Debian Bug report logs - #638236
libatlas3-base: when the LAPACK alternative points to ATLAS, the BLAS alternative should always point to ATLAS

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Jonathan Nieder <jrnieder@gmail.com>

To: submit@bugs.debian.org

Subject: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Wed, 17 Aug 2011 17:22:14 -0500

Package: libatlas3gf-base
Version: 3.8.4-3
Severity: important

Hi,

Trying to build r-base:

| make[5]: Entering directory `/tmp/r-base-2.13.1/src/library/grDevices'
| Warning in solve.default(rgb) :
|   unable to load shared object '/tmp/r-base-2.13.1/modules//lapack.so':
|   /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
| Error in solve.default(rgb) : lapack routines cannot be loaded
| Error: unable to load R code in package 'grDevices'
| Execution halted
| make[5]: *** [mklazy] Error 1

Hmm.  So:

| $ readlink /etc/alternatives/liblapack.so.3gf
| /usr/lib/atlas-base/atlas/liblapack.so.3gf
| $ dpkg-query -S /usr/lib/atlas-base/atlas/liblapack.so.3gf
| libatlas3gf-base: /usr/lib/atlas-base/atlas/liblapack.so.3gf
| # dpkg-query -W libatlas3gf-base
| libatlas3gf-base	3.8.4-3

And:

| $ python
| Python 2.7.2+ (default, Aug 16 2011, 09:23:59) 
| [GCC 4.6.1] on linux2
| Type "help", "copyright", "credits" or "license" for more information.
| >>> import numpy
| Traceback (most recent call last):
[...]
|     from numpy.linalg import lapack_lite
| ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv

Severity is just important because I don't know if it's just me.
Ideas?

Jonathan

| $ ls -l /etc/alternatives/libblas.so.3gf
| /usr/lib/openblas-base/libopenblas.so.0

-- System Information:
Debian Release: wheezy/sid
  APT prefers experimental
  APT policy: (990, 'experimental'), (500, 'proposed-updates'), (500, 'unstable'), (500, 'testing'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.0.0-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages libatlas3gf-base depends on:
ii  libc6                         2.13-16    Embedded GNU C Library: Shared lib
ii  libgcc1                       1:4.6.1-7  GCC support library
ii  libgfortran3                  4.6.1-7    Runtime library for GNU Fortran ap

libatlas3gf-base recommends no packages.

Versions of packages libatlas3gf-base suggests:
ii  liblapack3gf                  3.3.1-1    library of linear algebra routines

-- no debconf information

Message #10 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Jonathan Nieder <jrnieder@gmail.com>

To: 638236@bugs.debian.org

Subject: Re: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Wed, 17 Aug 2011 17:40:12 -0500

forcemerge 638236 624318
# declared dependencies are incomplete
severity 624318 serious
quit

Jonathan Nieder wrote:

> | $ ls -l /etc/alternatives/libblas.so.3gf
> | /usr/lib/openblas-base/libopenblas.so.0

Ah, so apparently this was the problem --- atlas relies on libblas.so.3gf
defining some private functions.

How about this patch?  It fixes the policy "must" violation (§3.5,
incomplete dependencies) by introducing a policy "should" violation
(§2.5, conflict with optional package).
---
 debian/changelog |    8 ++++++++
 debian/control   |    1 +
 2 files changed, 9 insertions(+), 0 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0d24ac4d..3339f19a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+atlas (3.8.4-3.1) local; urgency=low
+
+  * Declare incompatibility between libatlas3gf-base and other
+    libblas.so.3gf providers using a Breaks relation in debian/control
+    (Closes: #624318)
+
+ -- Jonathan Nieder <jrnieder@gmail.com>  Wed, 17 Aug 2011 17:37:24 -0500
+
 atlas (3.8.4-3) unstable; urgency=low
 
   * Revert change about devscripts being in the build-dep (see bug #628104)
diff --git a/debian/control b/debian/control
index e12ff657..a370d218 100644
--- a/debian/control
+++ b/debian/control
@@ -23,6 +23,7 @@ Conflicts: atlas2 (<< 3.2.1-1), libblas3gf (<< 1.2-5),
  libatlas3gf-corei7sse3 (<< 3.8.3-25), libatlas3gf-altivec (<< 3.8.3-25), 
  libatlas3gf-v9 (<< 3.8.3-25), libatlas3gf-ev6 (<< 3.8.3-25), 
  libatlas3gf-2.0 (<< 3.8.3-25)
+Breaks: libblas.so.3gf
 Replaces: atlas2 (<< 3.2.1-1),  libatlas3gf-sse (<< 3.8.3-25), 
  libatlas3gf-sse2 (<< 3.8.3-25), libatlas3gf-sse3 (<< 3.8.3-25), 
  libatlas3gf-core2sse3 (<< 3.8.3-25), libatlas3gf-amd64sse3 (<< 3.8.3-25),
-- 
1.7.6

