[gmx-users] error while install GMX4.5.5

[zhongjin]

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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