#10508: Update ATLAS to stable version 3.10.1
---------------------------------------------------------------------------------------------------------+
Reporter: vbraun
| Owner: tbd
Type: enhancement
| Status: needs_work
Priority: major
| Milestone: sage-5.10
Component: packages: standard
| Resolution:
Keywords: ATLAS spkg
| Work issues: linker errors
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, Jean-Pierre Flori
| Merged in:
Dependencies: #13160, #13395, #13392, #13416, #12994, #9906, #12883,
#13123, #13415, #14344, #14465 | Stopgaps:
---------------------------------------------------------------------------------------------------------+
Changes (by jpflori):
* work_issues: linker errors, rebase => linker errors
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://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0.spkg].
> 2. [http://boxen.math.washington.edu/home/jpflori/cvxopt-1.1.5.p1.spkg].
>
> '''Apply'''
> 1. [attachment:10508_root.patch] to the SAGE_ROOT repository
> 2. [attachment:trac_10508_doctest.rebased.patch] and
> [attachment:trac_10508_update_atlas_docs.patch] to the Sage repository.
> 3. [attachment:10508_scripts.patch] to `local/bin`.
>
> '''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://boxen.math.washington.edu/home/jpflori/atlas-3.10.1.p0.spkg].
2. [http://boxen.math.washington.edu/home/jpflori/cvxopt-1.1.5.p1.spkg].
'''Apply'''
1. [attachment:10508_root.patch] to the SAGE_ROOT repository
2. [attachment:trac_10508_doctest.rebased.patch] and
[attachment:trac_10508_update_atlas_docs.rebased.patch] to the Sage
repository.
3. [attachment:10508_scripts.patch] to `local/bin`.
'''Remove''' the lapack and blas packages.
--
Comment:
It seems somehow your last failures are caused by the fact that ATLAS
finds out the generic implementation of thread related functions is as
fast as the assembly one (whence the random failures I guess), and in the
end both implementaitons end up in the archive, and wen Volker's code
tries to make a shared library of this archive, it fails...
I'll investigate more on that later, as 'm not sure upstream which does
not really use shared libraries will care.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/10508#comment:443>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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