gmane.linux.ubuntu.motu.science

Re: MOTU-science for "official" development team delegation

Scott Howard — 2010-03-01T14:53:53

Thanks for the reply Morten, and figuring out how it's working. After
looking more closely at the new designated team system, you are right,
MOTU Science probably isn't tight enough. Also, it the team seems to
be functioning well as is: bug response times are fast, and packages
are being kept up to date. The tools (specifically:
http://qa.ubuntuwire.com/multidistrotools/science.html) are really
helpful to keeping that going. One more question though: How are new
packages added to the MOTU Science "watchlist" (either subscribed bug
or multidistrotools?)? Is it everything with debian section science,
math, etc? Thanks,
Scott

Re: MOTU-science for "official" development team delegation

Morten Kjeldgaard — 2010-03-01T12:53:48

On 07/02/2010, at 19.37, Scott Howard wrote:


I am afraid the team is too small and scattered to really make an  
effort. As it stands now, it is my feeling that the current purpose of  
the team *mostly* is that members can display an emblem on their LP  
page showing their interest in science packages. It is my impression  
that the team's members indeed are active in the day-to-day  
maintenance of these packages, they care about bugs, new releases etc.  
and report bugs on LP.

However, I am not sure that the team with its current strength can  
take on a more formal and active role. When joining Ubuntu as a MOTU  
is was my vision that it might be possible to make a branded "Science"  
Ubuntu version. However, I do not myself have the time or energy  
required to pull such a thing through, and in addition, some of the  
most active members from the past have retired. A more realistic goal  
might be to join forces with the edubuntu team, and perhaps form a  
"science" subgroup under that umbrella.


I have approved 3 new members today; welcome to you! Our current  
policy is that new applicants are required to have 500 bonus points.  
Science packages are often a little bit complex, and so Grant and I  
some tima ago decided that it was a good idea that applicants have  
demonstrated some activity and gained some experience before letting  
them in the team.

Cheers,
Morten

MOTU-science for "official" development team delegation

Scott Howard — 2010-02-07T18:37:37

Hello all again,

With the archive reorganization currently going on [1], I'd like to
gauge the team's interest (especially William Grant and Morten) in
becoming an official development team [2] for science packages.

As our team stands now, we have 9 members: 4 are full ubuntu-dev, one
more should ubuntu-dev (but hasn't applied, I think), one is inactive,
and the other three are at least -contributor level (but have not
applied yet). I think we are ready to take part in this new system. We
would have to make the non ubuntu-dev people "apply" to stay in the
team since they would have upload permissions. I'll be willing to take
on the communication with the technical board over the implementation
for this.

Regards,
Scott

[1] https://wiki.ubuntu.com/ArchiveReorganisation
[2] https://wiki.ubuntu.com/UbuntuDevelopers/TeamDelegation

Kamal Mostafa wants to join motu-science

Scott Howard — 2010-02-07T17:35:45

Hi All,

Kamal Mostafa has been active merging and fixing science library
packages. He's experienced developer, and would like to join
motu-science. Would someone be able to approve his membership on
launchpad? He has recently applied.
Thanks,
Scott

Re: Programing PICs with Ubuntu

Kamal Mostafa — 2010-01-10T07:24:25

Hi Léo-

Yes, Ubuntu includes several packages for building PIC binaries and
flash-programming PIC microcontrollers.  I do all of my PIC development
on an Ubuntu 9.10 system, using these packages:

        gputils - GNU PIC utilities
        
            (gputils is the build toolchain package, and includes
        programs:
             gpasm, gplink, and gplib)
        
        gpsim - Simulator for Microchip's PIC microcontrollers
        
        picp - command line utility to drive a PICSTART programmer

More PIC-related packages are also available.  This command will give
you a (partial?) list:

        $ apt-cache search microchip

Best regards,

 -Kamal Mostafa

Re: Bugmail for geda-gaf

Morten Kjeldgaard — 2010-01-06T22:11:18

On 06/01/2010, at 17.48, Peter Clifton wrote:


Done.

Cheers,
Morten

Bugmail for geda-gaf

Peter Clifton — 2010-01-06T16:48:55

I see MOTU Science is a bug contact for all the old separate geda-*,
libgeda source packages, which were removed from Lucid.

Since the upload of gEDA 1.6.0-3 (source package geda-gaf), I wonder if
the MOTU-Science team admins would like to subscribe themselves to
bugmail for that?

Best regards,

Peter C.

Programing PICs with Ubuntu

Léo Magalhães — 2009-11-09T01:20:24

Re: Eletronics simulations software

Aanjhan R — 2009-10-25T00:40:30

2009/10/25 Léo Magalhães <leomagalhaes2008-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>:

Did you add the DC Simulation block in the circuit? i.e after you put
down your voltage divider circuit you need to click on the
"components" tab on the left, choose "simulations" in the drop down
list and then drag and drop "dc simulation" box into the circuit
workspace. Now you have defined the action.

