<div class="gmail_quote">Dear experts,<div><br></div><div>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 :</div>
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<div><div>[root@icstcluster gromacs-4.5.1]# ./configure --prefix=/shared/apps/gromacs --enable-mpi --enable-double </div><div>checking build system type... x86_64-unknown-linux-gnu</div><div>checking host system type... x86_64-unknown-linux-gnu</div>
<div>checking for a BSD-compatible install... /usr/bin/install -c</div><div>checking whether build environment is sane... yes</div><div>checking for a thread-safe mkdir -p... /bin/mkdir -p</div><div>checking for gawk... gawk</div>
<div>checking whether make sets $(MAKE)... yes</div><div>checking how to create a ustar tar archive... gnutar</div><div>checking for cc... cc</div><div>checking for C compiler default output file name... a.out</div><div>
checking whether the C compiler works... yes</div>
<div>checking whether we are cross compiling... no</div><div>checking for suffix of executables... </div><div>checking for suffix of object files... o</div><div>checking whether we are using the GNU C compiler... yes</div>
<div>checking whether cc accepts -g... yes</div><div>checking for cc option to accept ISO C89... none needed</div><div>checking for style of include used by make... GNU</div><div>checking dependency style of cc... gcc3</div>
<div>checking dependency style of cc... gcc3</div><div>checking for mpxlc... no</div><div>checking for mpicc... mpicc</div><div>checking whether the MPI cc command works... yes</div><div>checking for MPI_IN_PLACE in collective operations... yes</div>
<div>checking for catamount... no</div><div>checking how to run the C preprocessor... mpicc -E</div><div>checking for grep that handles long lines and -e... /bin/grep</div><div>checking for egrep... /bin/grep -E</div><div>
checking whether ln -s works... yes</div><div>checking whether mpicc accepts -O3... yes</div><div>checking whether mpicc accepts -msse2... yes</div><div>checking whether mpicc accepts -funroll-all-loops... yes</div><div>
checking whether mpicc accepts -std=gnu99... yes</div>
<div>checking whether mpicc accepts -fexcess-precision=fast... no</div><div>checking whether mpicc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes</div><div>
checking whether byte ordering is bigendian... no</div><div>checking that size_t can hold pointers... yes</div><div>checking for SIGUSR1... yes</div><div>checking for pipes... yes</div><div>checking floating-point format... IEEE754 (little-endian byte and word order)</div>
<div>checking whether ln -s works... yes</div><div>checking whether make sets $(MAKE)... (cached) yes</div><div>checking for a sed that does not truncate output... /bin/sed</div><div>checking for ld used by mpicc... /usr/bin/ld</div>
<div>checking if the linker (/usr/bin/ld) is GNU ld... yes</div><div>checking for /usr/bin/ld option to reload object files... -r</div><div>checking for BSD-compatible nm... /usr/bin/nm -B</div><div>checking how to recognise dependent libraries... pass_all</div>
<div>checking dlfcn.h usability... yes</div><div>checking dlfcn.h presence... yes</div><div>checking for dlfcn.h... yes</div><div>checking whether we are using the GNU C++ compiler... yes</div><div>checking whether mpicc accepts -g... yes</div>
<div>checking dependency style of mpicc... gcc3</div><div>checking how to run the C++ preprocessor... mpicc -E</div><div>checking the maximum length of command line arguments... 32768</div><div>checking command to parse /usr/bin/nm -B output from mpicc object... failed</div>
<div>checking for objdir... .libs</div><div>checking for ar... ar</div><div>checking for ranlib... ranlib</div><div>checking for strip... strip</div><div>checking if mpicc supports -fno-rtti -fno-exceptions... no</div><div>
checking for mpicc option to produce PIC... -fPIC</div><div>checking if mpicc PIC flag -fPIC works... yes</div><div>checking if mpicc static flag -static works... no</div><div>checking if mpicc supports -c -o file.o... yes</div>
<div>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes</div><div>checking dynamic linker characteristics... GNU/Linux ld.so</div><div>checking how to hardcode library paths into programs... immediate</div>
<div>checking whether stripping libraries is possible... yes</div><div>checking if libtool supports shared libraries... yes</div><div>checking whether to build shared libraries... no</div><div>checking whether to build static libraries... yes</div>
