ADL: Running Vina on HPC Cluster

Serkan Altuntaş serkan at serkan.gen.tr
Thu Aug 9 16:06:47 PDT 2012


Hi,

As I know Vina uses a shared memory architecture and MPI is a distributed
memory architecture. If you set number of CPUs as the number of CPUs in
single node, Vina can take the advantage of those cores but other nodes
will be available to run other jobs. And you do not need to install MPI.

A node is every single *shared memory* computer with more than one CPUs
(cores) inside.

Sincerely,
Serkan Altuntaş

2012/8/9 Andrew Kalenkiewicz <ajkal at umich.edu>

> Dear AutoDock group,
>
> I have a quick question about Autodock Vina.
>
> To run vina multi-threaded across different nodes on a HPC cluster, do
> you require an MPI enabled version, or will Vina take the number of
> processors from a PBS submission script?
>
> Sincerely,
>
> Andrew Kalenkiewicz
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