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I am trying to figure out how to write a proper job file for the Sun Grid Engine so I can run a parallel computation using Mathematica on multiple nodes. Unfortunately almost all tutorials on the topic assume using MPI, which is not the case here.

In order to get this working, I need to find the answer to a few very specific questions:

  1. When I request multiple nodes, will the job file be run on all of them, or only on a single node? I need to run it only on a single node in this case, and start a single process which we can call controlling process.

  2. How can I access the names / IP addresses of all the other nodes? I think I have the answer to this one: the PE_HOSTFILE variable should point to a file that lists the names of all nodes.

  3. How can I let the controlling process start arbitrary processes at arbitrary times on any node that I can use? Should a simple ssh nodename command work for this, or would this require a password in a typical setup?

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1 Answer

up vote 5 down vote accepted
  1. The job script is run only on a single node by SGE. It is run on the first host listed in PE_HOSTFILE
  2. PE_HOSTFILEcan be parsed to get the names of all the nodes
  3. Using SSH without a passphrase internal to a cluster is a common setup, but it depends on who setup the machine you'll be using. I would ask them.

In addition, some HPC sites supply tools that might let you launch these tasks in a simpler manner. You should check with the site where you will be running.

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If ssh without a passphrase is not set up, which is the next most likely to work alternative for point 3.? –  Szabolcs Feb 12 '13 at 17:38
    
SSH without passphrase can be set up by you, actually. However, you can easily test it from your job script. Just pick off the second host from PE_HOSTFILE and try ssh $host uptime (or similar). If it doesn't work, you can setup your own passphraseless SSH. –  Bill Barth Feb 12 '13 at 17:52
    
Thanks for the advice, I can do that. –  Szabolcs Feb 12 '13 at 17:55
    
Unfortunately public key authentication seems to be disabled :-( –  Szabolcs Feb 12 '13 at 18:52
    
Did you try it within a job, or from outside? –  Bill Barth Feb 12 '13 at 19:06
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