pysparse-users

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

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

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,

Eddie Schwalbach

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

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

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

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

[Daniel W. <dan...@gm...>]

Was there a previous pysparse installation?

On Mon, May 10, 2010 at 12:59 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,
>
> Eddie Schwalbach
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Pysparse-users mailing list
> Pys...@li...
> https://lists.sourceforge.net/lists/listinfo/pysparse-users
>
>



-- 
Daniel Wheeler

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
>

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

[Daniel W. <dan...@gm...>]

Perhaps.It shouldn't matter, but you can just simply remove the
pysparse directory in site-packages, wherever it is. Can't hurt.

On Tue, May 11, 2010 at 1:46 PM, Eddie Schwalbach
<e-s...@no...> 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?
>
> 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
>
>



-- 
Daniel Wheeler

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
> >

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
> > >
>

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

[Daniel W. <dan...@gm...>]

On Thu, May 13, 2010 at 11:58 AM, Eddie Schwalbach
<e-s...@no...> wrote:
> 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

"clean" does nothing to the installed directories, it will just clean
up the working copy. I would always delete the build directory rather
than using "clean" anyway.

> (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.)

Very good. Look forward to it.

-- 
Daniel Wheeler