Serious bug in atlas, yet no action

Scott Howard showard314 at gmail.com
Wed Oct 7 18:42:28 BST 2009


Hello all,

The reason why Ubuntu has an old version of atlas is that Debian has
an old version of atlas. However, a week or two ago debian packaged
the newest version of atlas into the experimental section:
http://packages.qa.debian.org/a/atlas.html
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=382880

If it was earlier in the release cycle, it would be much simpler to
get atlas in to Karmic. However, since we are in feature freeze with
the release a few weeks away, we are almost bound to 3.6 since
upstream (in this case debian) released 3.8 too recently.

Science motus - if an upgrade to 3.8 fixes this problem, do you think
it is even worth trying to get a freeze exemption for an upgrade from
3.6 to 3.8? My guess is no, since several library names have changed
and other libraries have been removed which won't play nice with other
packages.

Upstream and Debian changelogs are below.


I'll try to package 3.8 later. Cyrus, if you'd like to try packaging,
you can get the source and package it by doing the following:

$ dget http://ftp.debian.org/debian/pool/main/a/atlas/atlas_3.8.3-2.dsc
$ dpkg-source -x atlas_3.8.3-2.dsc

Then build it (using pbuilder, for example - see the wiki for detailed
instructions).


ATLAS 3.8.3 released 02/21/09, Changes from 3.8.2:
   * Fixed bugs:
     - Numerous improvements to configure's architecture recognition
     - Fixed D/ZGEMM cleanup error on MIPS
     - Fixed TRMV tuning Makefile error
     - Fixed Makefile error preventing TRSM tuning
     - Worked around gcc's Solaris division bug
   * Backported Core2 and K10h GEMM kernels
     - Makes a *huge* perf diff on Intel boxes, slight improvement for K10h
   * Added arch defs for Corei7 (64 bit only)
ATLAS 3.8.2 released 06/06/08, Changes from 3.8.1:
   * Fixed bugs:
     - Pervasive performance bug in GEMM, affecting all architectures
     - Occasional access of C when BETA=0
   * Configure improvements:
     - Improved freebsd architecture probe
     - Improved linux cpu throttling probe
   * Added mu=4 SSE M cleanup for extra performance
ATLAS 3.8.1 released 02/22/08, Changes from 3.8.0:
   * Fixed bug in slvtst that counted complex flops same as real
   * Fixed bug causing wrong answer for row-major gemm C=A*A' or A'A
   * Fixed bug in configure causing Pentium-M to be IDed as CoreDuo
   * Fixed bug in tfc.c causing memory overwrite when too many samples taken
   * Improved L1 BLAS timers so they work like the rest of the package, and
     thus don't die all the time on tolerance failures
   * Improved ATLAS/tune/blas/gemm/mmsearch.c:
     - for x86, tried more registers, since smart compiler can reduce A & B
       regs to 2 (and possibly even 1)
     - Made it so search tries both load-C-at-top and load-C-at-bottom of
       M loop.  Bottom is superior for error, and ATLAS originally defaulted
       to load-C-at-top.
   * Added configure support for new K10h platform from AMD, as well as
     basic architectural defaults (no new kernels, just good search)







The debian changelog is below:
 atlas  (3.8.3-2) experimental; urgency=low

   * Improve CPU extension check

 -- Sylvestre Ledru <sylvestre at debian.org>  Sat, 26 Sep 2009 02:39:07 +0200
atlas (3.8.3-1) experimental; urgency=low

   * New upstream version (Closes: #382880)
   * debian/rules rewrited from scratch
   * Provides more documentation in the libatlas-doc packages
   * debian/copyright updated
   * Add myself to the uploader
   * Vcs-Browser & Vcs-Svn added
   * packages libatlas-3dnow-dev & libatlas3gf-3dnow obsoletes
   * packages libatlas-sse3-dev and libatlas3-sse3 added
   * libatlas-headers renamed to libatlas-dev
   * libatlas-dev is now in section libdevel
   * fakeroot debian/rules custom will generated a package called
     ../libatlas3gf-base_*.deb which will contain an optimized version of
     Atlas just for the current arch.
   * README.Debian updated to reflect the different changes
   * README.source added to explain where sources of the PDF are
   * Standards-Version updated to 3.8.3
   * compat updated to version 7
   * Camm & Ondrej removed as uploaders
   * Use of David Cournapeau's patches (many thanks for this great work)
   * Change of my email address since I am now DD


On Wed, Oct 7, 2009 at 11:31 AM, Cyrus Hall <hallc at lu.unisi.ch> wrote:
> On Tue, 2009-10-06 at 16:41 +0200, Cyrus Hall wrote:
>> I've recently run into what appears to be a known and reported problem
>> in Atlas 3.2.1
>
> Sorry, that should have read Atlas 3.6.0, not 3.2.1.  I was reading the
> wrong version number in aptitude.
>
> Scott, if you want to test any new build you make, you can also run the
> test posted at
>  https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/406520
> or
>  https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/376739
>
> You can switch between the SSE2 optimized version and the non-optimized
> version (which appears to function correctly) by using LD_PRELOAD:
>
> LD_PRELOAD=/usr/lib/libblas.so                 # Non-optimized version
> LD_PRELOAD=/usr/lib/sse2/atlas/libblas.so.3gf  # SSE2 optimized version
> (or whatever the appropriate directories are for a non-installed build.
> You can confirm LD_PRELOAD is working by checking the result of runtime
> linking with ldd.  This probably isn't news to anyone on this list...)
>
> I can tell you that the version you posted yesterday is still vulnerable
> to the bug, at least as tested by:
>  http://launchpadlibrarian.net/25714126/test.f
>
> Is there any particularly reason not to upgrade atlas to a version that
> isn't six years old?  The newest stable version of atlas is 3.8.3 from
> 18-02-09.  3.6.0 was released December of 2003.
>
> I can confirm that the test program works successfully with a build of
> 3.8.3 I made.
>
> I would be happy to package up 3.8.3 for ubuntu, at least for
> architectures I have access to (x86 CoreDuo and a x86-64 Opteron), if
> someone could offer me some pointers.  I am not familiar with apt beyond
> the level of a daily user, meaning I've never created packages for
> distribution before, but I'd be more than willing to give it a try.
>
> No matter, take away message here is that the new build does not fix the
> problem.  If I have more spare time later this week I'll try and see if
> I can't hunt down the version in which the problem went away.
>
> Cheers,
> Cyrus
>
>



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