[Beowulf] [EXTERNAL] Re: perl with OpenMPI gotcha?

[Lux, Jim (US 7140)]

If Joe has interpreted your need correctly, I’ll second the suggestion of pdsh – it’s simple, it works pretty well, it’s “transport” independent (I use it to manage a cluster of beagleboards over WiFi).  Typically I wind up with a shell script on the head node and some shell scripts on the worker nodes, and the head node script fires pdsh, which starts the worker bee scripts.



From: Beowulf <beowulf-bounces at beowulf.org> on behalf of Joe Landman <joe.landman at gmail.com>
Date: Friday, November 20, 2020 at 2:03 PM
To: "beowulf at beowulf.org" <beowulf at beowulf.org>
Subject: [EXTERNAL] Re: [Beowulf] perl with OpenMPI gotcha?



On 11/20/20 4:43 PM, David Mathog wrote:

[...]

Also, searching turned up very little information on using MPI with perl.
(Lots on using MPI with other languages of course.)
The Parallel::MPI::Simple module is itself almost a decade old.
We have a batch manager but I would prefer not to use it in this case.
Is there some library/method other than MPI which people typically use these days for this sort of compute cluster process control with Perl from the head node?



I can't say I've ever used Perl and MPI.  I suppose it is doable, but if you were doing it, I'd recommend encapsulating it with FFI::Platypus (https://metacpan.org/pod/FFI::Platypus<https://urldefense.us/v3/__https:/metacpan.org/pod/FFI::Platypus__;!!PvBDto6Hs4WbVuu7!afgHh9iIgQExswMZG_DhAJu2PzyrdLg5Tc8j9Dnc3LdGZ9ujD927YjcLBxKWv7faIxt-IWQ$>).

This however, doesn't seem tp be your problem per se.  Your problem sounds like "how do I launch a script on N compute nodes at once, and wait for it to complete".

If I have that correct, then you want to learn about pdsh (https://github.com/chaos/pdsh<https://urldefense.us/v3/__https:/github.com/chaos/pdsh__;!!PvBDto6Hs4WbVuu7!afgHh9iIgQExswMZG_DhAJu2PzyrdLg5Tc8j9Dnc3LdGZ9ujD927YjcLBxKWv7fa6GA3YiQ$> and info here: https://www.rittmanmead.com/blog/2014/12/linux-cluster-sysadmin-parallel-command-execution-with-pdsh/<https://urldefense.us/v3/__https:/www.rittmanmead.com/blog/2014/12/linux-cluster-sysadmin-parallel-command-execution-with-pdsh/__;!!PvBDto6Hs4WbVuu7!afgHh9iIgQExswMZG_DhAJu2PzyrdLg5Tc8j9Dnc3LdGZ9ujD927YjcLBxKWv7fatAD11t0$> ).

I write most of my admin scripts in perl, and you can use pdsh as a function within them.

However ...

MCE::Loop is your friend.

Combine that with something like this:

    $mounts=`ssh -o ConnectTimeout=20 $node grep o2ib /proc/mounts`;

and you can get pdsh-like control directly in Perl without invoking pdsh.

The general template looks like this:

#!/usr/bin/env perl

use strict;
use MCE::Loop;

MCE::Loop->init(
   max_workers => 25, chunk_size => 1
);

my $nfile=shift;

# grab file contents into @nodes array
my @nodes;
chomp(@nodes = split(/\n/,`cat $nfile`));

# looping over nodes, max_workers at a time
mce_loop {
   my ($mce, $chunk_ref, $chunk_id) = @_;
   # do stuff to node $_
} @nodes;



This will run 25 copies (max_workers) of the loop body over the @nodes array.  Incorporate the ssh bit above in the #do stuff area, and you get basically what I think you are asking for.

FWIW, I've been using this pattern for a few years, most recently on large supers over the past few months.





Thanks,

David Mathog



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