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

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

I removed the build directory, and reran the build and install steps with
the correct library paths and everything seems to be working now.  I guess
there was something in the build directory pointing to the wrong library
location from my initial install attempt that wasn't removed by

pythyon setup.py clean

Thanks for the help.

(Daniel, I now have FiPy up and running with Trilinos on our cluster, I'll
share scaling info with you after I run some tests.)

Eddie

On Tue, May 11, 2010 at 12:48 PM, Dominique Orban <dom...@gm...
> wrote:

> 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
> > >
>