#10508: Update ATLAS to stable version 3.10
-------------------------------------------------------+--------------------
Reporter: vbraun | Owner: tbd
Type: enhancement | Status:
needs_review
Priority: major | Milestone:
sage-5.4
Component: packages | Resolution:
Keywords: ATLAS | Work issues:
Report Upstream: Reported upstream. No feedback yet. | Reviewers:
Benjamin Jones
Authors: Volker Braun | Merged in:
Dependencies: #13160 | Stopgaps:
-------------------------------------------------------+--------------------
Changes (by vbraun):
* status: needs_work => needs_review
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 current spkg version is at
>
> http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.spkg
>
> '''Apply''' [attachment:trac_10508_root_repo.patch] to the SAGE_ROOT
> repository and [attachment: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.
The current spkg version is at
http://www.stp.dias.ie/~vbraun/Sage/spkg/atlas-3.10.0.spkg
http://www.stp.dias.ie/~vbraun/Sage/spkg/cvxopt-1.1.5.p1.spkg
'''Apply''' [attachment:trac_10508_root_repo.patch] to the SAGE_ROOT
repository and [attachment:10508_doctest.patch],
[attachment:trac_10508_update_atlas_docs.patch] to the Sage repository.
'''Remove''' the lapack and blas packages.
--
Comment:
I don't think we should be symlinking system libraries into local/lib if
we can avoid it. Really cvxopt is broken, it should be linking against the
accelerate blas but doesn't. In particular, we should correctly set
`BLAS_LIB_DIR` in cvxopt on Darwin. The update spkg fixes this. I've also
changed the atlas spkg back to not build by default on Darwin. Please test
the combination of both spkgs on your OSX machines.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/10508#comment:209>
Sage <http://www.sagemath.org>
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