[gmx-developers] Strange error message while making gromacs 4.0

Jim Kress ccl_nospam at kressworks.com
Mon Oct 27 00:12:40 CET 2008


Today I tried to build gromacs 4.0  Here is a summary of the commands and

[root at master gromacs-4.0]# ./configure --disable-shared --enable-x86-64-sse
--enable-ia64-asm --enable-cpu-optimization --disable-software-sqrt
--enable-all-static --enable-largefile

---lots of output---

[root at master gromacs-4.0]# make

---lots of output, then at the apparent end, I get the following:

mkdir .libs
ar cru .libs/libgmxpreprocess.a  add_par.o compute_io.o convparm.o gen_ad.o
gen_vsite.o genhydro.o gmxcpp.o gpp_atomtype.o gpp_bond_atomtype.o h_db.o
hackblock.o hizzie.o pdb2top.o pgutil.o readir.o readpull.o resall.o
sorting.o specbond.o ter_db.o tomorse.o topdirs.o topexcl.o topio.o
toppush.o topshake.o toputil.o tpbcmp.o vsite_parm.o xlate.o ranlib
.libs/libgmxpreprocess.a creating libgmxpreprocess.la (cd .libs && rm -f
libgmxpreprocess.la && ln -s ../libgmxpreprocess.la
cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP
-MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo
/bin/sh ../../libtool --tag=CC   --mode=link cc  -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops  -all-static -o
grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la
-lxml2  -L/usr/lib64 -lnsl -lfftw3f -lm   -lSM -lICE -lX11  
cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -static -o grompp grompp.o  ./.libs/libgmxpreprocess.a
-L/usr/lib64 ../mdlib/.libs/libmd.a ../gmxlib/.libs/libgmx.a -lxml2 -lnsl
-lfftw3f -lm -lSM -lICE -lX11
/usr/bin/ld: cannot find -lSM
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1
make[3]: Leaving directory `/root/gromacs-4.0/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/root/gromacs-4.0/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/gromacs-4.0/src'
make: *** [all-recursive] Error 1

Any suggestions about what I'm doing wrong and how to fix it?


Jim Kress

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