[gmx-users] Compilation problem on SGI ORIGIN 3800

[David van der Spoel]

Patrick Fuchs wrote:
> Hi gmx users,
> I'm trying to compile gromacs in // on an SGI ORIGIN 3800. For the 
> monoCPU version it went well (thanks to very good advices on previous 
> E-mails of the gmx list), but for the parallel version, I encountered a 
> problem. Here are the steps I followed :
> setenv CPPFLAGS "-I/opt/mpt/1.4.0.3/usr/include -I/usr/local/include"
> setenv LDFLAGS "-L/opt/mpt/1.4.0.3/usr/lib 
> -L/usr/local/lib/fftw2.1.5/lib32"
> setenv LIBS "-lmpi"
> ./configure --enable-mpi --prefix=/home/fuchs/software/gromacs 
> --program-suffix=_mpi --disable-float --disable-fortran --disable-nice
> -> This step went OK
> 
> make mdrun
> -> at the beginning it went OK
> ...
> (cd ./src/kernel && make mdrun ; exit 0)
>        /bin/sh ../../libtool --mode=link mpicc  -O3 
> -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON 
> -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 
> 1174 -D__INLINE_INTRINSICS -I/usr/freeware/include/libxml2   
> -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32  -woff 84 -o 
> mdrun  glaasje.o gctio.o init_sh.o  ionize.o do_gct.o relax_sh.o  
> xutils.o md.o mdrun.o genalg.o ../mdlib/libmd_mpi_d.la 
> ../gmxlib/libgmx_mpi_d.la  -lnsl -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw 
> -lm -lmpi -lXm -lXt  -lSM -lICE -lXext -lX11  -L/usr/freeware/lib32 
> -lxml2 -lz -lm
> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved.
This might be a problem.

> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved.
> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: 
> warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved.
> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.la' was moved.
> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.la' was moved.
> libtool: link: warning: library 
> `/usr/local/lib/fftw2.1.5/lib32/librfftw.la' was moved.libtool: link: 
> warning: library `/usr/local/lib/fftw2.1.5/lib32/libfftw.la' was moved.
> mpicc -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead 
> -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 
> -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS 
> -I/usr/freeware/include/libxml2 -woff 84 -o mdrun glaasje.o gctio.o 
> init_sh.o ionize.o do_gct.o relax_sh.o xutils.o md.o mdrun.o genalg.o  
> -L/opt/mpt/1.4.0.3/usr/lib -L/usr/local/lib/fftw2.1.5/lib32 
> ../mdlib/.libs/libmd_mpi_d.a -L/usr/freeware/lib32 
> ../gmxlib/.libs/libgmx_mpi_d.a -lnsl 
> /usr/local/lib/fftw2.1.5/lib32/librfftw_mpi.a 
> /usr/local/lib/fftw2.1.5/lib32/libfftw_mpi.a 
> /usr/local/lib/fftw2.1.5/lib32/librfftw.a 
> /usr/local/lib/fftw2.1.5/lib32/libfftw.a -lmpi -lXm -lXt -lSM -lICE 
> -lXext -lX11 -lxml2 -lz -lm
> cc: Warning: -OPT options are ignored
> cc: Warning: -OPT options are ignored
> cc: Warning: -SWP options are ignored
> cc: Warning: -OPT options are ignored
> uld:
> Object file format error in: glaasje.o: bad symbolic header (magic number)
Something wrong with this file, delete it.

> *** Error code 1 (bu21)
> *** Error code 1 (bu21)
> 
> I didn't find any similar case in the mailing list, and I'm wondering 
> where could it come from.
> Does someone have an idea on how to fix that ?
> Thanks !
> 
> Patrick
> 
Could it be that you have restarted the compilation with differen flags? 
In that case you will have to do
make distclean

On SGI machines it has always been a problem to install the compilers, 
this problem is however hard to distinguish from others.
You might want to start from scratch if make distclean doesn't do it.
-- 
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://xray.bmc.uu.se/~spoel
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