<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>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.</DIV>
<DIV>Second is the error while install GMX4.5.5. I use configure instead of CMake.</DIV>
<DIV>I have successfully installed GMX4.5.4 and GMX4.0.7 with these command .</DIV>
<DIV>I use GNU C compiler, and hareware is a 8 core Dell sever.</DIV>
<DIV> </DIV>
<DIV>Command line used is : </DIV>
<DIV> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>tar xzvf gromacs-<?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:chsdate w:st="on" Year="1899" Month="12" Day="30" IsLunarDate="False" IsROCDate="False">4.5.5</st1:chsdate>.tar.gz</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US> ./configure --prefix=/home/hzj1000/software/GMX/4.5.5 --with-gsl --with-fft=fftw3</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>make</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>and an error </SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>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<BR>/home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np'<BR>collect2: ld returned 1 exit status<BR>make[3]: *** [grompp] Error 1<BR>make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel'<BR>make[2]: *** [all-recursive] Error
1<BR>make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'<BR>make[1]: *** [all] Error 2<BR>make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src'<BR>make: *** [all-recursive] Error 1</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>The output of configure:</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>checking build system type... i686-pc-linux-gnu<BR>checking host system type... i686-pc-linux-gnu<BR>checking for a BSD-compatible install... /usr/bin/install -c<BR>checking whether build environment is sane... yes<BR>checking for a thread-safe mkdir -p... /bin/mkdir -p<BR>checking for gawk... gawk<BR>checking whether make sets $(MAKE)... yes<BR>checking how to create a ustar tar archive... gnutar<BR>checking for cc... cc<BR>checking for C compiler default output file name... a.out<BR>checking whether the C compiler works... yes<BR>checking whether we are cross compiling... no<BR>checking for suffix of executables... <BR>checking for suffix of object files... o<BR>checking whether we are using the GNU C compiler... yes<BR>checking
whether cc accepts -g... yes<BR>checking for cc option to accept ISO C89... none needed<BR>checking for style of include used by make... GNU<BR>checking dependency style of cc... gcc3<BR>checking dependency style of cc... gcc3<BR>checking how to run the C preprocessor... cc -E<BR>checking for grep that handles long lines and -e... /bin/grep<BR>checking for egrep... /bin/grep -E<BR>checking whether ln -s works... yes<BR>checking whether cc accepts -O3... yes<BR>checking whether cc accepts -msse2... yes<BR>checking whether cc accepts -funroll-all-loops... yes<BR>checking whether cc accepts -std=gnu99... yes<BR>checking whether cc accepts -fexcess-precision=fast... no<BR>checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes<BR>checking for ANSI C header files... yes<BR>checking for sys/types.h... yes<BR>checking for sys/stat.h... yes<BR>checking for stdlib.h...
yes<BR>checking for string.h... yes<BR>checking for memory.h... yes<BR>checking for strings.h... yes<BR>checking for inttypes.h... yes<BR>checking for stdint.h... yes<BR>checking for unistd.h... yes<BR>checking for unistd.h... (cached) yes<BR>checking sys/time.h usability... yes<BR>checking sys/time.h presence... yes<BR>checking for sys/time.h... yes<BR>checking sched.h usability... yes<BR>checking sched.h presence... yes<BR>checking for sched.h... yes<BR>checking for sysconf... yes<BR>checking for the pthreads library -lpthreads... no<BR>checking whether pthreads work without any flags... no<BR>checking whether pthreads work with -Kthread... no<BR>checking whether pthreads work with -kthread... no<BR>checking for the pthreads library -llthread... no<BR>checking whether pthreads work with -pthread... yes<BR>checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE<BR>checking if more special flags are required for pthreads... no<BR>checking for
cc_r... cc<BR>checking if atomic operations are supported... yes<BR>checking if pthread_setaffinity_np is available... yes<BR>checking whether byte ordering is bigendian... no<BR>checking that size_t can hold pointers... yes<BR>checking for SIGUSR1... yes<BR>checking for pipes... yes<BR>checking floating-point format... IEEE754 (little-endian byte and word order)<BR>checking whether ln -s works... yes<BR>checking whether make sets $(MAKE)... (cached) yes<BR>checking for a sed that does not truncate output... /bin/sed<BR>checking for ld used by cc ... /usr/bin/ld<BR>checking if the linker (/usr/bin/ld) is GNU ld... yes<BR>checking for /usr/bin/ld option to reload object files... -r<BR>checking for BSD-compatible nm... /usr/bin/nm -B<BR>checking how to recognise dependent libraries... pass_all<BR>checking dlfcn.h usability... yes<BR>checking dlfcn.h presence... yes<BR>checking for dlfcn.h... yes<BR>checking for g++... g++<BR>checking whether we are using
