[GE users] PVM, SSh and vendor-specific host file

Bisbal, Prentice PBisbal at LexPharma.com
Tue Oct 3 17:25:41 BST 2006


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Reuti, 

Thanks for the excellent advice. I modified my startpvm.sh script, and the applications work exactly as desired. You saved me a lot of time. Now, I'm having trouble with tight PVM integration, but that's for another e-mail (which has already been posted).

Prentice


-----Original Message-----
From: Reuti [mailto:reuti at staff.uni-marburg.de]
Sent: Thu 9/28/2006 4:57 PM
To: users at gridengine.sunsource.net
Subject: Re: [GE users] PVM, SSh and vendor-specific host file
 
Hi,

Am 28.09.2006 um 22:00 schrieb Bisbal, Prentice:

> I'm using SGE 6.0u8 with ssh, and PVM 3.4.5 with loose integration.  
> I didn't recompile my SSH with the tight-integration patch, so I'm  
> using ssh "loosely integrated"
>
> PVM+SGE works fine with the sample applications that come with the  
> PVM distribution (helloh, timings, for example). I'm having trouble  
> getting a commercial PVM application to work. The application  
> expects to have the hostfile specified to it as a commandline  
> argument:
>
> foo -pvmconf pvmconfigfile
>
> To make matters worse, pvmconfigfile has a non-standard syntax of  
> the form:
>
> host <hostname> <# processors to use>
>
> So if I have hostA and hostB and I want to use 2 processors on  
> each, the file would look like this:
>
> host hostA 2
> host hostB 2
>
> I have 3 questions:
>
> 1) Is it possible to reference the pvm pe_hostfile from within my  
> job script to create a new file with the desired format. For  
> example, can I do something like
>
> for host in `cat $pe_hostfile`; do
>         echo "host $host 2" >> pvmconfigfile
> done
>
> foo -pvmconf pvmconfigfile
>
> in my submit script? If not, how else can I get this too work? If I  
> omit the -pvmconf switch, the application runs in single-processor  
> mode.
yes, you can do this to ensure the correct number of processes  
started on each node. But the pseudo variable $pe_hostfile is only  
known as an argument to start_proc_args. You can use either  
$PE_HOSTFILE in the jobscript (with uppercase), or prepare the custom  
pvmconfigfile in the startpvm.sh, which would be the best place IMO  
and hidden to the user. You could do it like it's done for the MPI  
integration, i.e. write the modified file to $TMPDIR/machines and use  
it in your jobscript:

foo -pvmconf $TMPDIR/machines
>
>
> 2) Will specifying the hosts in a config file like this break the  
> interactions between SGE and PVM?
No, in fact your application is behaving in a nice way, as it will  
supersede the PVM built-in round-robin for the task distribution,  
which would need an even number of slots on all involved nodes.  
(Unless your application is adding the given hosts on its own and  
trying to start there the pmvds.)
> 3) Will my use of SSH interfere with PVM in anyway, especially when  
> I switch to PVM with tight-integration?
>
Yes, If you feel the need to use ssh, then you have to recompile it  
with the ssh-patch and follow the PVM Howto for tight integration.

HTH - Reuti

(For loose integration please be sure to set the PVM_VMID to allow  
more than one pvmd per node, which belong to different jobs.)

> Thanks for your help.
> -- 
> Prentice
>
>
>
> The contents of this communication, including any attachments, may  
> be confidential, privileged or otherwise protected from disclosure.  
> They are intended solely for the use of the individual or entity to  
> whom they are addressed. If you are not the intended recipient,  
> please do not read, copy, use or disclose the contents of this  
> communication. Please notify the sender immediately and delete the  
> communication in its entirety.
>

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