Message #19 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Sylvestre Ledru <sylvestre@debian.org>

To: Jonathan Nieder <jrnieder@gmail.com>, 638236@bugs.debian.org

Subject: Re: Bug#638236: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Thu, 18 Aug 2011 00:57:17 +0200

forcemerge 638236 598638
> Jonathan Nieder wrote:
> 
> > | $ ls -l /etc/alternatives/libblas.so.3gf
> > | /usr/lib/openblas-base/libopenblas.so.0
> 
> Ah, so apparently this was the problem --- atlas relies on libblas.so.3gf
> defining some private functions.
> 
> How about this patch?  
Sorry but no. It is not the right solution.

See here for the full description of the issue:
http://lists.debian.org/debian-dpkg/2011/02/msg00069.html
and the source of the issue:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=521813

Update blas to use the one provided by atlas and it should fix your
problem.

I am considering a potential improvement which might fix the issue.

Sorry about that,
Sylvestre

Message #24 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Jonathan Nieder <jrnieder@gmail.com>

To: Sylvestre Ledru <sylvestre@debian.org>

Cc: 638236@bugs.debian.org

Subject: Re: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Wed, 17 Aug 2011 18:06:11 -0500

Sylvestre Ledru wrote:

> It is not the right solution.

While I agree, it fixes (or works around and declares, if you prefer)
a serious bug, today.  So if other plans fall through, I would still
encourage you to consider it.

[...]
> I am considering a potential improvement which might fix the issue.

Thanks!  That's very good to hear.

Cheers,
Jonathan

Message #29 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Jonathan Nieder <jrnieder@gmail.com>

To: Sylvestre Ledru <sylvestre@debian.org>

Cc: 638236@bugs.debian.org

Subject: Re: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Sat, 15 Oct 2011 20:33:47 -0500

Sylvestre Ledru wrote:

> I am considering a potential improvement which might fix the issue.

Ping.  Any details about that, or any other way that people interested
in seeing this fixed can help out?

Message #34 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Encolpe Degoute <encolpe.degoute@free.fr>

To: Sylvestre Ledru <sylvestre@debian.org>

Cc: 638236@bugs.debian.org, Jonathan Nieder <jrnieder@gmail.com>

Subject: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chem

Date: Fri, 28 Oct 2011 01:33:37 +0200

Hello,

I got this working by removing the libopenblas-base package.

Regards
-- 
Encolpe DEGOUTE
http://encolpe.degoute.free.fr/
Logiciels libres, hockey sur glace et autres activités cérébrales

Message #47 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Laurent Bonnaud <Laurent.Bonnaud@inpg.fr>

To: 638236@bugs.debian.org

Subject: Re: undefined symbol: ATL_chem

Date: Fri, 15 Jun 2012 10:37:03 +0200

Hi,

this bug is still there in this package version:
 
Package: libatlas3-base
Version: 3.8.4-7

One easy way to check for the presence of this bug is:

$ php
PHP Warning:  PHP Startup: Unable to load dynamic library '/usr/lib/php5/20100525+lfs/php_mapscript.so' - /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv in Unknown on line 0

-- 
Laurent Bonnaud <Laurent.Bonnaud@inpg.fr>

Message #52 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Sébastien Villemot <sebastien.villemot@ens.fr>

To: Laurent Bonnaud <Laurent.Bonnaud@inpg.fr>

Cc: 638236@bugs.debian.org

Subject: Re: Bug#638236: undefined symbol: ATL_chem

Date: Fri, 15 Jun 2012 11:15:17 +0200

[Message part 1 (text/plain, inline)]

Laurent Bonnaud <Laurent.Bonnaud@inpg.fr> writes:


> this bug is still there in this package version:
>  
> Package: libatlas3-base
> Version: 3.8.4-7
>
> One easy way to check for the presence of this bug is:
>
> $ php
> PHP Warning:  PHP Startup: Unable to load dynamic library '/usr/lib/php5/20100525+lfs/php_mapscript.so' - /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv in Unknown on line 0

No, I think you've hit #576972.