the GNU C++ compiler... yes<BR>checking whether g++ accepts -g... yes<BR>checking dependency style of g++... gcc3<BR>checking how to run the C++ preprocessor... g++ -E<BR>checking the maximum length of command line arguments... 32768<BR>checking command to parse /usr/bin/nm -B output from cc object... ok<BR>checking for objdir... .libs<BR>checking for ar... ar<BR>checking for ranlib... ranlib<BR>checking for strip... strip<BR>checking if cc supports -fno-rtti -fno-exceptions... no<BR>checking for cc option to produce PIC... -fPIC<BR>checking if cc PIC flag -fPIC works... yes<BR>checking if cc static flag -static works... yes<BR>checking if cc supports -c -o file.o... yes<BR>checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes<BR>checking whether -lc should be explicitly linked in... no<BR>checking dynamic linker characteristics... GNU/Linux ld.so<BR>checking how to hardcode library paths
into programs... immediate<BR>checking whether stripping libraries is possible... yes<BR>checking for shl_load... no<BR>checking for shl_load in -ldld... no<BR>checking for dlopen... no<BR>checking for dlopen in -ldl... yes<BR>checking whether a program can dlopen itself... yes<BR>checking whether a statically linked program can dlopen itself... no<BR>checking if libtool supports shared libraries... yes<BR>checking whether to build shared libraries... yes<BR>checking whether to build static libraries... yes<BR>configure: creating libtool<BR>appending configuration tag "CXX" to libtool<BR>checking for ld used by g++... /usr/bin/ld<BR>checking if the linker (/usr/bin/ld) is GNU ld... yes<BR>checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes<BR>checking for g++ option to produce PIC... -fPIC<BR>checking if g++ PIC flag -fPIC works... yes<BR>checking if g++ static flag -static works... yes<BR>checking if g++ supports -c -o
file.o... yes<BR>checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes<BR>checking dynamic linker characteristics... GNU/Linux ld.so<BR>checking how to hardcode library paths into programs... immediate<BR>appending configuration tag "F77" to libtool<BR>checking for special C compiler options needed for large files... no<BR>checking for _FILE_OFFSET_BITS value needed for large files... 64<BR>checking for _LARGEFILE_SOURCE value needed for large files... 1<BR>checking for sqrt in -lm... yes<BR>checking for fftw3.h... yes<BR>checking for main in -lfftw3f... yes<BR>checking rpc/rpc.h usability... yes<BR>checking rpc/rpc.h presence... yes<BR>checking for rpc/rpc.h... yes<BR>checking for rpc/xdr.h... yes<BR>checking for xdr_float in -lnsl... yes<BR>checking limits.h usability... yes<BR>checking limits.h presence... yes<BR>checking for limits.h... yes<BR>checking for unistd.h... (cached) yes<BR>checking for unistd.h... (cached)
yes<BR>checking direct.h usability... no<BR>checking direct.h presence... no<BR>checking for direct.h... no<BR>checking for sys/types.h... (cached) yes<BR>checking for sys/time.h... (cached) yes<BR>checking dirent.h usability... yes<BR>checking dirent.h presence... yes<BR>checking for dirent.h... yes<BR>checking regex.h usability... yes<BR>checking regex.h presence... yes<BR>checking for regex.h... yes<BR>checking for working memcmp... yes<BR>checking return type of signal handlers... void<BR>checking for off_t... yes<BR>checking for vprintf... yes<BR>checking for _doprnt... no<BR>checking if malloc debugging is wanted... no<BR>checking for strcasecmp... yes<BR>checking for strdup... yes<BR>checking for gettimeofday... yes<BR>checking for cbrt... yes<BR>checking for isnan... yes<BR>checking for _isnan... no<BR>checking for isfinite... no<BR>checking for _isfinite... no<BR>checking for fsync... yes<BR>checking for fileno... yes<BR>checking for bool...
no<BR>checking for library containing posix_memalign... none required<BR>checking for library containing memalign... none required<BR>checking for _aligned_malloc... no<BR>checking size of int... 4<BR>checking size of long int... 4<BR>checking size of long long int... 8<BR>checking size of off_t... 8<BR>checking size of void*... 4<BR>checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include<BR>checking whether -R must be followed by a space... neither works<BR>checking for gethostbyname... yes<BR>checking for connect... yes<BR>checking for remove... yes<BR>checking for shmat... yes<BR>checking for IceConnectionNumber in -lICE... yes<BR>checking gsl/gsl_version.h usability... no<BR>checking gsl/gsl_version.h presence... no<BR>checking for gsl/gsl_version.h... no<BR>checking libxml/parser.h usability... no<BR>checking libxml/parser.h presence... no<BR>checking for libxml/parser.h... no<BR>checking for an ANSI C-conforming const...
