Date: Wed, 4 May 2005 14:20:21 -0400 (EDT) From: Gregory Crosswhite <cog@umd.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/80623: [patch] science/py-scipy links to wrong atlas library Message-ID: <200505041820.j44IKLJv092552@dragon.student.umd.edu> Resent-Message-ID: <200505041830.j44IU32g042377@freefall.freebsd.org>
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>Number: 80623
>Category: ports
>Synopsis: [patch] science/py-scipy links to wrong atlas library
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Wed May 04 18:30:02 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator: Gregory Crosswhite
>Release: FreeBSD 5.3-RELEASE i386
>Organization:
University of Maryland, College Park
>Environment:
System: FreeBSD dragon.student.umd.edu 5.3-RELEASE FreeBSD 5.3-RELEASE #1: Sun Mar 13 14:21:12 EST 2005 cog@dragon.stude
nt.umd.edu:/usr/obj/usr/src/sys/MYKERNEL i386
Applicable Installed Ports:
atlas-3.6.0,1 Automatically Tuned Linear Algebra Software (ATLAS)
py23-scipy-0.3 Scientific tools for Python
>Description:
In FreeBSD, the atlas libraries have a slightly different naming convention than that expected by SciPy. In particular,
the threaded versions of the libraries end in "_r", which SciPy does not expect. Thus, it links against the wrong
libraries. When you use the SciPy libraries, they throw an ImportError reporting that they are unable to find symbols
they need.
I have seen two such errors:
ImportError: /usr/local/lib/libptf77blas.so.1: Undefined symbol "ATL_cpttrsm"
when using the optimize package, and then, after a fix was applied for the above,
ImportError: /usr/local/lib/python2.3/site-packages/scipy/linalg/clapack.so: Undefined symbol "clapack_sgesv"
when using the linear algebra package.
>How-To-Repeat:
Build and install the science/scipy port.
Run python and type in the commands:
from scipy.optimize.optimize import *
fmin_bfgs
ImportError: /usr/local/lib/libptf77blas.so.1: Undefined symbol "ATL_cpttrsm"
>Fix:
Before building the port, change the file scipy_core/scipy_distutils/system_info.py so that
lines 547-549, which formally read
atlas_libs = self.get_libs('atlas_libs',
self._lib_names + ['atlas'])
lapack_libs = self.get_libs('lapack_libs',['lapack'])
now read
atlas_libs = self.get_libs('atlas_libs',
self._lib_names + ['atlas_r'])
lapack_libs = self.get_libs('lapack_libs',['alapack_r'])
(I changed the names of the libraries slightly: 'atlas'->'atlas_r' and 'lapack'->'alapack_r'.)
A patch has been included which does this automatically. It can just be dropped directly into the
"files/" directory in the science/py-scipy port.
>Release-Note:
>Audit-Trail:
>Unformatted:
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