On 03/03/2014 04:36 PM, Ron Palmer wrote:

Thanks Reuti for your comments. I will peruse that FAQ detail.

I just thought of the fact that each of these rack computers have 4
ethernet sockets, eth0 - eth3... I could connect the cluster on a
separate ethernet sockets via an extra switch not connected to the
internet or any other computers, and accept all communication among
them, and keep iptables up on the ethx connected to the outside world. I
guess I would have to set up routing tables or something. Ah, more
reading :-)

Thanks for your help.
Ron

Hi Ron

If those extra interfaces are not in use,
and if you have a spare switch,
you can setup a separate private subnet exclusively for MPI.
You need to configure the interfaces consistently (IP, subnet mask,
perhaps a gateway). Configuring them statically is easy:

https://access.redhat.com/site/documentation//en-US/Red_Hat_Enterprise_Linux/6/html-single/Deployment_Guide/index.html#s2-networkscripts-interfaces-eth0

Use a subnet that doesn't intersect the existent/original IP range.

http://en.wikipedia.org/wiki/Private_network

You could also create host names associated to those IPs (say
node01, node02, node02), resolve them via /etc/hosts on each computer,
set passwordless ssh across these newly named "hosts".
This may simpler/safer than messing with the iptables.

[Actually, the IP addresses you showed 192.168.X.Y, sound as a private
subnet already, not Internet, but that may be the subnet for your
organization/school/department already. So, you may set up a different
one on these three computers for MPI and very-local access.]

OpenMPI allows you to choose the interface that it will use,
so you can direct it to your very-local subnet:

http://www.open-mpi.org/faq/?category=tcp#tcp-selection

I hope this helps,
Gus

On 4/03/2014 00:13, Reuti wrote:

Am 03.03.2014 um 01:34 schrieb Ron Palmer:

Gus,
I have just replied with the details of the success, but I will
clarify your questions here, if it helps next time.

Re the actual application to be run, 'inversion', I have only
received binaries. I used to run them on gainsborough (without mpi)
and that worked fine.

Home directories are not nfs shared, they are individual and
separate, only the name is repeated.

I had tried password free ssh in all directions and permutations.

I had iptables down on sargeant and up on the other two.

Yes, I installed the gcc-gfortran.x86_64 AFTER I took those
screnshots, and the post install output was identical to the top one
(sargeant).

I am unsure about cpi and fortran...

Stuff remaining to get sorted out:
1. Get that hyperthreading set up - what is your suggestions? Disable
and let mpi manage the cores?

It depends on your applications, whether you can make use of it. Test
it with HT switched off, switched on and increase the number of
processes, until you see that any process is no longer running at 100%
and you judge that you don't tolerate this slow down.

It's not uncommon to see an improvement up to 150% with HT turned on,
but not 200% (depending on the workload).

2. run mpiexec with iptables up, need to figure out what traffic to
allow.

https://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_How_do_I_control_which_ports_MPICH_uses.3F


-- Reuti

Great many thanks to all, and Gus, Reuti and Rajeev in particular.

Cheers,
Ron

On 3/03/2014 10:09, Gustavo Correa wrote:

Hi Ron

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