error ...?? And how to overcome these???

I do not think your MPI compiler is working correctly. I suggest you 
find a small test case to probe whether it is.

Mark

> .
> .
> .
> .
> .
> .
> configure:5529: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.4"
> | #define PACKAGE_STRING "gromacs 4.5.4"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.4"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Tue Aug  7 10:46:37 IST 2012"
> | #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
> | #define GMX_MPI /**/
> | #define GMX_LIB_MPI /**/
> | #define MPI_IN_PLACE_EXISTS /**/
> | /* end confdefs.h.  */
> |
> | #if defined __QK_USER__
> | #else
> | #error not catamount
> | #endif
> |
> | int
> | main ()
> | {
> |
> |   ;
> |   return 0;
> | }
> configure:5551: result: no
> configure:6229: checking how to run the C preprocessor
> configure:6260: mpicc -E -I/usr/local/lib conftest.c
> configure:6260: $? = 0
> configure:6274: mpicc -E -I/usr/local/lib conftest.c
> conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
> compilation terminated.
> configure:6274: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.4"
> | #define PACKAGE_STRING "gromacs 4.5.4"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.4"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Tue Aug  7 10:46:37 IST 2012"
> | #define BUILD_USER "prashant at prashant"
> | #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
> | #define GMX_MPI /**/
> | #define GMX_LIB_MPI /**/
> | #define MPI_IN_PLACE_EXISTS /**/
> | #define F77_OR_C_FUNC(name,NAME) name
> | #define F77_OR_C_FUNC_(name,NAME) name
> | /* end confdefs.h.  */
> | #include <ac_nonexistent.h>
> configure:6299: result: mpicc -E
> configure:6319: mpicc -E -I/usr/local/lib conftest.c
> configure:6319: $? = 0
> configure:6333: mpicc -E -I/usr/local/lib conftest.c
> conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
> compilation terminated.
> configure:6333: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.4"
> | #define PACKAGE_STRING "gromacs 4.5.4"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.4"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Tue Aug  7 10:46:37 IST 2012"
> | #define BUILD_USER "prashant at prashant"
> | #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
> | #define GMX_MPI /**/
> | #define GMX_LIB_MPI /**/
> | #define MPI_IN_PLACE_EXISTS /**/
> | #define F77_OR_C_FUNC(name,NAME) name
> | #define F77_OR_C_FUNC_(name,NAME) name
> | /* end confdefs.h.  */
> | #include <ac_nonexistent.h>
> configure:6362: checking for grep that handles long lines and -e
> configure:6420: result: /usr/bin/grep
> configure:6425: checking for egrep
> configure:6487: result: /usr/bin/grep -E
> configure:6492: checking whether ln -s works
> configure:6496: result: yes
> configure:6895: checking whether mpicc accepts -O3
> configure:6913: result: yes
> configure:7193: checking whether mpicc accepts -msse2
> configure:7211: result: yes
> configure:7225: checking whether mpicc accepts -funroll-all-loops
> configure:7243: result: yes
> configure:7255: checking whether mpicc accepts -std=gnu99
> configure:7273: result: yes
> configure:7288: checking whether mpicc accepts -fexcess-precision=fast
> configure:7306: result: yes
> configure:7347: checking whether mpicc accepts  -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> -funroll-all-loops -std=gnu99 -fexcess-precision=fast
> configure:7365: result: yes
> configure:8089: checking whether byte ordering is bigendian
> configure:8104: mpicc -c  -O3 -fomit-frame-pointer -finline-functions
> -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
> -fexcess-precision=fast -I/usr/local/lib conftest.c >&5
> conftest.c:23:9: error: unknown type name 'not'
> conftest.c:23:15: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'universal'
> conftest.c:23:15: error: unknown type name 'universal'
> configure:8104: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.4"
> | #define PACKAGE_STRING "gromacs 4.5.4"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.4"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Tue Aug  7 10:46:37 IST 2012"
> | #define BUILD_USER "prashant at prashant"
> | #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
> | #define GMX_MPI /**/
> | #define GMX_LIB_MPI /**/
> | #define MPI_IN_PLACE_EXISTS /**/
> | #define F77_OR_C_FUNC(name,NAME) name
> | #define F77_OR_C_FUNC_(name,NAME) name
> | /* end confdefs.h.  */
> | #ifndef __APPLE_CC__
> | 	       not a universal capable compiler
> | 	     #endif
> | 	     typedef int dummy;
> |
> configure:8157: mpicc -c  -O3 -fomit-frame-pointer -finline-functions
> -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
> -fexcess-precision=fast -I/usr/local/lib conftest.c >&5
> configure:8157: $? = 0
> configure:8183: mpicc -c  -O3 -fomit-frame-pointer -finline-functions
> -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
> -fexcess-precision=fast -I/usr/local/lib conftest.c >&5
> conftest.c: In function 'main':
> conftest.c:37:4: error: unknown type name 'not'
> conftest.c:37:12: error: expected '=', ',', ';', 'asm' or
> '__attribute__' before 'endian'
> configure:8183: $? = 1
> configure: failed program was:
> | /* confdefs.h */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.5.4"
> | #define PACKAGE_STRING "gromacs 4.5.4"
> | #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
> | #define PACKAGE_URL ""
> | #define PACKAGE "gromacs"
> | #define VERSION "4.5.4"
> | #define GMX_SOFTWARE_INVSQRT /**/
> | #define GMX_QMMM_GAUSSIAN /**/
> | #define GMX_QMMM_ORCA /**/
> | #define BUILD_TIME "Tue Aug  7 10:46:37 IST 2012"
> .
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>
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> configure error : cannot compute sizeof ( off_t)...
>
>
>
> Thank you ...
>
> With best wishes and regards...