Dear all,
When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure command, I got the error information: 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... configure: error: in `/gromacs/gromacs-4.5.5': configure: error: C compiler cannot create executables See `config.log' for more details. The content of the config.log is the as following: This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gromacs configure 4.5.5, which was generated by GNU Autoconf 2.64. Invocation command line was $ ./configure --disable-float --prefix=/gromacs/gromacs-4.5.5 ## --------- ## ## Platform. ## ## --------- ## hostname = localhost.localdomain uname -m = i686 uname -r = 2.6.18-308.el5 uname -s = Linux uname -v = #1 SMP Tue Feb 21 20:05:41 EST 2012 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = i686 /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/kerberos/sbin PATH: /usr/kerberos/bin PATH: /usr/local/bin PATH: /usr/bin PATH: /bin PATH: /usr/X11R6/bin PATH: /home/sunyp/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:3028: checking build system type configure:3042: result: i686-pc-linux-gnu configure:3062: checking host system type configure:3075: result: i686-pc-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) 1.15.1 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) 4.1.2 20080704 (Red Hat 4.1.2-52) Copyright (C) 2006 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: i386-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=i386-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-52) 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 /gromacs/fftw-3.3.2/include conftest.c >&5 /gromacs/fftw-3.3.2/include: file not recognized: Is a directory collect2: ld returned 1 exit status configure:4434: $? = 1 configure:4471: result: 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 "gmx-users@gromacs.org" | #define PACKAGE_URL "" | #define PACKAGE "gromacs" | #define VERSION "4.5.5" | #define GMX_DOUBLE /**/ | #define GMX_SOFTWARE_INVSQRT /**/ | #define GMX_QMMM_GAUSSIAN /**/ | #define GMX_QMMM_ORCA /**/ | #define BUILD_TIME "Mon Oct 8 18:32:11 PDT 2012" | #define BUILD_USER "root@localhost.localdomain" | #define BUILD_MACHINE "Linux 2.6.18-308.el5 i686" | /* end confdefs.h. */ | #include <stdio.h> | int | main () | { | FILE *f = fopen ("conftest.out", "w"); | return ferror (f) || fclose (f) != 0; | | ; | return 0; | } configure:4477: error: in `/gromacs/gromacs-4.5.5': configure:4481: error: C compiler cannot create executables See `config.log' for more details. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=i686-pc-linux-gnu ac_cv_env_CCASFLAGS_set= ac_cv_env_CCASFLAGS_value= ac_cv_env_CCAS_set= ac_cv_env_CCAS_value= ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value=/gromacs/fftw-3.3.2/include ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_F77_set= ac_cv_env_F77_value= ac_cv_env_FFLAGS_set= ac_cv_env_FFLAGS_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBSUFFIX_set= ac_cv_env_LIBSUFFIX_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_XMKMF_set= ac_cv_env_XMKMF_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_host=i686-pc-linux-gnu ac_cv_path_install='/usr/bin/install -c' ac_cv_path_mkdir=/bin/mkdir ac_cv_prog_AWK=gawk ac_cv_prog_ac_ct_CC=cc ac_cv_prog_make_make_set=yes am_cv_prog_tar_ustar=gnutar ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run