Things should work after this.


Regards,
Aanjhan

Eletronics simulations software

Léo Magalhães — 2009-10-25T00:15:47

Re: Serious bug in atlas, yet no action

Cyrus Hall — 2009-10-08T11:38:57

Scott-

I wont have time to try and package 3.8.3 until this evening, but will
do so then.

In terms of the feature freeze, I have two comments.  First, it does
seem worth trying to get a non-broken version of the SSE2 version into
the repo.  The seriousness of this bug is very clear: a large number of
scientific computing tasks use atlas, and are at risk of producing
incorrect results.  This reflects poorly on Unbuntu and OSS in general.

However, if it's not desirable to ask for an exception, maybe it would
be possible to argue for the removal of the SSE2 optimized package in
Karmic.  This would not be an inconvenience for users, as the package
produces incorrect results anyway, and would in fact help them by making
sure they do not produce erroneous data.

Cheers,
Cyrus

On Wed, 2009-10-07 at 19:42 +0200, Scott Howard wrote:

Re: Serious bug in atlas, yet no action

Scott Howard — 2009-10-07T17:42:28

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-8fiUuRrzOP0dnm+yROfE0A< at >public.gmane.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-ZecRSD2H78cfv37vnLkPlQ< at >public.gmane.org> wrote:

Re: Serious bug in atlas, yet no action

Cyrus Hall — 2009-10-07T15:31:17

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

Re: Serious bug in atlas, yet no action

Scott Howard — 2009-10-07T00:35:42

Hello again,

I just packaged a merge from debian. You can try it at:
https://launchpad.net/~showard314/+archive/ppa

I haven't found any patches that directly address the problem, I don't
know if it's been triaged fully anywhere yet. This debian merge at the
PPA is just a try to see if we got lucky and something fixed it up in
debian over the past year. If this works I'll post a merge proposal to
debian.

Regards,
Scott

On Tue, Oct 6, 2009 at 5:55 PM, Scott Howard <showard314-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Re: Serious bug in atlas, yet no action

Scott Howard — 2009-10-06T21:55:20

Hi all,
I'm going to look at this too. I couldn't find any patch or
information on what the bug is. Debian is migrating to version 3.8,
and we have the possibility of merging in from debian:

https://merges.ubuntu.com/a/atlas/REPORT

from the debian changelog:

   * Removing debian/used_lapack_version in clean
   * Use the changelog from liblapack-dev to find the current lapack version as
     we don't build-depend on the lapack3 package.

that liblapack library is mentioned in the mail exchange that Cyrus
pointed us to. We can try to put a PPA up of the debian version and
test if that works ok.

Regards,
Scott

On Tue, Oct 6, 2009 at 3:57 PM, Morten Kjeldgaard <mok-F3bI4HJ04gslQiHFxVf3kg< at >public.gmane.org> wrote:

Re: Serious bug in atlas, yet no action

Morten Kjeldgaard — 2009-10-06T19:57:29

On 06/10/2009, at 16.41, Cyrus Hall wrote:


Thank you for drawing our attention to this bug. I will take a look at  
the problems. Anyone willing to pitch in, please do so! In particular,  
if you are aware of patches, make a note on the bugs.

Cheers,
Morten

Serious bug in atlas, yet no action

Cyrus Hall — 2009-10-06T14:41:11

Ciao all-

I've recently run into what appears to be a known and reported problem
in Atlas 3.2.1: the SSE2 optimized version is broken.  This version is
currently shipped with Jaunty, and is reported to still be broken in the
Karmic (see bug reports below).  There are numerous unassigned bug
reports in launchpad which appear related to the problem, some of which
are six months old:

https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/363510
https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/376739
https://bugs.launchpad.net/ubuntu/+source/atlas/+bug/406520

I understand that it is unusual to e-mail a dev list to call for action
on a particular bug, but the failure mode here seems particularly
serious.  Programs that depend on the broken library compile perfectly
fine, seem to return valid numerical results, and show no signs of being
broken unless one compares against correct results.  I fear that many of
my colleagues who use Octave and other numerical tools that depend on
Atlas are less in careful in such ways, and it concerns me that bogus
results are probably, at this moment, being accepted as valid in
research labs around the world.

The way I came across the bug was by compiling the new release of
Octave, 3.2.3.  Both the eig and eigs functions (eigenvalue
decompositions, for full and sparse matrices respectively) returned
unexpected results in make check.  For the set of messages related to
the problem, see the following threads on the Octave list:

https://www-old.cae.wisc.edu/pipermail/bug-octave/2009-September/009527.html

A fix for this bug seems critical to get into Karmic, and possibly into
older Ubuntu versions still supported.

Cheers,
Cyrus Hall

Want to join/help motu science

2009-08-25T02:22:45