[Debichem-devel] Bug#765794: Race condition when running scripts in "stdin" mode

[Vincent Fourmond]

Package: pymol
Version: 1.7.2.1-1
Severity: normal

  Hello,

  I've been trying to make a small script that drives pymol completely
uninteractively using a pymol -c -p command.

  Unfortunately, pymol is polling from stdin DURING the reading of
scripts from within a @ command, which leads to painful race
conditions, as I'm wrapping the call to scripts to a cd in/cd out
command.

  For instance, I'm running 

cd /home/vincent/Recherche/Proteines/CODH
@ CODH-clusters.pml
cd /home/vincent/tmp

The CODH-clusters.pml runs a series of pymol scripts by itself. 
 
  As you can see below, the cd /home/vincent/tmp comes between

select prot, ((all) and (not ((fes) or (nifes))))

and

select s, /////S3

  Both of these commands are within the
"CODH-Chydrogenoformans-definitions.pml" script. This is really
painful, since one cannot assume that because one sends commands
sequentially, the previous one is finished before the next one starts.

============================================================
PyMOL>cd /home/vincent/Recherche/Proteines/CODH
 cd: now in /home/vincent/Recherche/Proteines/CODH
PyMOL>@ CODH-clusters.pml
PyMOL>@ CODH-vue-generale.pml
PyMOL>@ CODH-Chydrogenoformans-definitions.pml
PyMOL>load ../PDB/1SU8.pdb.gz, Ch;
[...]
PyMOL>select prot, ((all) and (not ((fes) or (nifes))))
 Selector: selection "prot" defined with 11466 atoms.
PyMOL>cd /home/vincent/tmp
PyMOL>select s, /////S3
============================================================

  I'll try to see if this can be easily fixed...

       Vincent


-- System Information:
Debian Release: jessie/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (500, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.16.3+macbook (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages pymol depends on:
ii  freeglut3                         2.8.1-2
ii  libc6                             2.19-11
ii  libfreetype6                      2.5.2-2
ii  libgcc1                           1:4.9.1-16
ii  libgl1-mesa-glx [libgl1]          10.2.8-1
ii  libglew1.10                       1.10.0-3
ii  libglu1-mesa [libglu1]            9.0.0-2
ii  libpng12-0                        1.2.50-2
ii  libstdc++6                        4.9.1-16
ii  python                            2.7.8-1
ii  python-numpy [python-numpy-abi9]  1:1.8.2-2
ii  python-pmw                        1.3.2-6
ii  python-tk                         2.7.8-2
pn  python2.7:any                     <none>

Versions of packages pymol recommends:
ii  apbs  1.4-1

pymol suggests no packages.

-- no debconf information