Using PVM on the patas cluster


While the version of Condor we have installed does not currently support scheduling PVM applications, running PVM in parallel with Condor works fine. It does, however, require a small amount of setup on your account so PVM can run software on the compute nodes without asking for your password.

  1. Log into and run ssh-keygen to create an SSH key for yourself. Accept the default file location, and use a blank passphrase.
  2. Add the new key into your authorized_keys file, and restrict the file permissions:
    1. cat ~/.ssh/ >>~/.ssh/authorized_keys
    2. chmod 600 ~/.ssh/authorized_keys
  3. Add the host keys for the nodes to your known_hosts file: cat /opt/etc/ssh-host-keys >>~/.ssh/known_hosts


Try running pvm and adding a few of the compute nodes as hosts. You should get something like this:

user@patas:~$ pvm
pvm> add patas-n1
add patas-n1
1 successful
                    HOST     DTID
                 patas-n1    80000
pvm> add patas-n2
add patas-n2
1 successful
                    HOST     DTID
                 patas-n2    c0000
pvm> add patas-n3
add patas-n3
1 successful
                    HOST     DTID
                 patas-n3   100000

Usage notes

By default, PVM is set up to use the system's PVM installation, in /usr/share/pvm3. If the program you're running includes its own PVM implementation, you may need to change the settings of the PVM_ROOT and PVM_ARCH environment variables.

You can always find out what nodes are available by running condor_status and looking at the left column. Only the part of the hostname between the @ sign and the first dot is needed by PVM (e.g., "patas-n1").

If you are having trouble adding a node, check that the troublesome nodes don't have pvmd running already. Check the /tmp/ directory on the node for files like .pvm.socket.username, where "username" is your user name. You may have to remove this file to force pvmd to halt on this machine.

Usage with Logon software

The Logon tree distributes its own version of pvm and pvmd3, which reside in logon/lingo/lkb/bin/linux.x86.64/ (or ...linux.x86.32 if you are running a 32bit machine). As noted above, you will need to set your PVM_ROOT variable to this path. Logon's version of pvm does not seem to work well with short hostnames (eg. patas-n1) and so you should expand these (eg. These expansions may have to take place in your ~/.ssh/known_hosts and ~/.pvm_hosts files.

Start pvmd like this (assumes you have the Logon tree in your home directory):

~/logon/lingo/lkb/bin/linux.x86.64/pvmd3 ~/.pvm_hosts

-- Main.goodmami - 13 Apr 2009

This topic: Main > PVMOnPatas
Topic revision: r2 - 2009-04-13 - 08:38:53 - goodmami
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