install problem on Ubuntu 12.04 LTS

Questions about BrainVisa usage and installation

Moderators: denghien, riviere

Post Reply
User avatar
rvboutin
Posts: 36
Joined: Tue Feb 09, 2010 12:53 pm

install problem on Ubuntu 12.04 LTS

Post by rvboutin »

Hi,
I got a strange problem on 1 particular PC running Ubuntu 12.04 LTS 64bit. This issue does not happen on another computer I have running this OS. I must precise that I have BrainVisa/Anatomist 4.1.1 and 4.3.0 64 bit running on that machine fine, but I need to run Anatomist 32 bit because of a memory allocation bug in Anatomist 64 bit, which does not happen in the 32 bit version.
After unpacking brainvisa 4.3.0 (or 4.2.1), if I run

Code: Select all

./brainvisa-4.3.0/bin/bv_env
I got the following output:

Code: Select all

export BRAINVISA_UNENV_DCMDICTPATH=''
export BRAINVISA_UNENV_LD_LIBRARY_PATH=''
export BRAINVISA_UNENV_PATH='/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
export BRAINVISA_UNENV_PYTHONPATH=''
unset SIGRAPH_PATH
unset ANATOMIST_PATH
unset AIMS_PATH
export BRAINVISA_SHARE='/home/inveon-users/./brainvisa-4.3.0/share'
export LC_NUMERIC='C'
export PYTHONHOME='/home/inveon-users/./brainvisa-4.3.0'
export DCMDICTPATH='/home/inveon-users/./brainvisa-4.3.0/lib/dicom.dic'
export LD_LIBRARY_PATH='/home/inveon-users/./brainvisa-4.3.0/lib'
export PATH='/home/inveon-users/./brainvisa-4.3.0/bin/real-bin:/home/inveon-users/./brainvisa-4.3.0/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
export PYTHONPATH='/home/inveon-users/./brainvisa-4.3.0/python:/home/inveon-users/./brainvisa-4.3.0/lib/python2.5/site-packages'
and when I try to run

Code: Select all

./brainvisa-4.3.0/bin/anatomist
I got:

Code: Select all

/home/inveon-users/brainvisa-4.3.0/bin/bv_env: cannot execute /home/inveon-users/brainvisa-4.3.0/bin/real-bin/anatomist: No such file or directory
The rights are OK for the brainvisa folder and subfolder. The executable "anatomist" is in the real-bin folder... so I really don't understand... What make me angry :evil: is that I think I had the issue once before and was able to solve it... but I cannot remember how!!! How stupid that is :?
Any idea anyone?
Thanks,
Rv
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: install problem on Ubuntu 12.04 LTS

Post by riviere »

Hi Rv,

I guess you don't have 32 bit executables support installed on your system. Ubuntu does not install it by default any longer.
You can probably install basic 32 bit support (install at least lib32gcc1), but in recent distribs (I have Ubuntu 13.04 currently on my machine, and cannot check for 12.04 right now), it seems that not all libs are present in 32 bit version on Ubuntu repositories. I guess you may have difficulties for OpenGL libs for instance.

Which allocation bug are you talking about in Anatomist 64 bit ? Did you report it ? (I don't remember it but my memory is sometimes... a bit corrupted...)
We actually fixed a few issues about large volumes (needing 64 bit addressing) in the last months (in Anatomist, and in some IO file formats support) but using such large data need 64 bit anyway, so using a 32 bit version will probably not help.

Denis
User avatar
rvboutin
Posts: 36
Joined: Tue Feb 09, 2010 12:53 pm

Re: install problem on Ubuntu 12.04 LTS

Post by rvboutin »

Hi Denis,
Thanks for your reply. I have not reported the bug on the 64bit version but I will.
To answer your question, as a matter of fact I have 2 other computers running Ubuntu 12.04LTS 64 bit, one with the latest version running the latest kernel 3.5 and one a bit older running the 3.2 kernel. On both of them, I am able to run Anatomist 32bit without any problem, hence my incomprehension when it did not work on the third computer. I thought that the 32 bit compatibility issues were taken care of by the ia32 multi arch that comes with all version since Ubuntu 11.10?
The PC I am on at the moment, which I can run the 32bit version of anatomist on, has the ia32-libs and ia32-libs-multiarch:i386 installed, so I need to check on the computer that has a problem.
Thanks for pointing me in that direction. As this is quite urgent because of a Master student project that need finishing, and because fixing the bug in the 64bit version might take you a while, I'll give him a computer not bugging and still try to install a working 32bit version.
I'll however open a new thread to specifically report the bug in the 64bit version.
Cheers,
Rv
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
User avatar
rvboutin
Posts: 36
Joined: Tue Feb 09, 2010 12:53 pm

Re: install problem on Ubuntu 12.04 LTS

Post by rvboutin »

Follow up on that thread... I should have done it earlier.
The problem was indeed that all the ia32-libs and ia32-libs-multiarch:i386 need to be installed via Synaptic to have Anatomist 32bit working on a 64bit system.
Problem solved.
Rv
__________________________________
Hervé BOUTIN, PhD
Senior Research Scientist
University of Manchester
Faculty of Biology, Medicine and Health
email: herve.boutin@manchester.ac.uk
__________________________________
Post Reply