Dear experts, I have just install gromacs 4.5.1 on my cluster (using CentOS that was install openmpi1.5, Platform MPI, fftw3, g77, gcc , g++) but I have problem with size of int :
[r...@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs --enable-mpi --enable-double checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for MPI_IN_PLACE in collective operations... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether mpicc accepts -O3... yes checking whether mpicc accepts -msse2... yes checking whether mpicc accepts -funroll-all-loops... yes checking whether mpicc accepts -std=gnu99... yes checking whether mpicc accepts -fexcess-precision=fast... no checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking whether we are using the GNU C++ compiler... yes checking whether mpicc accepts -g... yes checking dependency style of mpicc... gcc3 checking how to run the C++ preprocessor... mpicc -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... failed checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag "F77" to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3... yes checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for rpc/xdr.h... yes checking for xdr_float in -lnsl... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking unistd.h usability... yes checking unistd.h presence... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/types.h usability... yes checking sys/types.h presence... yes checking for sys/types.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working memcmp... no checking return type of signal handlers... void checking for off_t... yes checking for vprintf... yes checking for _doprnt... no checking if malloc debugging is wanted... no checking for strcasecmp... yes checking for strdup... yes checking for gettimeofday... yes checking for cbrt... yes checking for isnan... yes checking for _isnan... no checking for isfinite... no checking for _isfinite... no checking for fsync... yes checking for fileno... yes checking for bool... no checking for library containing posix_memalign... none required checking for library containing memalign... none required checking for _aligned_malloc... no *checking size of int... 0* *checking size of long int... 0* *checking size of long long int... 0* *checking size of off_t... configure: error: in `/shared/apps/source/gromacs-4.5.1':* configure: error: cannot compute sizeof (off_t) Any idea about this? -- Son Tung Ngo Institute for Computational Science & Technology Email: [email protected] Website: http://icst.org.vn -- Son Tung Ngo Institute for Computational Science & Technology Email: [email protected] Website: http://icst.org.vn
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