<div>configure: creating libtool</div><div>appending configuration tag "CXX" to libtool</div><div>checking for ld used by mpicc... /usr/bin/ld -m elf_x86_64</div><div>checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes</div>
<div>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes</div><div>checking for mpicc option to produce PIC... -fPIC</div><div>checking if mpicc PIC flag -fPIC works... yes</div>
<div>checking if mpicc static flag -static works... no</div><div>checking if mpicc supports -c -o file.o... yes</div><div>checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes</div>
<div>checking dynamic linker characteristics... GNU/Linux ld.so</div><div>checking how to hardcode library paths into programs... immediate</div><div>appending configuration tag "F77" to libtool</div><div>checking for special C compiler options needed for large files... no</div>
<div>checking for _FILE_OFFSET_BITS value needed for large files... no</div><div>checking for _LARGEFILE_SOURCE value needed for large files... no</div><div>checking for sqrt in -lm... yes</div><div>checking for fftw3.h... yes</div>
<div>checking for main in -lfftw3... yes</div><div>checking rpc/rpc.h usability... yes</div><div>checking rpc/rpc.h presence... yes</div><div>checking for rpc/rpc.h... yes</div><div>checking for rpc/xdr.h... yes</div><div>
checking for xdr_float in -lnsl... yes</div><div>checking limits.h usability... yes</div><div>checking limits.h presence... yes</div><div>checking for limits.h... yes</div><div>checking unistd.h usability... yes</div><div>
checking unistd.h presence... yes</div><div>checking for unistd.h... yes</div><div>checking for unistd.h... (cached) yes</div><div>checking sys/types.h usability... yes</div><div>checking sys/types.h presence... yes</div>
<div>checking for sys/types.h... yes</div><div>checking sys/time.h usability... yes</div><div>checking sys/time.h presence... yes</div><div>checking for sys/time.h... yes</div><div>checking dirent.h usability... yes</div>
<div>checking dirent.h presence... yes</div><div>checking for dirent.h... yes</div><div>checking regex.h usability... yes</div><div>checking regex.h presence... yes</div><div>checking for regex.h... yes</div><div>checking for working memcmp... no</div>
<div>checking return type of signal handlers... void</div><div>checking for off_t... yes</div><div>checking for vprintf... yes</div><div>checking for _doprnt... no</div><div>checking if malloc debugging is wanted... no</div>
<div>checking for strcasecmp... yes</div><div>checking for strdup... yes</div><div>checking for gettimeofday... yes</div><div>checking for cbrt... yes</div><div>checking for isnan... yes</div><div>checking for _isnan... no</div>
<div>checking for isfinite... no</div><div>checking for _isfinite... no</div><div>checking for fsync... yes</div><div>checking for fileno... yes</div><div>checking for bool... no</div><div>checking for library containing posix_memalign... none required</div>
<div>checking for library containing memalign... none required</div><div>checking for _aligned_malloc... no</div><div><b><span style="background-color:rgb(255, 153, 102)">checking size of int... 0</span></b></div>
<div><b><span style="background-color:rgb(255, 153, 102)">checking size of long int... 0</span></b></div><div><b><span style="background-color:rgb(255, 153, 102)">checking size of long long int... 0</span></b></div>
<div><b><span style="background-color:rgb(255, 153, 102)">checking size of off_t... configure: error: in `/shared/apps/source/gromacs-4.5.1':</span></b></div><div>configure: error: cannot compute sizeof (off_t)</div>
<div><br></div><div>Any idea about this?</div><div><br></div>-- <br><div>Son Tung Ngo</div><div>Institute for Computational Science & Technology</div><div><br></div><div>Email: <a href="mailto:nstung@icst.org.vn" target="_blank">nstung@icst.org.vn</a></div>
<div>Website: <a href="http://icst.org.vn" target="_blank">http://icst.org.vn</a></div><br>
</div>
</div><br><br clear="all"><br>-- <br><div>Son Tung Ngo</div><div>Institute for Computational Science & Technology</div><div><br></div><div>Email: <a href="mailto:nstung@icst.org.vn" target="_blank">nstung@icst.org.vn</a></div>
<div>Website: <a href="http://icst.org.vn" target="_blank">http://icst.org.vn</a></div><br>