[MINC-users] Running MINC tools from the www user

[Burt Crépeault]

Hi Alex,

I went ahead and tried your suggestions, unfortunately I'm still
stuck. The /tmp folder still has plenty of space and it is writable by
anyone. I still get the following error from running the process:


   [7]:     [_www at pita.crulrg.local:/Library/WebServer/Documents/]
[2008-04-16 12:32:14] running:
   [8]:       /usr/local/minc2/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.1 0.01 -iterations 100
                -stop 0.001 -shrink 3 -auto_mask -nonotify -b_spline 1
-distance 100 -quiet -execute

                -clobber -nokeeptmp -tmpdir /tmp/nu_correct_1361/

'/Library/MEDICS/data/images/10188/bl/MR.T1.MP-RAGE/1004/Library.MEDICS.data.images.10188.bl.MR.T1.MP-RAGE.1004.1.10004.[mnc.d2m].Br.12_p2.mnc'


'/Library/MEDICS/data/images/10188/bl/MR.T1.MP-RAGE/1007/Library.MEDICS.data.images.10188.bl.MR.T1.MP-RAGE.1007.1.10007.[mnc.d2m+mnc.nuc].Br.22_p2.imp'
   [9]:
   [10]:     Assertion failed at line 742 in file templates/CachedArray.cc

   [11]:     nu_estimate_np_and_em: crashed while running volume_stats
(termination status=256)
   [12]:     nu_correct: crashed while running nu_estimate_np_and_em
(termination status=256)

I've listed my environment variables below:


       [TMPDIR] => /tmp
       [FOO] => /bar
       [PERL5LIB] =>
:/usr/local/minc2/lib:/Library/Perl/5.8.8:/usr/local/minc2/lib/perl5/site_perl/:/Users/burt/lib/perl
       [LD_LIBRARY_PATH] => :/Applications/MATLAB72/dip/Darwin/lib

       [PATH] =>
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/minc2/bin:/opt/local/bin:/opt/local/sbin:/bin:/usr/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/local/bin:/sbin:/usr/sbin:/usr/local/mysql/bin
       [PWD] => /Library/WebServer/Documents

       [SHLVL] => 1
       [DYLD_LIBRARY_PATH] => :/usr/local/minc2/external-libs

I tried the command at line [8] of my log directly in a terminal and
everything runs fine. There is a /tmp/nu_correct_xxxx dir that is
being created. However, that directory does not appear when the
process is launched from the web app, therefore your assumption that
CachedArray.cc is unable to create the temp file (or more likely dir)
appears to be correct.


This is where I'm stuck at the moment, any other ideas?


-- 
Burt Crépeault
Research Assistant
Centre de Recherche de l'Université Laval - Robert-Giffard
418-663-5741, ext 6844