[gmx-users] unable to compile from source

Peter C. Lai sirmoo at cowbert.2y.net
Wed Jul 3 17:26:01 CEST 2002

On Tue, Jul 02, 2002 at 11:03:41AM -0700, Erik Lindahl wrote:
> Peter C. Lai wrote:
> >I am having difficulty compiling gromacs 3.1.4 from source on an
> >SGI Octane using SGI's cc and f77. The linker errors out because
> >it is finding stuff that is prempting other functions in libc.
> >After the linker errors out, then the rest of make fails.
> >Are there any caveats to compiling on the SGI?
> >
> Hi Peter,
> Unless you post the exact error messages it's hard to suggest anything.
> Gromacs compiles just fine on a properly setup SGI system, but a lot of 
> SGI boxes
> are not properly configured for their new/old binary formats.

This is an IRIX 6.5.15m  system.

cc tries to link a bunch of .o's using the following line:

cc -r10000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -I
NLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -wof
f 1174 -D__INLINE_INTRINSICS -r10000 -mips4 -woff 84 -o pdb2gmx hizzie.o xlate.o
 specbond.o ter_db.o h_db.o genhydro.o pdb2top.o gen_ad.o gen_dum.o pgutil.o res
all.o hackblock.o add_par.o topexcl.o toputil.o topdirs.o pdb2gmx.o  -L/usr/loca
l/lib ../mdlib/.libs/libmd.a -L/usr/lib32/mips4/r10000 -L/usr/lib32/mips4 -L/usr
/lib32 ../gmxlib/.libs/libgmx.a -lnsl /usr/local/lib/librfftw.a /usr/local/lib/l
ibfftw.a -lXm -lXt -lSM -lICE -lXext -lX11 -lftn -lm

ld32 starts to complain now:

ld32: WARNING 85: definition of main in pdb2gmx.o preempts that definition
in /usr/lib32/mips4/libftn.so.
ld32: WARNING 85: definition of _ffs in /usr/lib32/libnsl.so preempts that
definition in /usr/lib32/mips4/libc.so.
ld32: WARNING 134: weak definition of ffs in /usr/lib32/libnsl.so preempts that
weak definition in /usr/lib32/mips4/libc.so.
ld32: WARNING 85: definition of _dial in /usr/lib32/libnsl.so preempts that
definition in /usr/lib32/mips4/libc.so.
ld32: WARNING 134: weak definition of dial in /usr/lib32/libnsl.so preempts that
weak definition in /usr/lib32/mips4/libc.so.
this continues on for a while with various inline functions in libnsl and libc
until ld32 quits after 50 warnings which reference only lines 85 and 134.
After ld32 quits, the rest of make dies because it is trying to reference
symbols from the libs that it was trying to link previously.

> >
> >
> >I tried installing the gromacs binaries from gromacs.org, but
> >it complains about finding the libraries (even though they
> >exist in the search path)
> >
> Don't know anything about that; those binaries are contributed by users, 
> but you might
> have to set LD_LIBRARY_PATH.
> Cheers,
> Erik
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Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology | Undergraduate Research Assistant

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