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

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Mon Oct 27 00:16:31 CET 2008

On Sun, 26 Oct 2008, Jim Kress wrote:

JK> Gentlemen,


JK> Today I tried to build gromacs 4.0  Here is a summary of the commands and
JK> results:
JK> [root at master gromacs-4.0]# ./configure --disable-shared --enable-x86-64-sse

this is not on topic, but compiling software as superuser is generally 
a _very_ bad idea. just consider what would happen if some script in
the build process does some "rm -rf /$this_has_a_blank/some_path/" ...

JK> --enable-ia64-asm --enable-cpu-optimization --disable-software-sqrt

either you have an ia64 or an x86_64 machine. you cannot have both at
the same time.

JK> --enable-all-static --enable-largefile

an all-static link is a bad idea on current linux machines (assuming
you are running linux...).

JK> ---lots of output---
JK> [root at master gromacs-4.0]# make
JK> ---lots of output, then at the apparent end, I get the following:
JK> mkdir .libs
JK> ar cru .libs/libgmxpreprocess.a  add_par.o compute_io.o convparm.o gen_ad.o
JK> gen_vsite.o genhydro.o gmxcpp.o gpp_atomtype.o gpp_bond_atomtype.o h_db.o
JK> hackblock.o hizzie.o pdb2top.o pgutil.o readir.o readpull.o resall.o
JK> sorting.o specbond.o ter_db.o tomorse.o topdirs.o topexcl.o topio.o
JK> toppush.o topshake.o toputil.o tpbcmp.o vsite_parm.o xlate.o ranlib
JK> .libs/libgmxpreprocess.a creating libgmxpreprocess.la (cd .libs && rm -f
JK> libgmxpreprocess.la && ln -s ../libgmxpreprocess.la
JK> libgmxpreprocess.la)
JK> cc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include
JK> -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer
JK> -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP
JK> -MF .deps/grompp.Tpo -c -o grompp.o grompp.c mv -f .deps/grompp.Tpo
JK> .deps/grompp.Po
JK> /bin/sh ../../libtool --tag=CC   --mode=link cc  -O3 -fomit-frame-pointer
JK> -finline-functions -Wall -Wno-unused -funroll-all-loops  -all-static -o
JK> grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la
JK> -lxml2  -L/usr/lib64 -lnsl -lfftw3f -lm   -lSM -lICE -lX11  
JK> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
JK> -funroll-all-loops -static -o grompp grompp.o  ./.libs/libgmxpreprocess.a
JK> -L/usr/lib64 ../mdlib/.libs/libmd.a ../gmxlib/.libs/libgmx.a -lxml2 -lnsl
JK> -lfftw3f -lm -lSM -lICE -lX11
JK> /usr/bin/ld: cannot find -lSM

you don't have the proper x11 libs installed.
try running configure with --without-x added.


JK> collect2: ld returned 1 exit status
JK> make[3]: *** [grompp] Error 1
JK> make[3]: Leaving directory `/root/gromacs-4.0/src/kernel'
JK> make[2]: *** [all-recursive] Error 1
JK> make[2]: Leaving directory `/root/gromacs-4.0/src'
JK> make[1]: *** [all] Error 2
JK> make[1]: Leaving directory `/root/gromacs-4.0/src'
JK> make: *** [all-recursive] Error 1
JK> Any suggestions about what I'm doing wrong and how to fix it?
JK> Regards,
JK> Jim Kress
JK> _______________________________________________
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Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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