Re: [Pysparse-users] Trouble finding the correct ATLAS LAPACK libraries with pysparse 1.2a1

[Eddie S. <e-s...@no...>]

Hi guys, thanks for the response.  Our machine went down for maintenance
this morning, as soon as its back up I'll send the requested outputs.

I haven't tested the ATLAS or LAPACK libraries, but I have been able to
compile other software against them (specifically Trilinos 9.0.3 including
the PyTrilinos module).  Not sure if it matters, but there are other
versions of ATLAS (3.9.16 and 3.9.24) at /software/ATLAS/#.#.##  where #'s
are the version numbers.  These newer versions don't have full LAPACK
support or shared versions of the libraries.

To answer your question Daniel, there was no previous install of PySparse
for the Python in my home directory, but I believe on the first attempt at
installing I used the default setup.py, perhaps this left something around
that's interfering with more recent attempts to install?  I did run

python setup.py clean

before modifying setup.py and rerunning the build/install steps.  Is there a
better way of removing/cleaning up before I try installing again?

Thanks again, and more info to follow when I can get access to the machine.

Eddie


On Tue, May 11, 2010 at 9:01 AM, Daniel Wheeler
<dan...@gm...>wrote:
Was there a previous pysparse installation?


On Tue, May 11, 2010 at 2:01 AM, Dominique Orban
<dom...@gm...>wrote:

> On Mon, May 10, 2010 at 5:59 PM, Eddie Schwalbach
> <e-s...@no...> wrote:
> > I'm trying to install pysparse on a Linux cluster with ATLAS 3.8.3 (which
> > was built with full LAPACK support).  ATLAS is located at
> > /software/ATLAS/3.8.3
> > and I'm using Python2.6.4 which is located in the nonstandard location
> > /home/ejs698/software (which is at the beginning of my PATH and
> PYTHONPATH).
> >
> > I've modified the setup.py file to include the appropriate (I think)
> library
> > directories:
> >
> > library_dirs_list=
> >
> ['/software/ATLAS/3.8.3/lib/','/home/ejs698/software/lib/','/usr/bin/lib/']
> > libraries_list = ['f77blas', 'cblas', 'atlas', 'lapack', 'gfortran']
> >
> > I also have the environment variables:
> > LD_LIBRARY_PATH
> >
> /opt/moab/lib:/opt/torque/lib::/software/ATLAS/3.8.3/lib:/home/ejs698/software/lib
> > ATLAS  /software/ATLAS/3.8.3  (this was necessary for getting numpy built
> > against the correct ATLAS libraries)
> >
> > I don't see errors when I run python setup.py install, or when I try
> >      from pysparse import *
> > However, if I attempt to run any of the tests in the Examples directory,
> I
> > get:
> >
> > [ejs698@quser04 Examples]$ python jdsym_test.py
> > Traceback (most recent call last):
> >   File "jdsym_test.py", line 1, in <module>
> >     from pysparse import spmatrix, jdsym, itsolvers
> > ImportError: /software/ATLAS/lib/liblapack.so: cannot open shared object
> > file: No such file or directory
> >
> > This seems to indicate that pysparse is looking in the wrong place for
> the
> > lapack libraries (the correct location is
> > /software/ATLAS/3.8.3/lib/liblapack.so).  Have I missed some environment
> > variable or setting in the setup.py to properly specify these library
> > locations?
> >
> > Any suggestions are appreciated,  and thanks in advance,
>
> Hello Eddie,
>
> There are no environment variables to set in Pysparse, so no, you
> haven't missed any.
>
> Could you please post the complete output of 'python setup.py build'
> as well as the result of 'ls -l
> /software/ATLAS/3.8.3/lib/liblapack.so'? I don't doubt your word that
> the library is there but am just trying to get the obvious things out
> of the way first. Also I presume you can run the ATLAS and LAPACK
> tests with your libraries?
>
> Thanks,
>
> --
> Dominique
>