Regression after upgrade to 14.04: undefined symbol: ATL_cpttrsm

Bug #1336202 reported by Achim Bohnet on 2014-07-01
12
This bug affects 2 people
Affects Status Importance Assigned to Milestone
atlas (Ubuntu)
Undecided
Unassigned

Bug Description

After upgrade from precise to trusty: a selfcompiled python program broke with:

> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py", line
> 153, in <module>
> from . import add_newdocs
> File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py",
> line 13, in <module>
> from numpy.lib import add_newdoc
> File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py",
> line 18, in <module>
> from .polynomial import *
> File
> "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line
> 19, in <module>
> from numpy.linalg import eigvals, lstsq, inv
> File
> "/usr/local/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line
> 50, in <module>
> from .linalg import *
> File "/usr/local/lib/python2.7/dist-packages/numpy/linalg/linalg.py",
> line 29, in <module>
> from numpy.linalg import lapack_lite, _umath_linalg
> ImportError:
> /usr/local/lib/python2.7/dist-packages/numpy/linalg/lapack_lite.so:
> undefined symbol: ATL_cpttrsm

checking the lib on trusty:

objdump -tTrR /usr/lib/libatlas.so.3gf | grep ATL_cpttrsm

and on precise:

[0]root@ex-kmos:~# lsb_release -a; objdump -tTrR /usr/lib/libatlas.so.3gf | grep ATL_cpttrsm
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.04.4 LTS
Release: 12.04
Codename: precise
00000000002eaf40 g DF .text 0000000000000197 Base ATL_cpttrsm
00000000002eacc0 g DF .text 0000000000000279 Base ATL_cpttrsm_nt
00000000002eac50 g DF .text 0000000000000068 Base ATL_cpttrsm0
000000000052aca0 R_X86_64_GLOB_DAT ATL_cpttrsm0
000000000052d530 R_X86_64_JUMP_SLOT ATL_cpttrsm_nt

So the ABI has changed (a symbol removed) but the SONAME of the lib the same.
That's AFAIU a bug. At least it broke programs here.

Achim

ProblemType: Bug
DistroRelease: Ubuntu 14.04
Package: libatlas3gf-base 3.10.1-4
ProcVersionSignature: Ubuntu 3.13.0-30.54-generic 3.13.11.2
Uname: Linux 3.13.0-30-generic x86_64
NonfreeKernelModules: openafs
ApportVersion: 2.14.1-0ubuntu3.2
Architecture: amd64
Date: Tue Jul 1 10:48:57 2014
PackageArchitecture: all
ProcEnviron:
 TERM=screen
 PATH=(custom, no user)
 XDG_RUNTIME_DIR=<set>
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: atlas
UpgradeStatus: Upgraded to trusty on 2014-06-30 (0 days ago)

Achim Bohnet (allee) wrote :
Launchpad Janitor (janitor) wrote :

Status changed to 'Confirmed' because the bug affects multiple users.

Changed in atlas (Ubuntu):
status: New → Confirmed
Frau Tukka (frautukka) wrote :

I get the same problem when I try to setup our python programs:
python setup.py install --record files.txt
Traceback (most recent call last):
  File "setup.py", line 18, in <module>
    import numpy
  File "/usr/local/lib/python2.7/dist-packages/numpy/__init__.py", line 153, in <module>
    from . import add_newdocs
  File "/usr/local/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/usr/local/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/usr/local/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 19, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/usr/local/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 50, in <module>
    from .linalg import *
  File "/usr/local/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: /usr/local/lib/python2.7/dist-packages/numpy/linalg/lapack_lite.so: undefined symbol: ATL_cpttrsm

Frau Tukka (frautukka) wrote :

Upgrading numpy via
# pip install --upgrade numpy
solved the issue for me.

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