[gmx-users] Trouble Installing GROMACS
shyamala iyer
shyamala.iyer at gmail.com
Sat Sep 8 20:28:40 CEST 2007
Hi,
I am new to GROMACS and I am having some trouble installing GROMACS in my
home directory.
The machine I am currently working on has fftw, gcc and binutils already
installed
fftw package installed: fftw3-3.0.1-4
When I execute ./configure --prefix=$HOME/gromacs, I get the error that C
compiler cannot create executables.
I have pasted my congif.log file below.
gcc is in my path
% gcc -v
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-java-awt=gtk
--host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)
Thanks,
Shyamala
config.log
-------------------------------------------
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 3.3.1, which was
generated by GNU Autoconf 2.59. Invocation command line was
$ ./configure --prefix=/hosts/nirvana/spare/home/shyamala/gromacs
## --------- ##
## Platform. ##
## --------- ##
hostname = nirvana.compbio.washington.edu
uname -m = x86_64
uname -r = 2.6.9-42.0.10.ELsmp
uname -s = Linux
uname -v = #1 SMP Fri Feb 16 17:13:42 EST 2007
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /home/ram/usr/protinfo/bin/scripts
PATH: /home/ram/usr/protinfo/bin/linux_ix86_64
PATH: /home/ram/usr/packages/bin/scripts
PATH: /home/ram/usr/packages/bin/linux_ix86_64
PATH: /home/ram/usr/extras/bin/scripts
PATH: /home/ram/usr/extras/bin/linux_ix86_64
PATH: /home/ram/usr/ramp/bin/scripts
PATH: /home/ram/usr/ramp/bin/linux_ix86_64
PATH: /home/ram/usr/rambin/bin/scripts
PATH: /home/ram/usr/rambin/bin/linux_ix86_64
PATH: /home/ram/bin/scripts
PATH: .
PATH: /bin
PATH: /sbin
PATH: /etc
PATH: /usr/bin
PATH: /usr/ucb
PATH: /usr/sbin
PATH: /usr/bsd
PATH: /usr/local/bin
PATH: /usr/bin/X11
PATH: /usr/etc
PATH: /home/ram/bin/linux_ix86_64
PATH: /home/ram/usr/bin/scripts
PATH: /home/ram/usr/bin/linux_ix86_64
PATH: /hosts/nirvana/spare/home/shyamala/bin
PATH: /hosts/nirvana/spare/home/shyamala/bin/NAMD_2.6_Linux-amd64
PATH: /hosts/nirvana/spare/home/shyamala/MGLTools-1.4.5/share/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1580: checking build system type
configure:1598: result: x86_64-unknown-linux-gnu
configure:1606: checking host system type
configure:1620: result: x86_64-unknown-linux-gnu
configure:1643: checking for a BSD-compatible install
configure:1698: result: /usr/bin/install -c
configure:1709: checking whether build environment is sane
configure:1752: result: yes
configure:1817: checking for gawk
configure:1833: found /bin/gawk
configure:1843: result: gawk
configure:1853: checking whether make sets $(MAKE)
configure:1873: result: yes
configure:2036: checking how to create a ustar tar archive
configure:2049: tar --version
tar (GNU tar) 1.14
Copyright (C) 2004 Free Software Foundation, Inc.
This program comes with NO WARRANTY, to the extent permitted by law.
You may redistribute it under the terms of the GNU General Public License;
see the file named COPYING for details.
Written by John Gilmore and Jay Fenlason.
configure:2052: $? = 0
configure:2092: tardir=conftest.dir && eval tar --format=ustar -chf -
"$tardir" >conftest.tar
configure:2095: $? = 0
configure:2099: tar -xf - <conftest.tar
configure:2102: $? = 0
configure:2115: result: gnutar
configure:2710: checking for C compiler version
configure:2713: gcc --version </dev/null >&5
gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3)
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:2716: $? = 0
configure:2718: gcc -v </dev/null >&5
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-java-awt=gtk
--host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)
configure:2721: $? = 0
configure:2723: gcc -V </dev/null >&5
gcc: `-V' option must have argument
configure:2726: $? = 1
configure:2749: checking for C compiler default output file name
configure:2752: gcc -O3 -Wall -pedantic -static $(HDRS) $(DEFINES)
conftest.c -lm >&5
gcc: $(HDRS): No such file or directory
gcc: $(DEFINES): No such file or directory
configure:2755: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME "GROMACS"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "3.3.1"
| #define PACKAGE_STRING "GROMACS 3.3.1"
| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "3.3.1"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Sat Sep 8 10:43:40 PDT 2007"
| #define BUILD_USER "shyamala at nirvana.compbio.washington.edu"
| #define BUILD_MACHINE "Linux 2.6.9-42.0.10.ELsmp x86_64"
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:2794: error: C compiler cannot create executables
See `config.log' for more details.
