Hi, everyone: when I compiled GMX4.5.5, I encountered a problem and failed many times， SOS!
Below is my config.log: /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/lib64/qt-3.3/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/local/sbin PATH: /usr/sbin PATH: /sbin PATH: /usr/local/grace/bin PATH: /usr/lib64/openmpi/bin PATH: /home/njn/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:3028: checking build system type configure:3042: result: x86_64-unknown-linux-gnu configure:3062: checking host system type configure:3075: result: x86_64-unknown-linux-gnu configure:3112: checking for a BSD-compatible install configure:3180: result: /usr/bin/install -c configure:3191: checking whether build environment is sane configure:3241: result: yes configure:3382: checking for a thread-safe mkdir -p configure:3421: result: /bin/mkdir -p configure:3434: checking for gawk configure:3450: found /usr/bin/gawk configure:3461: result: gawk configure:3472: checking whether make sets $(MAKE) configure:3494: result: yes configure:3569: checking how to create a ustar tar archive configure:3582: tar --version tar (GNU tar) 1.23 Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Written by John Gilmore and Jay Fenlason. configure:3585: $? = 0 configure:3625: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar configure:3628: $? = 0 configure:3632: tar -xf - <conftest.tar configure:3635: $? = 0 configure:3648: result: gnutar configure:4308: checking for cc configure:4324: found /usr/bin/cc configure:4335: result: cc configure:4366: checking for C compiler version configure:4375: cc --version >&5 cc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6) Copyright (C) 2010 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:4386: $? = 0 configure:4375: cc -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC) configure:4386: $? = 0 configure:4375: cc -V >&5 cc: '-V' option must have argument configure:4386: $? = 1 configure:4375: cc -qversion >&5 cc: unrecognized option '-qversion' cc: no input files configure:4386: $? = 1 configure:4408: checking for C compiler default output file name configure:4430: cc conftest.c >&5 configure:4434: $? = 0 configure:4471: result: a.out configure:4487: checking whether the C compiler works configure:4496: ./a.out configure:4500: $? = 0 configure:4515: result: yes configure:4522: checking whether we are cross compiling configure:4524: result: no configure:4527: checking for suffix of executables configure:4534: cc -o conftest conftest.c >&5 configure:4538: $? = 0 configure:4560: result: configure:4566: checking for suffix of object files configure:4588: cc -c conftest.c >&5 configure:4592: $? = 0 configure:4613: result: o configure:4617: checking whether we are using the GNU C compiler configure:4636: cc -c conftest.c >&5 configure:4636: $? = 0 configure:4645: result: yes configure:4654: checking whether cc accepts -g configure:4674: cc -c -g conftest.c >&5 configure:4674: $? = 0 configure:4715: result: yes configure:4732: checking for cc option to accept ISO C89 configure:4796: cc -c -g -O2 conftest.c >&5 configure:4796: $? = 0 configure:4809: result: none needed configure:4840: checking for style of include used by make configure:4868: result: GNU configure:4893: checking dependency style of cc configure:5003: result: gcc3 configure:5262: checking