[MINC-users] minc tools crash in matlab
Pierre Bellec
pbellec at bic.mni.mcgill.ca
Wed Feb 24 08:46:59 EST 2010
Hi everyone,
Here's an update on the crash of minc tools when used through matlab R2009b.
First, as Alex pointed out, I had an outdated version of the minc tools that
had not been cleaned up by installing the mincbundle package. After manually
deleting the minctools package, I got :
$ mincinfo -version
program: 2.0.17
libminc: 2.0.17
netcdf : "3.6.2" of Feb 8 2008 16:40:20 $
HDF5 : 1.6.5
Unfortunately, mincinfo still crashed when called through matlab.
>> system('mincinfo -help')
mincinfo: symbol lookup error: mincinfo: undefined symbol: ncopts
Claude found out what the problem is. The mincbundle package has been
compiled dynamically and relies on the NETCDF libraries
$ ldd /usr/local/bic/bin/mincinfo
linux-gate.so.1 => (0xb7ee8000)
libhdf5-1.6.5.so.0 => /usr/lib/libhdf5-1.6.5.so.0 (0xb7daa000)
libpthread.so.0 => /lib/tls/i686/cmov/libpthread.
so.0 (0xb7d92000)
libz.so.1 => /usr/lib/libz.so.1 (0xb7d7c000)
*libnetcdf.so.4 => /usr/lib/libnetcdf.so.4 (0xb7d4a000)*
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7d25000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7bd6000)
/lib/ld-linux.so.2 (0xb7ee9000)
However, matlab comes with its own NETCDF library, and puts them first in
the LD_LIBRARY_PATH.
>> system('ldd /usr/local/bic/bin/mincinfo')
linux-gate.so.1 => (0xb7f51000)
libhdf5-1.6.5.so.0 => /usr/lib/libhdf5-1.6.5.so.0 (0xb7e13000)
libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0xb7dfa000)
libz.so.1 => /usr/lib/libz.so.1 (0xb7de5000)
*libnetcdf.so.4 => /usr/local/matlabR2009b/bin/**glnx86/libnetcdf.so.4
(0xb7da9000)*
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7d84000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7c35000)
/lib/ld-linux.so.2 (0xb7f52000)
There is obviously an incompatibility between the version of NETCDF that's
bundled with matlab and the one assumed by mincbundle. The mincbundle
package may be perfectly correct, but in any case the matlab installer is
just an archive and does not check on compatibility or whatever ... it just
crashes my minc tools ! Now if I change the environment variables in the
matlab call I can force mincinfo to use the right libraries :
>> system('export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH; mincinfo')
Usage: mincinfo [<options>] <mincfile> [<mincfile> ...]
mincinfo -help
Replacing all system calls to MINC tool in NIAK by this kind of hack is
obviously not an option. As matlab does reinitialize the environment
variables at each system call, I don't see how to apply that change once and
for all to any system call. In other words, the following strategy won't
work :
>> system('export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH;');
>> system('mincinfo -help')
mincinfo: symbol lookup error: mincinfo: undefined symbol: ncopts
Changing the .bashrc won't work as well (because matlab forces its library
to be first). The only practical solution I have at this stage is to keep
using a static compilation of the minc tools. This will work for the time
being because I have access to the CIVET quarantine but it won't apply to a
random user. Please let me know if one of you guys can think of a better
solution for the future.
Cheers,
Pierre
Date: Sun, 21 Feb 2010 01:00:23 -0500
> From: Alex Zijdenbos <alex at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] minc tools crash in matlab
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> <e758a6651002202200g2c41a678g61b12af585490f23 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Pierre,
>
> As far as I know, 'mincbundle' for Hardy contains (at least) 2.0.17,
> and installs in /usr/local/bic, not /usr as your error message
> suggests. I suspect you may have also installed the minc-tools package
> which lives in the Hardy repositories, but which is rather
> outdated/obsolete. See what happens if you run 'apt-get remove
> libminc2-1'.
>
> -- Alex
>
> On Sat, Feb 20, 2010 at 5:59 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>
> wrote:
> > Pierre,
> >
> > I don't know how this mincbundle was created, but it looks
> > like it's looking for dynamic libraries (.so). Add the path
> > of libminc2.so.1 (should be somewhere in your mincbundle)
> > to LD_LIBRARY_PATH environment variable.
> >
> > Also, this mincbundle is old. minc 2.0.14. This will not
> > work well with your fmri studies.
> >
> > Claude
> - Afficher le texte des messages précédents -
>
> >
> >
> >> I just installed the "mincbundle" package on my laptop (with ubuntu
> hardy).
> >> The installation went smoothly and everything I tried so far in the
> shell
> >> worked just fine. Unfortunately, when I start Matlab (7.9.0, R2009b) and
> try
> >> to use the minc tools via system calls I get an error :
> >>
> >> >> ! mincinfo anat_subject1.mnc.gz
> >> mincinfo: symbol lookup error: /usr/lib/libminc2.so.1: undefined symbol:
> >> ncerr
> >>
> >> In a shell, the "mincinfo -version" gives :
> >>
> >> program: 2.0.14
> >> libminc: 2.0.14
> >> netcdf : "3.6.2" of Feb ?8 2008 16:40:20 $
> >> HDF5 ? : 1.6.5
> >>
> >> >From Octave everything works fine. If I source the CIVET quarantine
> >> "Feb-14-2008", I don't get any error in matlab.
> >>
> >> Any thoughts about how to fix that ?
> >>
> >> Pierre
> >>
> >> --
> >> Pierre Bellec
> >> Post-doctoral fellow
> >> McConnel Brain Imaging Center, Webster 2B
> >> Montreal Neurological Institute
> >> 3801 University Street
> >> Montreal, Quebec, Canada H3A 2B4
> >> http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
> >> tel: ? ? ? (001)(514) 398 5220
> >> fax: ? ? ?(001)(514) 398 8948
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
>
>
--
Pierre Bellec
Post-doctoral fellow
McConnel Brain Imaging Center, Webster 2B
Montreal Neurological Institute
3801 University Street
Montreal, Quebec, Canada H3A 2B4
http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
tel: (001)(514) 398 5220
fax: (001)(514) 398 8948
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