Re: Installing and running on Rocks cluster

From: Jeudy Blanco <jeudyb_at_gmail.com>
Date: Tue, 17 Jun 2014 22:47:02 -0600

I was able to solve my problem. I post the solution in case it helps others
in the future.

In Rocks, you can not run complex programs such as Gadget directly with
mpirun. You need to submit it using qsub, the queue manager. Instructions
for this can be found in Rocks documentation. After this, runs beautifully.

Regards


On Fri, Jun 13, 2014 at 10:39 PM, Jeudy Blanco <jeudyb_at_gmail.com> wrote:

> Hi,
>
> My name is Jeudy Blanco, researcher from Universidad de Costa Rica.
>
> I just finished installing a small cluster using Rocks (5.5) and installed
> Gadget. If I run the galaxy sample only in the master node, it runs fine,
> but if I try to run it using more machines in the cluster, it get stuck at
>
> "Running on 20 processors"
>
> No output, no cpu.txt or other files created. No error files. Very strange.
>
> This is the command I'm using to run the example:
>
> mpirun -np 20 -machinefile machines ./Gadget2 galaxy.param
>
> I know MPI (openmpi) in the cluster works because if I run a simple sample
> I can see response from all the nodes in the cluster.
>
> If anybody has experience in installing and running Gadget on a Rocks
> cluster, or if this has been answered in the past, please ping me or point
> me to the right direction.
>
> Thanks in advance.
>
Received on 2014-06-18 06:47:04