#10508: Update ATLAS to stable version 3.10
-----------------------------------------------------------------------------------------+
Reporter: vbraun
| Owner: tbd
Type: enhancement
| Status: needs_work
Priority: major
| Milestone: sage-5.8
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:
-----------------------------------------------------------------------------------------+
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.
>
> 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://www.stp.dias.ie/~vbraun/Sage/spkg/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]
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 (by kcrisman):
> > Right, but in the past we still needed the lapack stuff from Cygwin.
> >
> Yup to get the BLAS thing.
> But although it also provided the LAPACK part we built it anyway.
Well, anyway that needs to be fixed so that Cygwin knows where to find
what.
> > Looks like a missing include of MPIR, maybe?
> Did you use the p1 spkg I posted and linked toward the end of the
comments?
No, it was in comment:299 - that's scores of comments ago. If that is
really what is needed, then you should update the ticket description
(which I have now done).
Does that mean I shouldn't have used Volker's spkg for atlas either? Does
yours behave properly w.r.t. Cygwin?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/10508#comment:368>
Sage <http://www.sagemath.org>
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