linalg_utils missing dpotrf_wrap

[mcfarljm]

On Fedora 13, with the latest development version from github, I get this import error when importing pymc:

In [1]: import pymc

ImportError Traceback (most recent call last)

/usr/lib/python2.6/site-packages/pymc/init.pyc in ()
45 from CircularStochastic import *
46 import distributions
---> 47 import gp
48
49 # Optional modules

/usr/lib/python2.6/site-packages/pymc/gp/init.py in ()
20 from GPutils import *
21 from Mean import *
---> 22 from Covariance import *
23 from BasisCovariance import *
24 from FullRankCovariance import *

/usr/lib/python2.6/site-packages/pymc/gp/Covariance.py in ()
8 from numpy.linalg import cholesky, LinAlgError
9 from GPutils import regularize_array, trisolve, square_and_sum
---> 10 from linalg_utils import diag_call, dpotrf_wrap
11 from incomplete_chol import ichol, ichol_continue
12

ImportError: cannot import name dpotrf_wrap

I can verify using nm that linalg_utils.so does not contain dpotrf_wrap.

[apatil]

I don't get this error. Were there errors during compilation?

[mcfarljm]

No, I didn't notice any build errors on the console. Is there a log file I can check?

[mcfarljm]

Anand: the difference may be that my system doesn't have a system lapack, so it's using different code in setup.py. Can you try to recreate the issue by forcing lapack_info==False? It looks like on my build, blas_wrap.o isn't getting included in linalg_utils.so, so probably has something to do with setup.py...

[mcfarljm]

OK, I think the fix is to add the source for blas_wrap.f to linalg_utils at line 80 of setup.py:
config.add_extension(name='gp.linalg_utils',sources=['pymc/gp/linalg_utils.f', 'pymc/blas_wrap.f'] + f_sources)

(I also had to update the timestap on blas_wrap.f or else re-running setup.py was not triggering a re-generation of linalg_utilsmodule.c; seems like a minor deficiency in the distutils build system.)

[apatil]

Thanks John, could you please verify that commit 7d3755c fixes the problem?

[mcfarljm]

Yes, that works for me.

[apatil]

Cool.

[mcfarljm]

Closing: fixed by above commit