[gmx-users] compile Gromacs 3.2.1: line 0: unexpected EOF while looking for matching `"'
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 25 09:04:54 CET 2007
Mike Hanby wrote:
> I'm trying to compile Gromacs 3.2.1 (a user requested this version
> specifically). The configure succeeds, however make fails with:
>
> /bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
>
> /bin/sh: -c: line 1: syntax error: unexpected end of file
>
>
>
try without fortran, it won't do you any good anyway on Intel machines.
> The system is a 64bit RHEL 4 workstation, I'm using Intel Compilers: v
> 9.1.042
>
>
>
> Any idea what the heck it's complaining about? Here's my configure
> statement:
>
> ./configure CC=icc CXX=icpc FC=ifort F77=ifort F90=ifort --enable-sse
> --enable-fortran --prefix=/share/apps/gromacs/intel/gromacs-3.2.1-s64
>
>
>
>
>
> Here's the last several lines of the make output:
>
> ============================================================================================================
>
> if /bin/sh ../../libtool --mode=compile icc -DHAVE_CONFIG_H -I. -I.
>
> -I../../src -I/usr/X11R6/include -I../../include
> -DGMXLIBDIR=\"/share/apps/gromac s/intel/gromacs-3.2.1-s64/share/top\"
>
> -I/share/apps/intel/cce/9.1.042/include
>
> -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include -I/
>
> usr/include/libxml2 -O3 -I/usr/include/libxml2 -MT widget.lo -MD -MP
> -MF ".deps/widget.Tpo" \
>
> -c -o widget.lo `test -f 'widget.c' || echo './'`widget.c; \ then mv
> -f ".deps/widget.Tpo" ".deps/widget.Plo"; \ else rm -f
> ".deps/widget.Tpo"; exit 1; \ fi icc -DHAVE_CONFIG_H -I. -I. -I../../src
> -I/usr/X11R6/include -I../../include
> -DGMXLIBDIR=\"/share/apps/gromacs/intel/gromacs-3.2.1-s64/share/top\"
>
> -I/ share/apps/intel/cce/9.1.042/include
>
> -I/share/apps/fftw/intel/fftw-2.1.5-s64/include -I/usr/local/include
>
> -I/usr/include/libxml2 -O3 -I/usr/include/li bxml2 -MT widget.lo
>
> -MD -MP -MF .deps/widget.Tpo -c widget.c -o widget.o /bin/sh
> ../../libtool --mode=link icc -O3 -I/usr/include/libxml2
> -L/share/apps/intel/cce/9.1.042/lib
>
> -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o
>
> libgmx.la -rpath
>
> /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib
>
> -version-info 3:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo
>
> calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo
>
> ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo
>
> fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo
> macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo
>
> mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo
>
> pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo
>
> readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo
>
> smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo
>
> trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo
>
> wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo
> vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo
>
> -L/usr/ X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE
>
> -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm
> -L/share/apps/intel/cce/9.1.042/lib -L/share/ap
> ps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib" -L/usr/X11R6/lib
> -L/share/apps/intel/fce/9.1.036/lib
>
> -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/u
>
> sr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport
> -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl
>
> /bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
>
> /bin/sh: -c: line 1: syntax error: unexpected end of file
>
> make[3]: *** [libgmx.la] Error 2
>
> make[3]: Leaving directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib'
>
> make[2]: *** [all-recursive] Error 1
>
> make[2]: Leaving directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src'
>
> make[1]: *** [all] Error 2
>
> make[1]: Leaving directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src'
>
> make: *** [all-recursive] Error 1
>
> Making install in src
>
> make[1]: Entering directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src'
>
> Making install in gmxlib
>
> make[2]: Entering directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib'
>
> /bin/sh ../../libtool --mode=link icc -O3 -I/usr/include/libxml2
> -L/share/apps/intel/cce/9.1.042/lib
>
> -L/share/apps/fftw/intel/fftw-2.1.5-s64/lib -L/ usr/X11R6/lib -o
>
> libgmx.la -rpath
>
> /share/apps/gromacs/intel/gromacs-3.2.1-s64/x86_64-unknown-linux-gnu/lib
>
> -version-info 3:0:0 3dview.lo atomprop.lo block_tx.lo bondfree.lo
>
> calcgrid.lo calch.lo confio.lo copyrite.lo disre.lo do_fit.lo enxio.lo
>
> ewald_util.lo fatal.lo ffscanf.lo filenm.lo futil.lo gb util.lo
>
> fnbf.lo gmxfio.lo ifunc.lo index.lo cinvsqrtdata.lo invblock.lo
> macros.lo orires.lo main.lo maths.lo matio.lo mshift.lo mvdata.lo
>
> mvxvf.lo nam es.lo network.lo nrama.lo nrjac.lo nrnb.lo pargs.lo
>
> pbc.lo pdbio.lo princ.lo rando.lo random.lo gmx_random.lo rbin.lo
>
> readinp.lo replace.lo rmpbc.lo s hift_util.lo sortwater.lo
>
> smalloc.lo stat.lo statutil.lo strdb.lo string2.lo symtab.lo tpxio.lo
>
> trnio.lo trxio.lo txtdump.lo typedefs.lo viewit.lo wgm s.lo
>
> wman.lo writeps.lo xdrd.lo xtcio.lo xvgr.lo detectcpu.lo libxdrf.lo
> vec.lo dihres.lo xmlio.lo innerf.lo f77_wrappers.lo mgmx.lo widget.lo
>
> -L/usr/ X11R6/lib64 -lnsl -lsrfftw -lsfftw -lXm -lXt -lSM -lICE
>
> -lXext -lXp -lX11 -lxml2 -lz -lpthread -lm
> -L/share/apps/intel/cce/9.1.042/lib -L/share/ap
> ps/fftw/intel/fftw-2.1.5-s64/lib -L/usr/X11R6/lib" -L/usr/X11R6/lib
> -L/share/apps/intel/fce/9.1.036/lib
>
> -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -L/u
>
> sr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64 -lsvml -lifport
> -lifcore -limf -lm -lipgo -lirc -lgcc_s -lirc_s -ldl
>
> /bin/sh: -c: line 0: unexpected EOF while looking for matching `"'
>
> /bin/sh: -c: line 1: syntax error: unexpected end of file
>
> make[2]: *** [libgmx.la] Error 2
>
> make[2]: Leaving directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src/gmxlib'
>
> make[1]: *** [install-recursive] Error 1
>
> make[1]: Leaving directory
>
> `/home/makeuser/tmp/gromacs/gromacs-3.2.1_s64/gromacs-3.2.1/src'
>
> make: *** [install-recursive] Error 1
>
>
> ------------------------------------------------------------------------
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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