[SciPy-user] Building Scipy on Dell 64bit Xeon

David Noriega neruocomp at yahoo.com
Tue Jul 12 16:51:08 CDT 2005


Well I did some more looking around and found that my
problem was that I didnt have the 64bit package for
libg2c.  Its a bit weird with this system since it
installs both i386 and x86_64 for some packages.  Well
that fixed this problem, I have a new one. It seems I
need to build the ATLAS libraries with -fPIC

/usr/bin/g77 -shared
build/temp.linux-x86_64-2.4/build/src/Lib/optimize/lbfgsb-0.9/_lbfgsbmodule.o
build/temp.linux-x86_64-2.4/build/src/fortranobject.o
build/temp.linux-x86_64-2.4/Lib/optimize/lbfgsb-0.9/routines.o
-L/usr/local/lib/atlas -Lbuild/temp.linux-x86_64-2.4
-llapack -lf77blas -lcblas -latlas -lg2c -o
build/lib.linux-x86_64-2.4/scipy/optimize/_lbfgsb.so
/usr/bin/ld:
/usr/local/lib/atlas/liblapack.a(dpotrf.o): relocation
R_X86_64_32 against `a local symbol' can not be used
when making a shared object; recompile with -fPIC
/usr/local/lib/atlas/liblapack.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld:
/usr/local/lib/atlas/liblapack.a(dpotrf.o): relocation
R_X86_64_32 against `a local symbol' can not be used
when making a shared object; recompile with -fPIC
/usr/local/lib/atlas/liblapack.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
error: Command "/usr/bin/g77 -shared
build/temp.linux-x86_64-2.4/build/src/Lib/optimize/lbfgsb-0.9/_lbfgsbmodule.o
build/temp.linux-x86_64-2.4/build/src/fortranobject.o
build/temp.linux-x86_64-2.4/Lib/optimize/lbfgsb-0.9/routines.o
-L/usr/local/lib/atlas -Lbuild/temp.linux-x86_64-2.4
-llapack -lf77blas -lcblas -latlas -lg2c -o
build/lib.linux-x86_64-2.4/scipy/optimize/_lbfgsb.so"
failed with exit status 1

I'll keep you posted on my progress.  I also wanted to
point out something in scipy_distutils.  The way
cpuinfo.py is currently setup, it will not find that
this system uses a Xeon processor.  also it will fail
to recongize it as having sse3.  Looking at
/proc/cpuinfo, Xeon is not in all caps and sse3, while
it should be there, only comes up as ss.  But that
might just be a kernel thing as I fixed it in
cpuinfo.py.

--- David Noriega <neruocomp at yahoo.com> wrote:

> Well thats easier said then done on a fedora/redhat
> system.  I know enought to get rpmbuild to rebuild
> gcc
> for me, but how would I get it to recompile gcc with
> -fPIC.  Any ideas as to which file I should edit and
> where to put "-fPIC"?
> 
> --- Nicolas Pernetty <nicopernetty at yahoo.fr> wrote:
> 
> > On Tue, 12 Jul 2005 08:07:10 -0700 (PDT), David
> > Noriega
> > <neruocomp at yahoo.com> wrote :
> > 
> > > Hello, I've been put in charge of setting up a
> > Dell
> > > 64bit Xeon workstation and on the side I've been
> > tring
> > > to get scipy to install, but I haven't had any
> > luck. 
> > > I compiled LAPACK, BLAS, and ATLAS sucsesfuly
> and
> > > scipy finds them.  Its when I try to build scipy
> > that
> > > I get problems.  I try just plain "./setup.py
> > build"
> > > and I get these errors:
> > 
> > Hello,
> > 
> > > /usr/bin/ld:
> > >
> >
>
/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/libg2c.a(s_stop.o):
> > > relocation R_X86_64_32 against `a local symbol'
> > can
> > > not be used when making a shared object;
> recompile
> > > with -fPIC
> > 
> > It seems that your gcc installation is somewhat
> > messed up (libg2c hasn't
> > been compiled with -fPIC)
> > IMHO, best you can do to see if it's the problem
> is
> > to compile your own
> > gcc (try 3.4.3 instead of 4.0.0 which seems a
> little
> > buggy). Don't be
> > afraid : it's not that hard.
> > 
> > Regards,
> > 
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user at scipy.net
> > http://www.scipy.net/mailman/listinfo/scipy-user
> > 
> 
> 
> Don't fear that philosophy's an impious way
> --superstition's more likely to lead folk astray.
> 
> ~Lucretius, De rerum natura, Book One
> 
> http://mindbender.deviantart.com
> 
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Don't fear that philosophy's an impious way
--superstition's more likely to lead folk astray.

~Lucretius, De rerum natura, Book One

http://mindbender.deviantart.com


		
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