octave segmentation fault with libopenblas-base

Bug #1181234 reported by Federico Carotenuto
10
This bug affects 2 people
Affects Status Importance Assigned to Milestone
openblas (Ubuntu)
Expired
Undecided
Unassigned

Bug Description

The installation of the libopenblas-base package (version 0.1.1-6) causes octave 3.6.2 to produce a "segmentation fault" at launch-time and installation-time (if the installation is attempted with the libopenblas-base package installed) on Ubuntu 12.10 x64.

The bug has been replicated to pinpoint its cause: removing libopenblas and installing octave produced a functioning version of the octave software. Re-installing the libopenblas-base package afterwards immediatly caused the segmentation fault at octave's launch-time.

Revision history for this message
Julian Taylor (jtaylor) wrote :

what is the cpu you are using?
can you provide a backtrace and disassembly with gdb?

can you try the openblas package from ubuntu 13.04 raring. openblas 0.1.1 has many issues.

Revision history for this message
Federico Carotenuto (pooka-85) wrote :

The CPU I'm using is an Intel Core i7-3770 @3.4 GHz with 8 cores.

I'm sorry I'm not a huge linux expert and I've never used gdb: can you tell me how to do the backtrace (or point me to a good tutorial)?

Due to software compatibility I cannot update to 13.04: is there a way just to add the repo of openblas?

Thank you very much

Revision history for this message
Julian Taylor (jtaylor) wrote :

you should be able to just install the package from here:
https://launchpad.net/ubuntu/+source/openblas

dpkg -i <package-file.deb>
apt-get install -f

for the backtrace:
gdb /usr/bin/octave
set logging on
run
backtrace full
disassemble

Julian Taylor (jtaylor)
Changed in openblas (Ubuntu):
status: New → Incomplete
Revision history for this message
Federico Carotenuto (pooka-85) wrote :

Unfortunately I cannot swap the OpenBLAS libraries for the new version since the WRF-CHEM model running on the workstation depends on them.

Attached there's the gdb output

Revision history for this message
Julian Taylor (jtaylor) wrote :

you should still be able to update the library, the version in raring is compatible with the one in precise.

it seems to be related to openmp, try disabling it:
OMP_NUM_THREADS=1 octave

Revision history for this message
Federico Carotenuto (pooka-85) wrote :

I've tried setting the number of threads to 1, but installing octave generates the same error.

I've still not updated openblas, though, I'm sorry but I'm not very familiar with launchpad: I see it offers me the possibility to download a .tar.gz package, but I do not know how to point dpkg to the updated openblas deb as you suggested.

Revision history for this message
Julian Taylor (jtaylor) wrote :

click on the little arrow next to saucy or raring, under package files you get a couple deb file download links, select libopenblas-base for the right architecture. Download, then:

dpkg -i <package-file.deb>
apt-get install -f

to revert back to precise version
sudo apt-get install libopenblas-base/precise

Revision history for this message
Launchpad Janitor (janitor) wrote :

[Expired for openblas (Ubuntu) because there has been no activity for 60 days.]

Changed in openblas (Ubuntu):
status: Incomplete → Expired
Revision history for this message
xyzdragon (xyzdragon) wrote :

I have the same bug with Octave 3.8.2 and Openblas 0.2.12-1. After removing libopenblas-base octave works again. But Openblas was installed in the first place as a dependency for Yade. See also https://savannah.gnu.org/bugs/?45651

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