<div>Hi,</div>
<div> </div>
<div>I am new to GROMACS and I am having some trouble installing GROMACS in my<br>home directory.<br>The machine I am currently working on has fftw, gcc and binutils already<br>installed<br>fftw package installed: fftw3-3.0.1-4
</div>
<div> </div>
<div>When I execute ./configure --prefix=$HOME/gromacs, I get the error that C compiler cannot create executables.</div>
<div>I have pasted my congif.log file below.</div>
<div> </div>
<div>gcc is in my path</div>
<div>% gcc -v<br>Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs<br>Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux
<br>Thread model: posix<br>gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)<br> </div>
<div>Thanks,</div>
<div>Shyamala</div>
<div> </div>
<div>config.log</div>
<div>-------------------------------------------</div>
<div><font size="2">
<p>This file contains any messages produced by compilers while</p>
<p>running configure, to aid debugging if configure makes a mistake.</p>
<p>It was created by GROMACS configure 3.3.1, which was</p>
<p>generated by GNU Autoconf 2.59. Invocation command line was</p>
<p>$ ./configure --prefix=/hosts/nirvana/spare/home/shyamala/gromacs</p>
<p>## --------- ##</p>
<p>## Platform. ##</p>
<p>## --------- ##</p>
<p>hostname = <a href="http://nirvana.compbio.washington.edu">nirvana.compbio.washington.edu</a></p>
<p>uname -m = x86_64</p>
<p>uname -r = 2.6.9-42.0.10.ELsmp</p>
<p>uname -s = Linux</p>
<p>uname -v = #1 SMP Fri Feb 16 17:13:42 EST 2007</p>
<p>/usr/bin/uname -p = unknown</p>
<p>/bin/uname -X = unknown</p>
<p>/bin/arch = x86_64</p>
<p>/usr/bin/arch -k = unknown</p>
<p>/usr/convex/getsysinfo = unknown</p>
<p>hostinfo = unknown</p>
<p>/bin/machine = unknown</p>
<p>/usr/bin/oslevel = unknown</p>
<p>/bin/universe = unknown</p>
<p>PATH: /home/ram/usr/protinfo/bin/scripts</p>
<p>PATH: /home/ram/usr/protinfo/bin/linux_ix86_64</p>
<p>PATH: /home/ram/usr/packages/bin/scripts</p>
<p>PATH: /home/ram/usr/packages/bin/linux_ix86_64</p>
<p>PATH: /home/ram/usr/extras/bin/scripts</p>
<p>PATH: /home/ram/usr/extras/bin/linux_ix86_64</p>
<p>PATH: /home/ram/usr/ramp/bin/scripts</p>
<p>PATH: /home/ram/usr/ramp/bin/linux_ix86_64</p>
<p>PATH: /home/ram/usr/rambin/bin/scripts</p>
<p>PATH: /home/ram/usr/rambin/bin/linux_ix86_64</p>
<p>PATH: /home/ram/bin/scripts</p>
<p>PATH: .</p>
<p>PATH: /bin</p>
<p>PATH: /sbin</p>
<p>PATH: /etc</p>
<p>PATH: /usr/bin</p>
<p>PATH: /usr/ucb</p>
<p>PATH: /usr/sbin</p>
<p>PATH: /usr/bsd</p>
<p>PATH: /usr/local/bin</p>
<p>PATH: /usr/bin/X11</p>
<p>PATH: /usr/etc</p>
<p>PATH: /home/ram/bin/linux_ix86_64</p>
<p>PATH: /home/ram/usr/bin/scripts</p>
