[SciPy-user] scipy fblas.so functions not found

Charlie Yanaitis charles.yanaitis@rochester....
Thu Jun 14 11:39:53 CDT 2007


Lev,

Lev Givon <lev <at> columbia.edu> writes:

> 
> Received from Lev Givon on Thu, Jun 14, 2007 at 09:41:22AM EDT:
> > Received from Charlie Yanaitis on Thu, Jun 14, 2007 at 08:12:26AM EDT:
> > > I'm hoping somebody could offer some advice. I've been stymied for a
> > > while trying to build/install a good working version of scipy-0.5.2
> > > on a Saturn Cluster that's running Red Hat RHEL4-U4. I'm using gcc
> > > version 3.4.6 and python-2.5. I've tried to build the Atlas
> > > variation, but was unsuccessful, so I back-tracked and reverted to
> > > building and installing numpy and then scipy. Going this route,
> > > scipy at least built and installed OK, but now, the fblas.so library
> > > is missing functions and a user reported to me that they got the
> > > following error:
> > > 
> > > ImportError: /usr/local/lib/python2.5/site-packages/scipy/linalg/fblas.so:
> > > undefined symbol: srotmg_
> > > 
> > > If anybody can offer some advice on a fix or work around for this, I'd
> > > appreciate it!
> > > 
> > > Thanks in advance!
> > > 
> > > Charlie Yanaitis
> > 
> > The lapack libraries you are using probably were not compiled against
> > the full blas source (the lapack source package from netlib includes
> > an incomplete subset of the blas source files). You might want to try
> > rebuilding the lapack rpm from Fedora 6 or 7 on your system; it
> > appears to include a patch providing the missing blas routines.
> > 
> > 							L.G.
> 
> I neglected to mention that Fedora also includes an atlas rpm that you
> might want to try rebuilding on RHEL instead of the lapack package.
> 
> 							L.G.
> 
 
Thanks for the advice. I went ahead and got the atlas libraries for
Linux_HAMMER64SSE2, put the libraries in place and got the following
error when building scipy-0.5.2: 

/usr/bin/ld: /usr/local/lib/libf77blas.a(dscal.o): relocation R_X86_64_PC32
against `atl_f77wrap_dscal__' can not be used when making a shared object;
recompile with -fPIC

The above error is what has stymied me with the Atlas version all along. I even
got the source code for Atlas and tried to build it myself with gcc, with -fPIC.
Here's the lines in the Makefile:

SHELL = /bin/sh
CC = gcc
NM = -o
OJ = -c
F77 = /usr/bin/g77
F77FLAGS = -fomit-frame-pointer -O -m64 -fPIC
FLINKER = $(F77)
FLINKFLAGS = $(F77FLAGS)
FCLINKFLAGS = $(FLINKFLAGS)

It builds fine, but when I try to build scipy-0.5.2, I get the above error to
"recompile with -fPIC", when I *did* build Atlas with -fPIC. It's been pretty
frustrating.

Thanks!

Charlie





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