Re: [igraph] Python-Igraph cannot find Igraph

[Tamas Nepusz]

Hi Alessandro,

> Unfortunately, in order to take advantage of the cluster I should  
> use the queue shell, and in that case I got the following error:
>
>
> ImportError: /homeb/antonucc/igraph/core.so: undefined symbol:  
> igraph_vector_destroy
>
> As I remember, this probably means that the Python interpreter is  
> not able to find igraph.
Yes, that's right, but I'm not sure how to solve it as I've never used  
Sun Grid Engine. What I'd try is the following:

1. Instead of symlinking the igraph libraries (libigraph.so and such),  
I would add the directory containing them to the LD_LIBRARY_PATH  
environment variable. For instance, in my university machine, I have a  
local lib/ subdirectory in my home containing all the libraries that I  
built from source and it is permanently added to my LD_LIBRARY_PATH in  
~/.profile as follows:

LD_LIBRARY_PATH=~/lib ; export LD_LIBRARY_PATH

(this works only if you're using bash or a bash-compatible shell)

2. When submitting the job to the grid engine, export your  
LD_LIBRARY_PATH to the exec nodes so they will also use it as a custom  
library path. I guess this can be done by qsub -v LD_LIBRARY_PATH, but  
I'm not sure. I'm shamelessly stealing the syntax from http://biowiki.org/HowToUseSunGridEngine 
.

--
Tamas