Looks like your BLAS alternative is set to Refblas or Openblas, while
your LAPACK alternative is set to ATLAS.

You must make sure that they are consistent:

 sudo update-alternatives --config libblas.so.3
 sudo update-alternatives --config liblapack.so.3

Best,

-- 
Sébastien Villemot
Researcher in Economics & Debian Maintainer
http://www.dynare.org/sebastien
Phone: +33-1-40-77-84-04 - GPG Key: 4096R/381A7594

[Message part 2 (application/pgp-signature, inline)]

Message #57 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Sébastien Villemot <sebastien.villemot@ens.fr>

To: Laurent Bonnaud <Laurent.Bonnaud@inpg.fr>

Cc: 638236@bugs.debian.org

Subject: Re: Bug#638236: undefined symbol: ATL_chem

Date: Fri, 15 Jun 2012 11:18:52 +0200

[Message part 1 (text/plain, inline)]

Laurent Bonnaud <Laurent.Bonnaud@inpg.fr> writes:

> this bug is still there in this package version:

Sorry, you are right (I was confusing two bugs).

This bug is still present, and it is the reason why it is not yet
closed…

If you have any idea on how to solve this, it is very welcome.

-- 
Sébastien Villemot
Researcher in Economics & Debian Maintainer
http://www.dynare.org/sebastien
Phone: +33-1-40-77-84-04 - GPG Key: 4096R/381A7594

[Message part 2 (application/pgp-signature, inline)]

Message #64 received at 638236@bugs.debian.org (full text, mbox, reply):

From: Sébastien Villemot <sebastien.villemot@ens.fr>

To: 576972@bugs.debian.org, 598638@bugs.debian.org, 624318@bugs.debian.org, 638236@bugs.debian.org, 676726@bugs.debian.org

Subject: Workaround implemented in atlas 3.8.4-8

Date: Thu, 28 Jun 2012 11:16:36 +0200

[Message part 1 (text/plain, inline)]

Hi,

It seems impossible to elegantly solve this bug without having hooks in
update-alternatives (a wishlist bug is filed for that).

In the meantime, a workaround has been implemented in order to minimize
the incidence of this bug.

Starting from version 3.8.4-8 of Atlas, the Lapack alternative provided
by Atlas has a lower priority than the one provided by Netlib's
reference Lapack. That means that the bug will never hit as long as the
alternatives are left in automatic mode (which is the default).

The downside is that one won't automatically benefit from the
optimizations made by Atlas into Lapack, unless the alternative is
manually modified.

The decision to implement this solution has been made jointly by
Sylvestre Ledru (maintainer), Julien Cristau (Release Team) and myself,
during the Debian Science Sprint kindly sponsored by ESRF, Grenoble,
France.

-- 
Sébastien Villemot
Researcher in Economics & Debian Maintainer
http://www.dynare.org/sebastien
Phone: +33-1-40-77-84-04 - GPG Key: 4096R/381A7594

[Message part 2 (application/pgp-signature, inline)]

Message #79 received at 576972-close@bugs.debian.org (full text, mbox, reply):

