Dear Developers,
The issue was resolved by writing a wrapper script that passed a
variable with other name and redefined it to LD_LIBRARY_PATH later.
But just FYI I give some comments/answers below. Once again, thanks
for support.
Cheers,
Igor.
>> After a recent update of the gridengine at our cluster, the
>> LD_LIBRARY_PATH variable cannot be passed to individual nodes ("due to
>> some security reasons"). Hence fipy doesn't know about location of
>> trilinos libraries and instead of running in parallel it runs in one
>> thread but at the number of nodes specified to mpirun. I patched
>> python to contain RUNPATH pointing to trilinos libs using
>> http://nixos.org/patchelf.html but it gave no result.
>
>
> It is obviously finding some trilinos libraries from somewhere otherwise it
> wouldn't be running at all (unless it is using a different solver). What is
> the path to the libraries that it is currently finding and what is the path
> to the libraries that you want to use?
The simple test script (testmpi.py) didn't use any solvers at all.
from fipy.tools import parallel
if parallel.procID == 0:
print "I'm running on", parallel.Nproc, "processors."
If I did
mpirun -np 4 python testmpi.py
and LD_LIBRARY_PATH was empty
it returned 4 times:
"I'm running on 1 processors"
if LD_LIBRARY_PATH=/opt/trilinos/lib
it returned
I'm running on 4 preocessors
>> By which executable/module is LD_LIBRARY_PATH read?
>
>
> In general, trilinos needs it to be set. I am not sure whether that is
> always true or when you have it installed in non-standard locations. Have
> you installed it in a standard place? If you are on a cluster then maybe
> not.
it is installed in non-default location
>> Is there a way I can explicitly set the locations of all the libraries
>> fipy requires?
>
>
> Where do you set the LD_LIBRARY_PATH currently?
>
>>
>> Can I force fipy to use python RPATH?
>
>
> Never heard of RPATH.
http://en.wikipedia.org/wiki/Rpath
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