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

[Dominique O. <dom...@gm...>]

On Tue, May 11, 2010 at 12:46:43PM -0500, Eddie Schwalbach wrote:
> 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?

It is much safer to 'rm -rf build'. I find the Distutils aren't as
reliable as Make.
 
> 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
> >