Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
Hi Gromacs Friends, After your reply, Itried in another way . I install the openmpi and fftw3 to the /opt/.. at the time of make (for gromacs) I encouner with error suggesting to recompile with -fPIC.. As per instruction in website, I added glag --enable-shared to the fftw, but again at the time of gromacs configuration I encounter the sane error suggesting to recompile with -fPIC So I used following coomand line ( as per instruction in website) ./configure --with-fft=fftw3 --enable-mpi --program-suffix=_mpi --prefix=/opt/gmx_4.5.4 --disable-shared make make install make tests make links make install-mdrun make links output . Libraries have been installed in: /opt/gmx_4.5.4/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,--rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. -- test -z /opt/gmx_4.5.4/lib/pkgconfig || /usr/bin/mkdir -p /opt/gmx_4.5.4/lib/pkgconfig /usr/bin/install -c -m 644 libgmx_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig' make[3]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib' make[2]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib' make[1]: Leaving directory `/opt/gromacs-4.5.4/src/gmxlib' (cd ./src/mdlib make install ; exit 0) make[1]: Entering directory `/opt/gromacs-4.5.4/src/mdlib' make[2]: Entering directory `/opt/gromacs-4.5.4/src/mdlib' test -z /opt/gmx_4.5.4/lib || /usr/bin/mkdir -p /opt/gmx_4.5.4/lib /bin/sh ../../libtool --mode=install /usr/bin/install -c libmd_mpi.la '/opt/gmx_4.5.4/lib' /usr/bin/install -c .libs/libmd_mpi.lai /opt/gmx_4.5.4/lib/libmd_mpi.la /usr/bin/install -c .libs/libmd_mpi.a /opt/gmx_4.5.4/lib/libmd_mpi.a chmod 644 /opt/gmx_4.5.4/lib/libmd_mpi.a ranlib /opt/gmx_4.5.4/lib/libmd_mpi.a PATH=$PATH:/sbin ldconfig -n /opt/gmx_4.5.4/lib -- Libraries have been installed in: /opt/gmx_4.5.4/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,--rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. -- test -z /opt/gmx_4.5.4/lib/pkgconfig || /usr/bin/mkdir -p /opt/gmx_4.5.4/lib/pkgconfig /usr/bin/install -c -m 644 libmd_mpi.pc '/opt/gmx_4.5.4/lib/pkgconfig' make[2]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib' make[1]: Leaving directory `/opt/gromacs-4.5.4/src/mdlib' (cd ./src/kernel make install-libLTLIBRARIES ; exit 0) make[1]: Entering directory `/opt/gromacs-4.5.4/src/kernel' test -z /opt/gmx_4.5.4/lib || /usr/bin/mkdir -p /opt/gmx_4.5.4/lib /bin/sh ../../libtool --mode=install /usr/bin/install -c libgmxpreprocess_mpi.la '/opt/gmx_4.5.4/lib' /usr/bin/install -c .libs/libgmxpreprocess_mpi.lai /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.la /usr/bin/install -c .libs/libgmxpreprocess_mpi.a /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a chmod 644 /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a ranlib /opt/gmx_4.5.4/lib/libgmxpreprocess_mpi.a PATH=$PATH:/sbin ldconfig -n /opt/gmx_4.5.4/lib -- Libraries have been installed in: /opt/gmx_4.5.4/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,--rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. -- make[1]: Leaving
[gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
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???
.
.
.
.
.
.
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@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@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@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@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@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 */
|
Re: [gmx-users] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
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@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@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@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@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@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'