aclocal-1.11' AMDEPBACKSLASH='' AMDEP_FALSE='' AMDEP_TRUE='' AMTAR='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run tar' AR='' AS='' ASFLAGS='' AUTOCONF='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run autoconf' AUTOHEADER='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run autoheader' AUTOMAKE='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run automake-1.11' AWK='gawk' CC='cc' CCAS='' CCASDEPMODE='' CCASFLAGS='' CCDEPMODE='' CC_FOR_BUILD='' CFLAGS='' CPP='' CPPFLAGS='/gromacs/fftw-3.3.2/include' CXX='' CXXCPP='' CXXDEPMODE='' CXXFLAGS='' CYGPATH_W='echo' DEFS='' DEPDIR='' DLLTOOL='' DLOPEN_LIBS='' ECHO='echo' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' F77='' F77LINK='$(LINK)' FFLAGS='' FFT_LIBS='' FLIBS='' GMX_BLUEGENE_FALSE='' GMX_BLUEGENE_TRUE='' GMX_DOUBLE_FALSE='#' GMX_DOUBLE_TRUE='' GMX_EXTERNAL_BLAS_FALSE='' GMX_EXTERNAL_BLAS_TRUE='#' GMX_EXTERNAL_LAPACK_FALSE='' GMX_EXTERNAL_LAPACK_TRUE='#' GMX_FAHCORE_FALSE='' GMX_FAHCORE_TRUE='' GMX_FORTRAN_FALSE='' GMX_FORTRAN_TRUE='' GMX_IA32_SSE2_FALSE='' GMX_IA32_SSE2_TRUE='' GMX_IA32_SSE_FALSE='' GMX_IA32_SSE_TRUE='' GMX_IA64_ASM_FALSE='' GMX_IA64_ASM_TRUE='' GMX_POWER6_FALSE='' GMX_POWER6_TRUE='' GMX_PPC_ALTIVEC_FALSE='' GMX_PPC_ALTIVEC_TRUE='' GMX_SOFTWARE_INVSQRT_FALSE='#' GMX_SOFTWARE_INVSQRT_TRUE='' GMX_X86_64_SSE2_FALSE='' GMX_X86_64_SSE2_TRUE='' GMX_X86_64_SSE_FALSE='' GMX_X86_64_SSE_TRUE='' GREP='' GSL_LIBS='' INCLUDES='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' LDFLAGS='' LIBOBJS='' LIBS='' LIBSUFFIX='' LIBTOOL='' LMKL='' LN_S='' LTLIBOBJS='' MAKEINFO='${SHELL} /gromacs/gromacs-4.5.5/config/missing --run makeinfo' MKDIR_P='/bin/mkdir -p' MPICC='' NO_LA_FILES_FALSE='' NO_LA_FILES_TRUE='#' OBJDUMP='' OBJEXT='' PACKAGE='gromacs' PACKAGE_BUGREPORT='gmx-users@gromacs.org' PACKAGE_NAME='gromacs' PACKAGE_STRING='gromacs 4.5.5' PACKAGE_TARNAME='gromacs' PACKAGE_URL='' PACKAGE_VERSION='4.5.5' PATH_SEPARATOR=':' PKG_CFLAGS=' -DGMX_DOUBLE -DGMX_SOFTWARE_INVSQRT' PKG_FFT='' PKG_FFT_LIBS='' PKG_GSL='' PKG_XML='' PTHREAD_CC='' PTHREAD_CFLAGS='' PTHREAD_LIBS='' RANLIB='' RPM='' SET_MAKE='' SHARED_VERSION_INFO='6:0:0' SHELL='/bin/sh' 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='' X_CFLAGS='' X_EXTRA_LIBS='' X_LIBS='' X_PRE_LIBS='' ac_ct_CC='cc' ac_ct_CXX='' 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='' am__isrc='' am__leading_dot='.' am__quote='' am__tar='tar --format=ustar -chf - "$$tardir"' am__untar='tar -xf -' bindir='${exec_prefix}/bin' build='i686-pc-linux-gnu' build_alias='' build_cpu='i686' build_os='linux-gnu' build_vendor='pc' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' have_git='' host='i686-pc-linux-gnu' host_alias='' host_cpu='i686' host_os='linux-gnu' host_vendor='pc' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='${SHELL} /gromacs/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='/gromacs/gromacs-4.5.5' 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 "gmx-users@gromacs.org" #define PACKAGE_URL "" #define PACKAGE "gromacs" #define VERSION "4.5.5" #define GMX_DOUBLE /**/ #define GMX_SOFTWARE_INVSQRT /**/ #define GMX_QMMM_GAUSSIAN /**/ #define GMX_QMMM_ORCA /**/ #define BUILD_TIME "Mon Oct 8 18:32:11 PDT 2012" #define BUILD_USER "root@localhost.localdomain" #define BUILD_MACHINE "Linux 2.6.18-308.el5 i686" configure: exit 77 Could you help me with that? Thanks! Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists