Thanks Mark for your reply. First I want to know do I have to update GMX? for example, when GMX4.5.5 come out, and I use GMX4.5.5 instead of GMX4.5.4. I think GMX4.0.7 is even more stable. Second is the error while install GMX4.5.5. I use configure instead of CMake. I have successfully installed GMX4.5.4 and GMX4.0.7 with these command . I use GNU C compiler, and hareware is a 8 core Dell sever. Command line used is : tar xzvf gromacs-4.5.5.tar.gz ./configure --prefix=/home/hzj1000/software/GMX/4.5.5 --with-gsl --with-fft=fftw3 make and an error cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so ../mdlib/.libs/libmd.so /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath -Wl,/home/hzj1000/software/GMX/4.5.5/lib /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 The output of configure: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-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 how to run the C preprocessor... cc -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 cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... 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 cc ... /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 for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no 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 for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld) 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... 64 checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... 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 for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking direct.h usability... no checking direct.h presence... no checking for direct.h... no checking for sys/types.h... (cached) yes checking for sys/time.h... (cached) 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... yes 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... 4 checking size of long int... 4 checking size of long long int... 8 checking size of off_t... 8 checking size of void*... 4 checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include checking whether -R must be followed by a space... neither works checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking gsl/gsl_version.h usability... no checking gsl/gsl_version.h presence... no checking for gsl/gsl_version.h... no checking libxml/parser.h usability... no checking libxml/parser.h presence... no checking for libxml/parser.h... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for inline... inline checking for C/C++ restrict keyword... __restrict checking for uid_t... yes checking for gid_t... yes checking for sig_atomic_t... yes checking whether your compiler can handle assembly files (*.s)... yes checking whether as fully supports ia32 SSE... yes checking whether byte ordering is bigendian... (cached) no checking if the compiler supports gcc inline assembly... yes checking if the compiler supports MSVC inline assembly... no checking if dlopen supported... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/gmxlib/Makefile config.status: creating src/gmxlib/libgmx.pc config.status: creating src/gmxlib/gmx_blas/Makefile config.status: creating src/gmxlib/gmx_lapack/Makefile config.status: creating src/gmxlib/selection/Makefile config.status: creating src/gmxlib/statistics/Makefile config.status: creating src/gmxlib/trajana/Makefile config.status: creating src/gmxlib/thread_mpi/Makefile config.status: creating src/gmxlib/nonbonded/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_c/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_power6/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile config.status: creating include/Makefile config.status: creating include/types/Makefile config.status: creating include/thread_mpi/Makefile config.status: creating include/thread_mpi/atomic/Makefile config.status: creating src/mdlib/Makefile config.status: creating src/mdlib/libmd.pc config.status: creating src/kernel/Makefile config.status: creating src/kernel/libgmxpreprocess.pc config.status: creating src/tools/Makefile config.status: creating src/tools/libgmxana.pc config.status: creating src/ngmx/Makefile config.status: creating src/contrib/Makefile config.status: creating scripts/Makefile config.status: creating admin/Makefile config.status: creating share/Makefile config.status: creating share/tutor/Makefile config.status: creating share/tutor/gmxdemo/Makefile config.status: creating share/tutor/nmr1/Makefile config.status: creating share/tutor/nmr2/Makefile config.status: creating share/tutor/water/Makefile config.status: creating share/tutor/mixed/Makefile config.status: creating share/tutor/methanol/Makefile config.status: creating share/tutor/speptide/Makefile config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/top/gmx.ff/Makefile config.status: creating share/top/gmx2.ff/Makefile config.status: creating share/top/encadv.ff/Makefile config.status: creating share/top/encads.ff/Makefile config.status: creating share/top/oplsaa.ff/Makefile config.status: creating share/top/gromos43a1.ff/Makefile config.status: creating share/top/gromos43a2.ff/Makefile config.status: creating share/top/gromos45a3.ff/Makefile config.status: creating share/top/gromos53a5.ff/Makefile config.status: creating share/top/gromos53a6.ff/Makefile config.status: creating share/top/charmm27.ff/Makefile config.status: creating share/top/amber94.ff/Makefile config.status: creating share/top/amber96.ff/Makefile config.status: creating share/top/amberGS.ff/Makefile config.status: creating share/top/amber99.ff/Makefile config.status: creating share/top/amber99sb.ff/Makefile config.status: creating share/top/amber99sb-ildn.ff/Makefile config.status: creating share/top/amber03.ff/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating man/man7/Makefile config.status: creating Doxyfile config.status: creating src/config.h config.status: executing depfiles commands Best wishes! Zhongjin He
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