[gmx-users] (no subject)

[yp sun]

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 at 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 at 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 at 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 at 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 at 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