<p>PATH: /home/ram/usr/bin/linux_ix86_64</p>
<p>PATH: /hosts/nirvana/spare/home/shyamala/bin</p>
<p>PATH: /hosts/nirvana/spare/home/shyamala/bin/NAMD_2.6_Linux-amd64</p>
<p>PATH: /hosts/nirvana/spare/home/shyamala/MGLTools-1.4.5/share/bin</p>
<p> </p>
<p>## ----------- ##</p>
<p>## Core tests. ##</p>
<p>## ----------- ##</p>
<p>configure:1580: checking build system type</p>
<p>configure:1598: result: x86_64-unknown-linux-gnu</p>
<p>configure:1606: checking host system type</p>
<p>configure:1620: result: x86_64-unknown-linux-gnu</p>
<p>configure:1643: checking for a BSD-compatible install</p>
<p>configure:1698: result: /usr/bin/install -c</p>
<p>configure:1709: checking whether build environment is sane</p>
<p>configure:1752: result: yes</p>
<p>configure:1817: checking for gawk</p>
<p>configure:1833: found /bin/gawk</p>
<p>configure:1843: result: gawk</p>
<p>configure:1853: checking whether make sets $(MAKE)</p>
<p>configure:1873: result: yes</p>
<p>configure:2036: checking how to create a ustar tar archive</p>
<p>configure:2049: tar --version</p>
<p>tar (GNU tar) 1.14</p>
<p>Copyright (C) 2004 Free Software Foundation, Inc.</p>
<p>This program comes with NO WARRANTY, to the extent permitted by law.</p>
<p>You may redistribute it under the terms of the GNU General Public License;</p>
<p>see the file named COPYING for details.</p>
<p>Written by John Gilmore and Jay Fenlason.</p>
<p>configure:2052: $? = 0</p>
<p>configure:2092: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar</p>
<p>configure:2095: $? = 0</p>
<p>configure:2099: tar -xf - <conftest.tar</p>
<p>configure:2102: $? = 0</p>
<p>configure:2115: result: gnutar</p>
<p>configure:2710: checking for C compiler version</p>
<p>configure:2713: gcc --version </dev/null >&5</p>
<p>gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3)</p>
<p>Copyright (C) 2006 Free Software Foundation, Inc.</p>
<p>This is free software; see the source for copying conditions. There is NO</p>
<p>warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.</p>
<p>configure:2716: $? = 0</p>
<p>configure:2718: gcc -v </dev/null >&5</p>
<p>Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs</p>
<p>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
</p>
<p>Thread model: posix</p>
<p>gcc version 3.4.6 20060404 (Red Hat 3.4.6-3)</p>
<p>configure:2721: $? = 0</p>
<p>configure:2723: gcc -V </dev/null >&5</p>
<p>gcc: `-V' option must have argument</p>
<p>configure:2726: $? = 1</p>
<p>configure:2749: checking for C compiler default output file name</p>
<p>configure:2752: gcc -O3 -Wall -pedantic -static $(HDRS) $(DEFINES) conftest.c -lm >&5</p>
<p>gcc: $(HDRS): No such file or directory</p>
<p>gcc: $(DEFINES): No such file or directory</p>
<p>configure:2755: $? = 1</p>
<p>configure: failed program was:</p>
<p>| /* confdefs.h. */</p>
<p>| </p>
<p>| #define PACKAGE_NAME "GROMACS"</p>
<p>| #define PACKAGE_TARNAME "gromacs"</p>
<p>| #define PACKAGE_VERSION "3.3.1"</p>
<p>| #define PACKAGE_STRING "GROMACS 3.3.1"</p>
<p>| #define PACKAGE_BUGREPORT "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"</p>
<p>| #define PACKAGE "gromacs"</p>
<p>| #define VERSION "3.3.1"</p>
<p>| #define GMX_SOFTWARE_SQRT</p>
<p>| #define GMX_QMMM_GAUSSIAN</p>
<p>| #define BUILD_TIME "Sat Sep 8 10:43:40 PDT 2007"</p>
<p>| #define BUILD_USER "<a href="mailto:shyamala@nirvana.compbio.washington.edu">shyamala@nirvana.compbio.washington.edu</a>"</p>
<p>| #define BUILD_MACHINE "Linux 2.6.9-42.0.10.ELsmp x86_64"</p>
<p>| /* end confdefs.h. */</p>
<p>| </p>
<p>| int</p>
<p>| main ()</p>
<p>| {</p>
<p>| </p>
<p>| ;</p>
<p>| return 0;</p>
<p>| }</p>
<p>configure:2794: error: C compiler cannot create executables</p>
<p>See `config.log' for more details.</p>
<p>## ---------------- ##</p>
<p>## Cache variables. ##</p>
<p>## ---------------- ##</p>
<p>ac_cv_build=x86_64-unknown-linux-gnu</p>
<p>ac_cv_build_alias=x86_64-unknown-linux-gnu</p>
<p>ac_cv_env_CC_set=set</p>
<p>ac_cv_env_CC_value=gcc</p>
<p>ac_cv_env_CFLAGS_set=set</p>
<p>ac_cv_env_CFLAGS_value='-O3 -Wall -pedantic -static $(HDRS) $(DEFINES)'</p>
<p>ac_cv_env_CPPFLAGS_set=</p>
<p>ac_cv_env_CPPFLAGS_value=</p>
<p>ac_cv_env_CPP_set=</p>
<p>ac_cv_env_CPP_value=</p>
<p>ac_cv_env_CXXCPP_set=</p>
<p>ac_cv_env_CXXCPP_value=</p>
<p>ac_cv_env_CXXFLAGS_set=</p>
<p>ac_cv_env_CXXFLAGS_value=</p>
<p>ac_cv_env_CXX_set=</p>
<p>ac_cv_env_CXX_value=</p>
<p>ac_cv_env_F77_set=</p>
<p>ac_cv_env_F77_value=</p>
<p>ac_cv_env_FFLAGS_set=set</p>
<p>ac_cv_env_FFLAGS_value='-x f77-cpp-input -O3 -Wall -static $(HDRS) $(DEFINES)'</p>
<p>ac_cv_env_LDFLAGS_set=</p>
<p>ac_cv_env_LDFLAGS_value=</p>
<p>ac_cv_env_build_alias_set=</p>
<p>ac_cv_env_build_alias_value=</p>
<p>ac_cv_env_host_alias_set=</p>
<p>ac_cv_env_host_alias_value=</p>
<p>ac_cv_env_target_alias_set=</p>
<p>ac_cv_env_target_alias_value=</p>
<p>ac_cv_host=x86_64-unknown-linux-gnu</p>
<p>ac_cv_host_alias=x86_64-unknown-linux-gnu</p>
<p>ac_cv_path_install='/usr/bin/install -c'</p>
<p>ac_cv_prog_AWK=gawk</p>
<p>ac_cv_prog_make_make_set=yes</p>
<p>am_cv_prog_tar_ustar=gnutar</p>
<p>## ----------------- ##</p>
<p>## Output variables. ##</p>
<p>## ----------------- ##</p>
<p>ACLOCAL='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run aclocal-1.9'</p>
<p>AMDEPBACKSLASH=''</p>
