Topographica on Hector

Today Adrian helped me out with the libgfortran bug: the library I was looking for was inside one of the subdirectories of gcc, namely /opt/gcc/4.5.2/snos/lib. I have no clue why find /opt/ -name 'libgfortran.so.3' wasn't picking it up.


The next issue - topographica not being able to find it's source code (the topo module). This was fixed by adding  the following line into my .pbs script:

export PYTHONPATH=$PBS_O_WORKDIR/topo:$PYTHONPATH

The next issue was matplotlib unable to create .matplotlib directory anywhere:

RuntimeError: Failed to create /home/d04/d04/s0676011/.matplotlib; 
consider setting MPLCONFIGDIR to a writable directory for matplotlib configuration data

I tried $HOME, $PBS_O_WORKDIR, work and topographica directories and even ./  . Nothing helped, I'm still not sure why. Neither did any solutions I found on the web. What fixed that problem was tracing the import and adding exception to the file that was importing matplotlib (topo/misc/commandline.py):

try:
    # Import matplotlib, if available, and use a non-GUI backend by default
    import matplotlib
    matplotlib_imported=True
    from matplotlib import rcParams
    rcParams['backend']='Agg'
except ImportError:
    print "Warning: Could not import matplotlib; pylab plots will not work."
except RuntimeError as e: #KKALERT: added this to be able to run on hector                   
    print "Warning: pylab plots will not work:",e

Thing I'm stuck with at the moment:

File "/esfs2/d04/d04/s0676011/topographica/lib/python2.6/site-packages/weave/catalog.py", line 129, in create_dir os.mkdir(p) OSError: [Errno 17] File exists: '/home/d04'

Starting to think that launching Topographica on Hector is a project on it's own...