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 : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
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