<p>AMDEP_FALSE=''</p>
<p>AMDEP_TRUE=''</p>
<p>AMTAR='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run tar'</p>
<p>AR=''</p>
<p>AS=''</p>
<p>ASFLAGS=''</p>
<p>AUTOCONF='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run autoconf'</p>
<p>AUTOHEADER='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run autoheader'</p>
<p>AUTOMAKE='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run automake-1.9'</p>
<p>AWK='gawk'</p>
<p>CC='gcc'</p>
<p>CCAS=''</p>
<p>CCASFLAGS=''</p>
<p>CCDEPMODE=''</p>
<p>CC_FOR_BUILD=''</p>
<p>CFLAGS='-O3 -Wall -pedantic -static $(HDRS) $(DEFINES)'</p>
<p>CPP=''</p>
<p>CPPFLAGS=''</p>
<p>CXX=''</p>
<p>CXXCPP=''</p>
<p>CXXDEPMODE=''</p>
<p>CXXFLAGS=''</p>
<p>CYGPATH_W='echo'</p>
<p>DEFS=''</p>
<p>DEPDIR=''</p>
<p>DLLTOOL=''</p>
<p>ECHO='echo'</p>
<p>ECHO_C=''</p>
<p>ECHO_N='-n'</p>
<p>ECHO_T=''</p>
<p>EGREP=''</p>
<p>EXEEXT=''</p>
<p>F77=''</p>
<p>F77LINK='$(LINK)'</p>
<p>FFLAGS='-x f77-cpp-input -O3 -Wall -static $(HDRS) $(DEFINES)'</p>
<p>FLIBS=''</p>
<p>GMXANA_LIBOBJS=''</p>
<p>GMXLIB_LIBOBJS=''</p>
<p>GMX_DOUBLE_FALSE=''</p>
<p>GMX_DOUBLE_TRUE='#'</p>
<p>GMX_EXTERNAL_BLAS_FALSE=''</p>
<p>GMX_EXTERNAL_BLAS_TRUE='#'</p>
<p>GMX_EXTERNAL_LAPACK_FALSE=''</p>
<p>GMX_EXTERNAL_LAPACK_TRUE='#'</p>
<p>GMX_FORTRAN_FALSE=''</p>
<p>GMX_FORTRAN_TRUE='#'</p>
<p>GMX_IA32_3DNOW_FALSE=''</p>
<p>GMX_IA32_3DNOW_TRUE=''</p>
<p>GMX_IA32_SSE2_FALSE=''</p>
<p>GMX_IA32_SSE2_TRUE=''</p>
<p>GMX_IA32_SSE_FALSE=''</p>
<p>GMX_IA32_SSE_TRUE=''</p>
<p>GMX_IA64_ASM_DOUBLE_FALSE=''</p>
<p>GMX_IA64_ASM_DOUBLE_TRUE=''</p>
<p>GMX_IA64_ASM_SINGLE_FALSE=''</p>
<p>GMX_IA64_ASM_SINGLE_TRUE=''</p>
<p>GMX_PPC_ALTIVEC_FALSE=''</p>
<p>GMX_PPC_ALTIVEC_TRUE=''</p>
<p>GMX_PREFETCH_FORCES_FALSE=''</p>
<p>GMX_PREFETCH_FORCES_TRUE='#'</p>
<p>GMX_SOFTWARE_SQRT_FALSE='#'</p>
<p>GMX_SOFTWARE_SQRT_TRUE=''</p>
<p>GMX_THREAD_FALSE=''</p>
<p>GMX_THREAD_TRUE='#'</p>
<p>GMX_X86_64_SSE2_FALSE=''</p>
<p>GMX_X86_64_SSE2_TRUE=''</p>
<p>GMX_X86_64_SSE_FALSE=''</p>
<p>GMX_X86_64_SSE_TRUE=''</p>
<p>INCLUDES=''</p>
<p>INSTALL_DATA='${INSTALL} -m 644'</p>
<p>INSTALL_PROGRAM='${INSTALL}'</p>
<p>INSTALL_SCRIPT='${INSTALL}'</p>
<p>INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'</p>
<p>LDFLAGS=''</p>
<p>LIBOBJS=''</p>
<p>LIBS='-lm'</p>
<p>LIBSUFFIX=''</p>
<p>LIBTOOL=''</p>
<p>LN_S=''</p>
<p>LTLIBOBJS=''</p>
<p>MAKEINFO='${SHELL} /hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/missing --run makeinfo'</p>
<p>MDLIB_LIBOBJS=' qm_gaussian.lo'</p>
<p>MPICC=''</p>
<p>OBJDUMP=''</p>
<p>OBJEXT=''</p>
<p>PACKAGE='gromacs'</p>
<p>PACKAGE_BUGREPORT='<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>'</p>
