[gmx-users] compile Gromacs 3.2.1: line 0: unexpected EOF while looking for matching `"'

Mike Hanby mhanby at uab.edu
Wed Jan 24 19:17:21 CET 2007 

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

 

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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