yes<BR>checking for size_t... yes<BR>checking whether struct tm is in sys/time.h or time.h... time.h<BR>checking for inline... inline<BR>checking for C/C++ restrict keyword... __restrict<BR>checking for uid_t... yes<BR>checking for gid_t... yes<BR>checking for sig_atomic_t... yes<BR>checking whether your compiler can handle assembly files (*.s)... yes<BR>checking whether as fully supports ia32 SSE... yes<BR>checking whether byte ordering is bigendian... (cached) no<BR>checking if the compiler supports gcc inline assembly... yes<BR>checking if the compiler supports MSVC inline assembly... no<BR>checking if dlopen supported... yes<BR>configure: creating ./config.status<BR>config.status: creating Makefile<BR>config.status: creating src/Makefile<BR>config.status: creating src/gmxlib/Makefile<BR>config.status: creating src/gmxlib/libgmx.pc<BR>config.status: creating src/gmxlib/gmx_blas/Makefile<BR>config.status: creating
src/gmxlib/gmx_lapack/Makefile<BR>config.status: creating src/gmxlib/selection/Makefile<BR>config.status: creating src/gmxlib/statistics/Makefile<BR>config.status: creating src/gmxlib/trajana/Makefile<BR>config.status: creating src/gmxlib/thread_mpi/Makefile<BR>config.status: creating src/gmxlib/nonbonded/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_c/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile<BR>config.status: creating
src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_power6/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_single/Makefile<BR>config.status: creating src/gmxlib/nonbonded/nb_kernel_f77_double/Makefile<BR>config.status: creating include/Makefile<BR>config.status: creating include/types/Makefile<BR>config.status: creating include/thread_mpi/Makefile<BR>config.status: creating include/thread_mpi/atomic/Makefile<BR>config.status: creating src/mdlib/Makefile<BR>config.status: creating src/mdlib/libmd.pc<BR>config.status: creating src/kernel/Makefile<BR>config.status: creating src/kernel/libgmxpreprocess.pc<BR>config.status: creating src/tools/Makefile<BR>config.status: creating src/tools/libgmxana.pc<BR>config.status: creating src/ngmx/Makefile<BR>config.status: creating src/contrib/Makefile<BR>config.status: creating scripts/Makefile<BR>config.status: creating
admin/Makefile<BR>config.status: creating share/Makefile<BR>config.status: creating share/tutor/Makefile<BR>config.status: creating share/tutor/gmxdemo/Makefile<BR>config.status: creating share/tutor/nmr1/Makefile<BR>config.status: creating share/tutor/nmr2/Makefile<BR>config.status: creating share/tutor/water/Makefile<BR>config.status: creating share/tutor/mixed/Makefile<BR>config.status: creating share/tutor/methanol/Makefile<BR>config.status: creating share/tutor/speptide/Makefile<BR>config.status: creating share/template/Makefile<BR>config.status: creating share/top/Makefile<BR>config.status: creating share/top/gmx.ff/Makefile<BR>config.status: creating share/top/gmx2.ff/Makefile<BR>config.status: creating share/top/encadv.ff/Makefile<BR>config.status: creating share/top/encads.ff/Makefile<BR>config.status: creating share/top/oplsaa.ff/Makefile<BR>config.status: creating share/top/gromos43a1.ff/Makefile<BR>config.status: creating
share/top/gromos43a2.ff/Makefile<BR>config.status: creating share/top/gromos45a3.ff/Makefile<BR>config.status: creating share/top/gromos53a5.ff/Makefile<BR>config.status: creating share/top/gromos53a6.ff/Makefile<BR>config.status: creating share/top/charmm27.ff/Makefile<BR>config.status: creating share/top/amber94.ff/Makefile<BR>config.status: creating share/top/amber96.ff/Makefile<BR>config.status: creating share/top/amberGS.ff/Makefile<BR>config.status: creating share/top/amber99.ff/Makefile<BR>config.status: creating share/top/amber99sb.ff/Makefile<BR>config.status: creating share/top/amber99sb-ildn.ff/Makefile<BR>config.status: creating share/top/amber03.ff/Makefile<BR>config.status: creating share/html/Makefile<BR>config.status: creating share/html/images/Makefile<BR>config.status: creating share/html/online/Makefile<BR>config.status: creating man/Makefile<BR>config.status: creating man/man1/Makefile<BR>config.status: creating
man/man7/Makefile<BR>config.status: creating Doxyfile<BR>config.status: creating src/config.h<BR>config.status: executing depfiles commands</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US>Best wishes! Zhongjin He</SPAN></DIV>
<DIV><SPAN style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 10.5pt; mso-fareast-font-family: 宋体; mso-bidi-font-family: 宋体; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA" lang=EN-US></SPAN> </DIV></td></tr></table>