Procheck ps seems to fail to be montaged causing cing to crash

[GoogleCodeExporter]

Perhaps this is a non-reproducable bug?

What is the expected output? What do you see instead?
===========================================================
===========================================
| CING: Common Interface for NMR structure Generation version 0.9 (r657)        
AW,JFD,GWV 
2004-2009 |
===========================================================
===========================================
User: jd              on: nmr.cmbi.umcn.nl (darwin)                     at: Wed 
Nov  4 10:33:55 2009
Enforcing a redo
Moving CCPN directory from [linkNmrStarData] to [1vnd]
==> Importing data from Ccpn project "1vnd"
Non-standard (residues and their) atoms added:
PRO : [ 77]
==> Ccpn molecule '1vnd' imported
WARNING: Lower distance bound is negative assuming CING prefers to unset lower 
bound as if 
unexisting; please check your data.
==> Ccpn project imported
-------------------------------------------------------
==> Saving <Project 1vnd>
==> Running shiftx
0.........1.........2.........
==> Calculating secondary structure by DSSP
==> Running What If checks on 2310 residues for an estimated (7 residues/s): 
330 seconds; 
please wait
0.........1.........2.........
==> Running procheck_nmr
Writing to: 1vnd.cing/Export/Aqua/1vnd.noe
Writing to: 1vnd.cing/Export/Aqua/1vnd.tor
==> Finished aqpc successfully
==> Finished procheck_nmr successfully
Running Wim Vranken's FormatConverter from script 
$CINGROOT/python/cing/Scripts/FC/convertCcpn2Nmrstar.py
==> NMR-STAR project written at /Volumes/tera4/NRG-
CING/data/vn/1vnd/1vnd.cing/1vnd/Wattos/project.str
==> Running Wattos for an estimated (5,000 atoms/s): 3465 seconds; please wait
Took number of seconds:    135.8
==> validateRestraints, output to 1vnd.cing/1vnd/Cing/restraints.txt
Skipping molecule.mergeResonances because there are no resonances
==> checkSaltbridges, output to 1vnd.cing/1vnd/Cing/saltbridges.txt
==> Disulfide analysis, output to 1vnd.cing/1vnd/Cing/disulfides.txt
Found assignments for the following spin types: {'13C': False, '15N': False}
==> summary, output to 1vnd.cing/1vnd/Cing/summary.txt
==> Generating Macros
WARNING: value < minValue (-3.06 > -3.0) got limited to bound
==> Initializing HTML objects
==> Generating CING HTML code and images.
Creating Whatif html
0..
Creating Procheck html
0.........1montage(17347) malloc: *** mmap(size=16777216) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
montage(17347) malloc: *** mmap(size=16777216) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

Original issue reported on code.google.com by jurge...@gmail.com on 6 Nov 2009 at 9:36

[GoogleCodeExporter]

Original comment by jurge...@gmail.com on 6 Nov 2009 at 9:37

• Added labels: Entry-1vnd

[GoogleCodeExporter]

Reproduced on Stella.
Seems to cause an out of memory message for montage from macports:
ImageMagick 6.5.7-0_0

This entry is unusual in that it has 151 pages in the 1vnd_11_rstraints.ps
Trying to montage that into a single png with 151 pages might just be too much.

Reducing the number of pages to 100:
/opt/local/bin/montage -limit file 2 -geometry +10+10 -density 144 
./1vnd.cing/1vnd/Procheck/1vnd_02_allramach.pdf'[0-99]' 
./1vnd.cing/1vnd/Procheck/t.png

Fixed in r665

Original comment by jurge...@gmail.com on 6 Nov 2009 at 11:53

• Changed state: Fixed