[gmx-users] Compilation problem on SGI ORIGIN 3800

[Patrick Fuchs]

David van der Spoel a écrit :

> 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.

Thank you David,
I made a distclean and then used the following :
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"
setenv MPICC cc
./configure --enable-mpi --prefix=/home/fuchs/software/gromacs 
--program-suffix=_mpi --disable-float --disable-nice
make mdrun
And it worked ! The thing missing was the line 'setenv MPICC cc', and 
that makes all the difference. The option --disable-fortran has no 
effect wether it's used or not, as long as 'setenv MPICC cc' has been set.
Ciao,

Patrick

-- 
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : Patrick.Fuchs at ebgm.jussieu.fr
Web Site: http://www.ebgm.jussieu.fr/~fuchs