[Networkit] Use of NetworKit in a Torque / PBS scheduling environment

Christian Staudt christian.staudt at kit.edu
Thu Dec 4 00:03:26 CET 2014


Hi Steve,

if I get your question right, you are asking how to run NetworKit on a cluster which you can only access via a job scheduler. Keep in mind that NetworKit uses shared-memory parallelism, so you would be restricted to a single node of the cluster (unlike the MPI program you gave as an example).

If the job scheduler is similar to the one I have used, it accepts arbitrary shell commands. NetworKit is a Python module that works with any Python interpreter. So if the system has Python installed, just submit a call to a Python script. If you have to do without Python, an executable written in C++ and linked against the NetworKit core library is also an option.

Does this work for you?

Best,
Chris





Am 03.12.2014 um 23:00 schrieb Steve Koch <stevekochscience at gmail.com>:

> I'm wondering if there are examples or tutorials for using NewtorKit on a cluster that uses a Torque / PBS scheduling environment? I am new to NetworKit and am helping a user (who is new to both NetworKit and HPC) potentially use the platform within our University's HPC center. I can see from the examples how to use the parallelized code using ipython on a multicore machine. However, I'm not sure whether the admins at the HPC center will allow installation / use of ipython. I'm wondering if there are any examples out there where people are using NetworKit and launching jobs on a cluster using a PBS script?
> 
> Apologies if my question isn't too clear. I don't have a lot of experience w/ intrinsically parallel code. I am slightly familiar with quantum chemistry and molecular dynamics codes that are run from a bash command within the PBS script with a line like:
> 
> mpirun -np $ncores -machinefile $PBS_NODEFILE ParallelCode.x
> 
> Thank you for any help!
> 
> --Steve Koch
> University of New Mexico
> <ATT00001.c>

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