#10508: Update ATLAS to stable version 3.10
-----------------------------------------------------------------------------------------+
Reporter: vbraun
| Owner: tbd
Type: enhancement
| Status: needs_work
Priority: major
| Milestone: sage-5.9
Component: packages
| Resolution:
Keywords: ATLAS
| Work issues:
Report Upstream: Reported upstream. No feedback yet.
| Reviewers: Benjamin Jones, Karl-Dieter Crisman, Dmitrii
Pasechnik, Georg Weber, François Bissey, John Palmieri
Authors: Volker Braun, Jeroen Demeyer
| Merged in:
Dependencies: #13160, #13395, #13392, #13416, #12994, #9906, #12883,
#13123, #13415 | Stopgaps:
-----------------------------------------------------------------------------------------+
Changes (by kcrisman):
* milestone: sage-5.8 => sage-5.9
Old description:
> The new atlas release now builds netlib lapack itself, so the lapack
> tarball is now included in the ATLAS spkg.
>
> * Updated to newest upstream source, various patches are no longer
> required
> * `SAGE_ATLAS_LIB=path` now searches in `path/libatlas.so` instead of
> `path/lib/libatlas.so` so it works for people with atlas in `/lib64`,
> too.
> * Threading is now enabled by default
> * Flush before `os.system` (#13210)
>
> Upstream has made some attempt at changing the layout of the shared
> libraries, which is now different from the static libraries. The atlas
> spkg contains a stub autoconf/libtools project that unpacks the static
> libraries and repacks them into equivalent shared libraries.
>
> By default, ATLAS will now try twice to get timings and fail immediately
> if throttling is enabled. If auto-tuning fails build with
> `SAGE_ATLAS_ARCH=fast`, and if that fails with `SAGE_ATLAS_ARCH=base`. On
> x86, the fast and base targets are the new ATLAS generic targets x86SSE3
> and x86SSE2/x86x87.
>
> The updated cvxopt spkg fixes a blas path issue on Darwin, and is rebased
> to the most recent cvxopt package to include a Cygwin fix.
>
> There is an
> [https://sourceforge.net/tracker/?func=detail&aid=3570164&group_id=23725&atid=379483
> upstream problem] where compilation sometimes crashes during `xextract`
> because of a buffer overflow due to small fixed-sized buffers for
> filenames.
>
> Updated '''spkg'''s:
> 1. [http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.p1.spkg]
> 2. [http://boxen.math.washington.edu/home/jpflori/cvxopt-1.1.5.p1.spkg]
>
> '''Apply''' [attachment:10508_root_after_13415.patch] to the SAGE_ROOT
> repository and [attachment:trac_10508_doctest.patch],
> [attachment:trac_10508_update_atlas_docs.patch] to the Sage repository.
>
> '''Remove''' the lapack and blas packages.
New description:
The new atlas release now builds netlib lapack itself, so the lapack
tarball is now included in the ATLAS spkg.
* Updated to newest upstream source, various patches are no longer
required
* `SAGE_ATLAS_LIB=path` now searches in `path/libatlas.so` instead of
`path/lib/libatlas.so` so it works for people with atlas in `/lib64`, too.
* Threading is now enabled by default
* Flush before `os.system` (#13210)
Upstream has made some attempt at changing the layout of the shared
libraries, which is now different from the static libraries. The atlas
spkg contains a stub autoconf/libtools project that unpacks the static
libraries and repacks them into equivalent shared libraries.
By default, ATLAS will now try twice to get timings and fail immediately
if throttling is enabled. If auto-tuning fails build with
`SAGE_ATLAS_ARCH=fast`, and if that fails with `SAGE_ATLAS_ARCH=base`. On
x86, the fast and base targets are the new ATLAS generic targets x86SSE3
and x86SSE2/x86x87.
The updated cvxopt spkg fixes a blas path issue on Darwin, and is rebased
to the most recent cvxopt package to include a Cygwin fix.
There is an
[https://sourceforge.net/tracker/?func=detail&aid=3570164&group_id=23725&atid=379483
upstream problem] where compilation sometimes crashes during `xextract`
because of a buffer overflow due to small fixed-sized buffers for
filenames.
Updated '''spkg'''s:
1. [http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.p1.spkg],
updated to [
http://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0.spkg]
* Optionally, the next upstream
[http://boxen.math.washington.edu/home/jpflori/atlas-3.11.8.p0.spkg]
2. [http://boxen.math.washington.edu/home/jpflori/cvxopt-1.1.5.p1.spkg]
'''Apply''' [attachment:10508_root_after_13415.patch] to the SAGE_ROOT
repository and [attachment:trac_10508_doctest.patch],
[attachment:trac_10508_update_atlas_docs.patch] to the Sage repository.
'''Remove''' the lapack and blas packages.
--
Comment:
Yours still has Volker's fix
{{{
if conf['Darwin?'] and not os.environ.has_key('SAGE_ATLAS_ARCH'):
print 'Skipping build of ATLAS on intel OS X'
if conf['PPC?']: # OSX 10.4 PPC linker needs help to find the
accelerate blas
veclib_dir = '/System/Library/Frameworks/Accelerate.framework/' +
\
'Versions/A/Frameworks/vecLib.framework/Versions/A'
for lib in [ 'libBLAS.dylib', 'libLAPACK.dylib']:
ln(os.path.join(veclib_dir, lib),
os.path.join(conf['SAGE_LOCAL'], 'lib', lib))
sys.exit(0)
}}}
so this should be okay. And ia64 works fine now for installing (according
to jhpalmieri - what about tests, I assume not done yet on iras?).
----
What are the work issues for this ticket? It's hard to tell from all the
comments - maybe they should be put in "work issues" :-)
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/10508#comment:371>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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