From: Sébastien Villemot <sebastien@debian.org>

To: 576972-close@bugs.debian.org

Subject: Bug#576972: fixed in atlas 3.10.2-2

Date: Tue, 05 Aug 2014 19:33:49 +0000

Source: atlas
Source-Version: 3.10.2-2

We believe that the bug you reported is fixed in the latest version of
atlas, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 576972@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Sébastien Villemot <sebastien@debian.org> (supplier of updated atlas package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Tue, 05 Aug 2014 18:13:33 +0200
Source: atlas
Binary: libatlas3-base libatlas3gf-base libatlas-base-dev libatlas-dev libatlas-test libatlas-doc
Architecture: source all amd64
Version: 3.10.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Sébastien Villemot <sebastien@debian.org>
Description:
 libatlas-base-dev - Automatically Tuned Linear Algebra Software, generic static
 libatlas-dev - Automatically Tuned Linear Algebra Software, C header files
 libatlas-doc - Automatically Tuned Linear Algebra Software, documentation
 libatlas-test - Automatically Tuned Linear Algebra Software, test programs
 libatlas3-base - Automatically Tuned Linear Algebra Software, generic shared
 libatlas3gf-base - Transitional package to libatlas3-base
Closes: 576972
Changes:
 atlas (3.10.2-2) unstable; urgency=medium
 .
   * shared_libraries.diff: no longer include ATLAS-specific symbols in
     libblas.so and liblapack.so. Rather dynamically link those libraries with
     libatlas.so. This makes it possible to use liblapack.so from ATLAS with a
     libblas.so coming from somewhere else. Thanks to Guillem Jover for
     suggesting this solution. (Closes: #576972)
   * Revert back to a higher priority in the LAPACK alternatives.
     The priority had been lowered in 3.8.4-8 in order to minimize the incidence
     of #576972, so this is no longer needed.
Checksums-Sha1:
 44e2068df19fafa6f600effd088206cdf8b7fd07 2422 atlas_3.10.2-2.dsc
 fbe8e103c791b00efa9c915122f17210a0d1b8f9 109640 atlas_3.10.2-2.debian.tar.xz
 303b22405fe6328de117e94cf4d3126b097ea320 51138 libatlas3gf-base_3.10.2-2_all.deb
 3a9bf98a2ca69d4aeb16891e29e611c3085af3aa 68086 libatlas-dev_3.10.2-2_all.deb
 d7ba71298f634ec4583e82a04eab22fd3a9e466b 1148810 libatlas-doc_3.10.2-2_all.deb
 38b61bb4dada606d9e3613e626142ed070fe7af1 2490864 libatlas3-base_3.10.2-2_amd64.deb
 4c985c6108bc25d5b77427f9814be4132b319212 3097166 libatlas-base-dev_3.10.2-2_amd64.deb
 64e618bdb5074933e8270ca9c427ffee0f02ff78 1777854 libatlas-test_3.10.2-2_amd64.deb
Checksums-Sha256:
 6b851bcac272f873daef03e815cfe8d6b649b0775be4cde7a46b8634816da22e 2422 atlas_3.10.2-2.dsc
 cdec7950fa6926e56194bc5b72de2bc3f17bc3238cd48c55546ab3dfcac5c716 109640 atlas_3.10.2-2.debian.tar.xz
 b9003002edcb93baa695825f860f18dc9d3c18d643fb09f626d0388ecc7647c9 51138 libatlas3gf-base_3.10.2-2_all.deb
 27cceee5ad4ec3eb0a16cb5f7c15b703195d86331fbb3e804a6c90e8a89b8a13 68086 libatlas-dev_3.10.2-2_all.deb
 8ff1869e1c1a2897814cb1e03e5e982091d79f3596fb294a32c3953e059d05a4 1148810 libatlas-doc_3.10.2-2_all.deb
 b32522cc5536f0bab8fac3aa35d0b1393ab8da20c8dba1f66f8a20bd609a55cc 2490864 libatlas3-base_3.10.2-2_amd64.deb
 547d6ab4d2630c2a5a0ef74f53e5c3e1cb25c162e859f0f555e834e9d690eb73 3097166 libatlas-base-dev_3.10.2-2_amd64.deb
 5c1b76d5f3215121c55a2a933dd708e8d97c3b131f44e9346da06cf46890b0bb 1777854 libatlas-test_3.10.2-2_amd64.deb
Files:
 23fe49f33f8fa1daf6598fc9d89f422e 51138 oldlibs optional libatlas3gf-base_3.10.2-2_all.deb
 d83589fa0f703e1ebcfce996b021c977 68086 libdevel optional libatlas-dev_3.10.2-2_all.deb
 a629460e5b4b4b27753bb4dddae55a1d 1148810 doc optional libatlas-doc_3.10.2-2_all.deb
 da3a534794e01dd82d21af7edb0e8c1e 2490864 libs optional libatlas3-base_3.10.2-2_amd64.deb
 069f6ad5eaffc56ff1d6cad2ed1a8a5c 3097166 libdevel optional libatlas-base-dev_3.10.2-2_amd64.deb
 137fb8a7a55c3ac910d284f482c75ee0 1777854 devel extra libatlas-test_3.10.2-2_amd64.deb
 dbfc23de4b16969f03e367189e0b9fb4 2422 devel optional atlas_3.10.2-2.dsc
 68adc578ab4886f36e9dfb3eea8bb249 109640 devel optional atlas_3.10.2-2.debian.tar.xz

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