<p>PACKAGE_NAME='GROMACS'</p>
<p>PACKAGE_STRING='GROMACS 3.3.1'</p>
<p>PACKAGE_TARNAME='gromacs'</p>
<p>PACKAGE_VERSION='3.3.1'</p>
<p>PATH_SEPARATOR=':'</p>
<p>RANLIB=''</p>
<p>RPM=''</p>
<p>SET_MAKE=''</p>
<p>SHARED_VERSION_INFO='4:0:0'</p>
<p>SHELL='/bin/sh'</p>
<p>STRIP=''</p>
<p>USE_X11_FALSE=''</p>
<p>USE_X11_TRUE=''</p>
<p>VERSION='3.3.1'</p>
<p>X_CFLAGS=''</p>
<p>X_EXTRA_LIBS=''</p>
<p>X_LIBS=''</p>
<p>X_PRE_LIBS=''</p>
<p>ac_ct_AR=''</p>
<p>ac_ct_AS=''</p>
<p>ac_ct_CC=''</p>
<p>ac_ct_CXX=''</p>
<p>ac_ct_DLLTOOL=''</p>
<p>ac_ct_F77=''</p>
<p>ac_ct_OBJDUMP=''</p>
<p>ac_ct_RANLIB=''</p>
<p>ac_ct_STRIP=''</p>
<p>am__fastdepCC_FALSE=''</p>
<p>am__fastdepCC_TRUE=''</p>
<p>am__fastdepCXX_FALSE=''</p>
<p>am__fastdepCXX_TRUE=''</p>
<p>am__include=''</p>
<p>am__leading_dot='.'</p>
<p>am__quote=''</p>
<p>am__tar='tar --format=ustar -chf - "$$tardir"'</p>
<p>am__untar='tar -xf -'</p>
<p>bindir='${exec_prefix}/bin'</p>
<p>build='x86_64-unknown-linux-gnu'</p>
<p>build_alias=''</p>
<p>build_cpu='x86_64'</p>
<p>build_os='linux-gnu'</p>
<p>build_vendor='unknown'</p>
<p>datadir='${prefix}/share'</p>
<p>exec_prefix='NONE'</p>
<p>host='x86_64-unknown-linux-gnu'</p>
<p>host_alias=''</p>
<p>host_cpu='x86_64'</p>
<p>host_os='linux-gnu'</p>
<p>host_vendor='unknown'</p>
<p>includedir='${prefix}/include'</p>
<p>infodir='${prefix}/info'</p>
<p>install_sh='/hosts/nirvana/spare/home/shyamala/gromacs-3.3.1/config/install-sh'</p>
<p>libdir='${exec_prefix}/lib'</p>
<p>libexecdir='${exec_prefix}/libexec'</p>
<p>localstatedir='${prefix}/var'</p>
<p>mandir='${prefix}/man'</p>
<p>mkdir_p='mkdir -p --'</p>
<p>oldincludedir='/usr/include'</p>
<p>prefix='/hosts/nirvana/spare/home/shyamala/gromacs'</p>
<p>program_transform_name='s,x,x,'</p>
<p>sbindir='${exec_prefix}/sbin'</p>
<p>sharedstatedir='${prefix}/com'</p>
<p>sysconfdir='${prefix}/etc'</p>
<p>target_alias=''</p>
<p>## ----------- ##</p>
<p>## confdefs.h. ##</p>
<p>## ----------- ##</p>
<p>#define BUILD_MACHINE "Linux 2.6.9-42.0.10.ELsmp x86_64"</p>
<p>#define BUILD_TIME "Sat Sep 8 10:43:40 PDT 2007"</p>
<p>#define BUILD_USER "<a href="mailto:shyamala@nirvana.compbio.washington.edu">shyamala@nirvana.compbio.washington.edu</a>"</p>
<p>#define GMX_QMMM_GAUSSIAN</p>
<p>#define GMX_SOFTWARE_SQRT</p>
<p>#define PACKAGE "gromacs"</p>
<p>#define PACKAGE_BUGREPORT "<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>"</p>
<p>#define PACKAGE_NAME "GROMACS"</p>
<p>#define PACKAGE_STRING "GROMACS 3.3.1"</p>
<p>#define PACKAGE_TARNAME "gromacs"</p>
<p>#define PACKAGE_VERSION "3.3.1"</p>
<p>#define VERSION "3.3.1"</p>
<p>configure: exit 77</p></font></div>