dependency style of cc configure:5370: result: gcc3 configure:6229: checking how to run the C preprocessor configure:6260: cc -E conftest.c configure:6260: $? = 0 configure:6274: cc -E conftest.c conftest.c:19:28: error: ac_nonexistent.h: No such file or directory configure:6274: $? = 1 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "gromacs" | #define PACKAGE_TARNAME "gromacs" | #define PACKAGE_VERSION "4.5.5" | #define PACKAGE_STRING "gromacs 4.5.5" | #define PACKAGE_BUGREPORT "[email protected]" | #define PACKAGE_URL "" | #define PACKAGE "gromacs" | #define VERSION "4.5.5" | #define GMX_SOFTWARE_INVSQRT /**/ | #define GMX_QMMM_GAUSSIAN /**/ | #define GMX_QMMM_ORCA /**/ | #define BUILD_TIME "Wed Sep 21 12:48:07 CST 2011" | #define BUILD_USER "njn@njn-SL" | #define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64 x86_64" | #define F77_OR_C_FUNC(name,NAME) name | #define F77_OR_C_FUNC_(name,NAME) name | /* end confdefs.h. */ | #include <ac_nonexistent.h>"' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run aclocal-1.11' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run tar' AR='ar' AS='cc ' ASFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99' AUTOCONF='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run autoconf' AUTOHEADER='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run autoheader' AUTOMAKE='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run automake-1.11' AWK='gawk' CC='cc ' CCAS='cc ' CCASDEPMODE='depmode=gcc3' CCASFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include' CCDEPMODE='depmode=gcc3' CC_FOR_BUILD='cc' CFLAGS=' -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include' CPP='cc -E' CPPFLAGS='' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS=' -pthread -I./include' CYGPATH_W='echo' DEFS='-DHAVE_CONFIG_H' DEPDIR='.deps' DLLTOOL='dlltool' DLOPEN_LIBS='-ldl' ECHO='echo' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='/bin/grep -E' EXEEXT='' F77='' F77LINK='$(LINK)' FFLAGS='' FFT_LIBS='-lfftw3f' FLIBS='' GMX_BLUEGENE_FALSE='' GMX_BLUEGENE_TRUE='#' GMX_DOUBLE_FALSE='' GMX_DOUBLE_TRUE='#' GMX_EXTERNAL_BLAS_FALSE='' GMX_EXTERNAL_BLAS_TRUE='#' GMX_EXTERNAL_LAPACK_FALSE='' GMX_EXTERNAL_LAPACK_TRUE='#' GMX_FAHCORE_FALSE='' GMX_FAHCORE_TRUE='#' GMX_FORTRAN_FALSE='' GMX_FORTRAN_TRUE='#' GMX_IA32_SSE2_FALSE='' GMX_IA32_SSE2_TRUE='#' GMX_IA32_SSE_FALSE='' GMX_IA32_SSE_TRUE='#' GMX_IA64_ASM_FALSE='' GMX_IA64_ASM_TRUE='#' GMX_POWER6_FALSE='' GMX_POWER6_TRUE='#' GMX_PPC_ALTIVEC_FALSE='' GMX_PPC_ALTIVEC_TRUE='#' GMX_SOFTWARE_INVSQRT_FALSE='#' GMX_SOFTWARE_INVSQRT_TRUE='' GMX_X86_64_SSE2_FALSE='' GMX_X86_64_SSE2_TRUE='#' GMX_X86_64_SSE_FALSE='#' GMX_X86_64_SSE_TRUE='' GREP='/bin/grep' GSL_LIBS='' INCLUDES=' -I/usr/include/libxml2' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS=' ' LIBOBJS='' LIBS='-lnsl -lm ' LIBSUFFIX='' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LMKL='' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/missing --run makeinfo' MKDIR_P='/bin/mkdir -p' MPICC='' NO_LA_FILES_FALSE='' NO_LA_FILES_TRUE='#' OBJDUMP='objdump' OBJEXT='o' PACKAGE='gromacs' PACKAGE_BUGREPORT='[email protected]' PACKAGE_NAME='gromacs' PACKAGE_STRING='gromacs 4.5.5' PACKAGE_TARNAME='gromacs' PACKAGE_URL='' PACKAGE_VERSION='4.5.5' PATH_SEPARATOR=':' PKG_CFLAGS=' -DGMX_SOFTWARE_INVSQRT -DGMX_THREADS' PKG_FFT='fftw3f' PKG_FFT_LIBS='' PKG_GSL='' PKG_XML='libxml-2.0' PTHREAD_CC='cc' PTHREAD_CFLAGS='-pthread' PTHREAD_LIBS='' RANLIB='ranlib' RPM='rpm' SET_MAKE='' SHARED_VERSION_INFO='6:0:0' SHELL='/bin/sh' STRIP='strip' THREAD_PARALLEL_FALSE='#' THREAD_PARALLEL_TRUE='' USE_VERSION_H_FALSE='' USE_VERSION_H_TRUE='#' USE_X11_FALSE='#' USE_X11_TRUE='' VERSION='4.5.5' XMKMF='' XML_LIBS='-lxml2' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS=' -lSM -lICE' ac_ct_CC='cc' ac_ct_CXX='g++' ac_ct_F77='' am__EXEEXT_FALSE='' am__EXEEXT_TRUE='#' am__fastdepCCAS_FALSE='#' am__fastdepCCAS_TRUE='' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__quote='' am__tar='tar --format=ustar -chf - "$$tardir"' am__untar='tar -xf -' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='${prefix}' have_git='' host='x86_64-unknown-linux-gnu' host_alias='' host_cpu='x86_64' host_os='linux-gnu' host_vendor='unknown' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /home/njn/Desktop/gromacs-4.5.5/config/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='/bin/mkdir -p' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='/home/njn/zms/1gmx4.5.5' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "gromacs" #define PACKAGE_TARNAME "gromacs" #define PACKAGE_VERSION "4.5.5" #define PACKAGE_STRING "gromacs 4.5.5" #define PACKAGE_BUGREPORT "[email protected]" #define PACKAGE_URL "" #define PACKAGE "gromacs" #define VERSION "4.5.5" #define GMX_SOFTWARE_INVSQRT /**/ #define GMX_QMMM_GAUSSIAN /**/ #define GMX_QMMM_ORCA /**/ #define BUILD_TIME "Wed Sep 21 12:48:07 CST 2011" #define BUILD_USER "njn@njn-SL" #define BUILD_MACHINE "Linux 2.6.32-131.0.15.el6.x86_64 x86_64" #define F77_OR_C_FUNC(name,NAME) name #define F77_OR_C_FUNC_(name,NAME) name #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_UNISTD_H 1 #define HAVE_SYS_TIME_H 1 #define HAVE_SCHED_H 1 #define HAVE_SYSCONF 1 #define HAVE_PTHREAD 1 #define THREAD_PTHREADS /**/ #define HAVE_PTHREAD_SETAFFINITY 1 #define GMX_THREADS /**/ #define GMX_MPI /**/ #define HAVE_SIGUSR1 /**/ #define HAVE_PIPES /**/ #define FLOAT_FORMAT_IEEE754 /**/ #define HAVE_DLFCN_H 1 #define HAVE_FSEEKO 1 #define HAVE_LIBM 1 #define HAVE_LIBFFTW3F 1 #define GMX_FFT_FFTW3 /**/ #define HAVE_RPC_RPC_H 1 #define HAVE_RPC_XDR_H 1 #define HAVE_LIBNSL 1 #define HAVE_LIMITS_H 1 #define HAVE_UNISTD_H 1 #define HAVE_UNISTD_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_TIME_H 1 #define HAVE_DIRENT_H 1 #define HAVE_REGEX_H 1 #define RETSIGTYPE void #define HAVE_VPRINTF 1 #define HAVE_STRCASECMP 1 #define HAVE_STRDUP 1 #define HAVE_GETTIMEOFDAY 1 #define HAVE_CBRT 1 #define HAVE_ISNAN 1 #define HAVE_FSYNC 1 #define HAVE_FILENO 1 #define HAVE_POSIX_MEMALIGN 1 #define HAVE_MEMALIGN 1 #define SIZEOF_INT 4 #define SIZEOF_LONG_INT 8 #define SIZEOF_LONG_LONG_INT 8 #define SIZEOF_OFF_T 8 #define SIZEOF_VOIDP 8 #define HAVE_LIBXML_PARSER_H 1 #define HAVE_LIBXML2 1 #define restrict __restrict #define HAVE_UID_T 1 #define HAVE_GID_T 1 #define HAVE_SIG_ATOMIC_T 1 #define GMX_X86_64_SSE /**/ #define GMX_DLOPEN /**/ configure: exit 0 I'm a rookie, and can't solve it, please help me!!! SOS! -- Sincerely yours Dr Ji-Nan Niu School of Materials Science and Engineering. China University of Mining and Technology. Jiangsu Province, XuZhou 221116 P. R. China
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