#7831: numpy-1.5.0 fixes for FreeBSD
--------------------------------------------+-------------------------------
Reporter: pjeremy | Owner: pjeremy
Type: defect | Status: needs_work
Priority: major | Milestone: sage-4.6.1
Component: FreeBSD | Keywords:
Author: Peter Jeremy | Upstream: None of the above -
read trac for reasoning.
Reviewer: Mike Hansen, Minh Van Nguyen | Merged:
Work_issues: |
--------------------------------------------+-------------------------------
Old description:
> * !__init!__.py needs a sage-specific patch to prefer sage_fortran on
> FreeBSD. Without this, numpy reports:
> {{{
> Running from numpy source directory.
> F2PY Version 2
> blas_opt_info:
> blas_mkl_info:
> libraries mkl,vml,guide not found in
> /home/peter/sage/sage-4.3/local/lib
> NOT AVAILABLE
>
> atlas_blas_threads_info:
> Setting PTATLAS=ATLAS
> libraries ptf77blas,ptcblas,atlas_r not found in
> /home/peter/sage/sage-4.3/local/lib
> NOT AVAILABLE
>
> atlas_blas_info:
> libraries f77blas,cblas,atlas_r not found in
> /home/peter/sage/sage-4.3/local/lib
> NOT AVAILABLE
>
> /home/peter/sage/sage-4.3/spkg/build/numpy-1.3.0.p2/src/numpy/distutils/system_info.py:1383:
> UserWarning:
> Atlas (http://math-atlas.sourceforge.net/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [atlas]) or by setting
> the ATLAS environment variable.
> warnings.warn(AtlasNotFoundError.__doc__)
> blas_info:
> FOUND:
> libraries = ['blas']
> library_dirs = ['/home/peter/sage/sage-4.3/local/lib']
> language = f77
>
> FOUND:
> }}}
>
> This also causes matplotlib to die with
> {{{
> REQUIRED DEPENDENCIES
> numpy: no
> * You must install numpy 1.1 or later to build
> * matplotlib.
> }}}
>
> * By default, numpy references threaded atlas libraries, as well as a
> custom variant on the lapack library, on FreeBSD. The reasoning behind
> this is unclear - there is nothing in the numpy documentation to indicate
> whether a threaded or non-threaded atlas is needed and the publicly
> available SVN logs do not mention this code. A query to the numpy mailing
> list elicited a response that either threaded or non-threaded atlas can
> be used and suggesting that the special-casing for FreeBSD may be
> obsolete. By default, atlas is built non-threaded and r-2.6.1.p23 assumes
> a non-threaded atlas and fails when only the threaded libraries are
> installed. Based on this, the special casing for FreeBSD was removed from
> numpy - it now uses the same libraries irrespective of the host OS. This
> part of the patch could potentially be integrated upstream but this has
> not been done yet.
New description:
* By default, numpy references threaded atlas libraries, as well as a
custom variant on the lapack library, on FreeBSD. The reasoning behind
this is unclear - there is nothing in the numpy documentation to indicate
whether a threaded or non-threaded atlas is needed and the publicly
available SVN logs do not mention this code. A query to the numpy mailing
list elicited a response that either threaded or non-threaded atlas can be
used and suggesting that the special-casing for FreeBSD may be obsolete.
By default, atlas is built non-threaded and r-2.6.1.p23 assumes a non-
threaded atlas and fails when only the threaded libraries are installed.
Based on this, the special casing for FreeBSD was removed from numpy - it
now uses the same libraries irrespective of the host OS. This part of the
patch could potentially be integrated upstream but this has not been done
yet.
* A patch to spkg-install is required to ensure that the <math.h> in
$SAGE_LOCAL/include is used in place of the system <math.h>, otherwise the
additional maths functions provided by cephes are not prototyped, leading
to lots of "implicit declaration" warnings whilst compiling (eg)
numpy/core/src/npymath/npy_math_complex.c.src
--
Comment(by pjeremy):
The __init__.py changes don't appear to be needed any longer but the
remaining fixes are still required.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/7831#comment:10>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
--
You received this message because you are subscribed to the Google Groups
"sage-trac" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/sage-trac?hl=en.
