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

Steve Koch stevekochscience at gmail.com
Thu Dec 4 00:32:03 CET 2014


Thank you Chris! This is exactly what I needed to learn. I hadn't realized
that it required shared-memory parallelism. Our center does have a
shared-memory
machine <http://www.carc.unm.edu/systems-software/systems.html>, 1 node, 64
cores (32+32), 256 GB shared memory. The center has an excellent
applications team and the NetworKit has excellent documentation, so I'm
guessing they'll be able to get it up and running for us.

Thank you again!
--Steve

On Wed, Dec 3, 2014 at 4:03 PM, Christian Staudt <christian.staudt at kit.edu>
wrote:

> 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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