[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
rama david
ramadavidgroup at gmail.com
Tue Aug 7 19:17:43 CEST 2012
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???
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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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configure error : cannot compute sizeof ( off_t)...
Thank you ...
With best wishes and regards...
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