Day 3

Day3
03/12/2009 16:48

Hi.

There was a problem with mpi4py on Jupiter (not on my laptop though) that was bothering me for quite some time. When trying to do "from mpi4py import MPI" from Python prompt, the system gave:

/topographica/bin/python: symbol lookup error: topographica/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int

(sometimes it was complaining about other .so files). Chris (a PhD student that helps me with this project) has found a solution for that: before executing the topographica startup script cast a bash voodoo spell

export LD_PRELOAD=topographica/lib/libmpi.so

(solution found at http://code.google.com/p/petsc4py/issues/detail?id=14)


Today I spent quite a few hours trying to add this export statement to topographica's startup script:

#!/disk/scratch/fast/s********/topographica/bin/python
# Startup script for Topographica

import topo

topo.release='0.9.6'
topo.version='10827'

# Process the command-line arguments
from sys import argv
from topo.misc.commandline import process_argv
process_argv(argv[1:])

and failed miserably. Doing

import os;
os.setenv["LD_PRELOAD"] = "topographica/lib/libmpi.so"

(or environ instead of setenv) didn't give any results. I'll leave that for now, can't spend any more time on this issue.