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-unknown-linux-gnu
ac_cv_build_alias=x86_64-unknown-linux-gnu
ac_cv_env_CC_set=set
ac_cv_env_CC_value=gcc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-O3 -Wall -pedantic -static $(HDRS) $(DEFINES)'
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
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=set
ac_cv_env_FFLAGS_value='-x f77-cpp-input -O3 -Wall -static $(HDRS)
$(DEFINES)'
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_host=x86_64-unknown-linux-gnu
ac_cv_host_alias=x86_64-unknown-linux-gnu
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_make_make_set=yes
am_cv_prog_tar_ustar=gnutar
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL}
/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run aclocal-1.9'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run tar'
AR=''
AS=''
ASFLAGS=''
AUTOCONF='${SHELL}
/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run autoconf'
AUTOHEADER='${SHELL}
/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run autoheader'
AUTOMAKE='${SHELL}
/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run automake-1.9'
AWK='gawk'
CC='gcc'
CCAS=''
CCASFLAGS=''
CCDEPMODE=''
CC_FOR_BUILD=''
CFLAGS='-O3 -Wall -pedantic -static $(HDRS) $(DEFINES)'
CPP=''
CPPFLAGS=''
CXX=''
CXXCPP=''
CXXDEPMODE=''
CXXFLAGS=''
CYGPATH_W='echo'
DEFS=''
DEPDIR=''
DLLTOOL=''
ECHO='echo'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
F77=''
F77LINK='$(LINK)'
FFLAGS='-x f77-cpp-input -O3 -Wall -static $(HDRS) $(DEFINES)'
FLIBS=''
GMXANA_LIBOBJS=''
GMXLIB_LIBOBJS=''
GMX_DOUBLE_FALSE=''
GMX_DOUBLE_TRUE='#'
GMX_EXTERNAL_BLAS_FALSE=''
GMX_EXTERNAL_BLAS_TRUE='#'
GMX_EXTERNAL_LAPACK_FALSE=''
GMX_EXTERNAL_LAPACK_TRUE='#'
GMX_FORTRAN_FALSE=''
GMX_FORTRAN_TRUE='#'
GMX_IA32_3DNOW_FALSE=''
GMX_IA32_3DNOW_TRUE=''
GMX_IA32_SSE2_FALSE=''
GMX_IA32_SSE2_TRUE=''
GMX_IA32_SSE_FALSE=''
GMX_IA32_SSE_TRUE=''
GMX_IA64_ASM_DOUBLE_FALSE=''
GMX_IA64_ASM_DOUBLE_TRUE=''
GMX_IA64_ASM_SINGLE_FALSE=''
GMX_IA64_ASM_SINGLE_TRUE=''
GMX_PPC_ALTIVEC_FALSE=''
GMX_PPC_ALTIVEC_TRUE=''
GMX_PREFETCH_FORCES_FALSE=''
GMX_PREFETCH_FORCES_TRUE='#'
GMX_SOFTWARE_SQRT_FALSE='#'
GMX_SOFTWARE_SQRT_TRUE=''
GMX_THREAD_FALSE=''
GMX_THREAD_TRUE='#'
GMX_X86_64_SSE2_FALSE=''
GMX_X86_64_SSE2_TRUE=''
GMX_X86_64_SSE_FALSE=''
GMX_X86_64_SSE_TRUE=''
INCLUDES=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LDFLAGS=''
LIBOBJS=''
LIBS='-lm'
LIBSUFFIX=''
LIBTOOL=''
LN_S=''
LTLIBOBJS=''
MAKEINFO='${SHELL}
/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing
--run makeinfo'
MDLIB_LIBOBJS=' qm_gaussian.lo'
MPICC=''
OBJDUMP=''
OBJEXT=''
PACKAGE='gromacs'
PACKAGE_BUGREPORT='gmx-users at gromacs.org'
PACKAGE_NAME='GROMACS'
PACKAGE_STRING='GROMACS 3.3.1'
PACKAGE_TARNAME='gromacs'
PACKAGE_VERSION='3.3.1'
PATH_SEPARATOR=':'
RANLIB=''
RPM=''
SET_MAKE=''
SHARED_VERSION_INFO='4:0:0'
SHELL='/bin/sh'
STRIP=''
USE_X11_FALSE=''
USE_X11_TRUE=''
VERSION='3.3.1'
X_CFLAGS=''
X_EXTRA_LIBS=''
X_LIBS=''
X_PRE_LIBS=''
ac_ct_AR=''
ac_ct_AS=''
ac_ct_CC=''
ac_ct_CXX=''
ac_ct_DLLTOOL=''
ac_ct_F77=''
ac_ct_OBJDUMP=''
ac_ct_RANLIB=''
ac_ct_STRIP=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE=''
am__include=''
am__leading_dot='.'
am__quote=''
am__tar='tar --format=ustar -chf - "$$tardir"'
am__untar='tar -xf -'
bindir='${exec_prefix}/bin'
build='x86_64-unknown-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='unknown'
datadir='${prefix}/share'
exec_prefix='NONE'
host='x86_64-unknown-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='unknown'
includedir='${prefix}/include'
infodir='${prefix}/info'
install_sh='/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1
/config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
prefix='/hosts/nirvana/spare/home/shyamala/gromacs'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define BUILD_MACHINE "Linux 2.6.9-42.0.10.ELsmp x86_64"
#define BUILD_TIME "Sat Sep 8 10:43:40 PDT 2007"
#define BUILD_USER "shyamala at nirvana.compbio.washington.edu"
#define GMX_QMMM_GAUSSIAN
#define GMX_SOFTWARE_SQRT
#define PACKAGE "gromacs"
#define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
#define PACKAGE_NAME "GROMACS"
#define PACKAGE_STRING "GROMACS 3.3.1"
#define PACKAGE_TARNAME "gromacs"
#define PACKAGE_VERSION "3.3.1"
#define VERSION "3.3.1"
configure: exit 77
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