[Beowulf] Cannot use more than two nodes on cluster

Vincent Diepeveen diep at xs4all.nl
Thu Sep 20 08:00:46 PDT 2012


Hi Antti,

You describe just 1 master and 1 slave works.
Is it 1 specific slave that works and not the other slaves?

So you have machines M0, S0,S1,S2

Is only M0 + S0 working and not M0+S1 nor M0+S2 ?

What parallel shell are you using to start the jobs?
Is it the free pdsh?

What command do you issue to start the jobs?
How many processes do you start at once and are the 3 slave nodes  
having the same number of cores?

Somewhere there must have a limit set; in most environments it's  
possible to restrict users in how many processes
they're allowed to execute simultaneously.

Maybe the default of the environment you use has this limit set to 2  
nodes.

What network is your cluster using?

On Sep 20, 2012, at 4:37 PM, Antti Korhonen wrote:

> I tested ssh with all combinations and that part is working as  
> designed.
>
> I can start job manually on any single node.
> I can start jobs on any two  nodes , as long as other node is master.
> All other combinations hang  and jobs do not start.
>
> I read through few install guides and did not find any steps I missed.
> I am using Ubuntu 12.04, in case that makes any difference.
>
>   Antti
>
> -----Original Message-----
> From: beowulf-bounces at beowulf.org [mailto:beowulf- 
> bounces at beowulf.org] On Behalf Of Jörg Saßmannshausen
> Sent: Thursday, September 20, 2012 1:42 AM
> To: beowulf at beowulf.org
> Subject: Re: [Beowulf] Cannot use more than two nodes on cluster
>
> Hi all,
>
> have you tried the following: ssh master -> node1 -> node2, i.e.  
> ssh from the master to node1 and from there to node2?
> You do not have a situation where the remote host-key is not in the  
> database and hence you get asked about adding that key to the local  
> database?
>
> If that is working with all permutations, another possibility is  
> that your host list is somehow messed up when you are submitting  
> parallel jobs. Can you start the jobs manually by providing a host  
> list to the MPI program you are using? Does that work or do you  
> have problems here as well?
>
> My two pennies
>
> Jörg
>
>
> On Thursday 20 September 2012 07:40:56 Antti Korhonen wrote:
>> Passwordless SSH works between all nodes.
>> Firewalls are disabled.
>>
>>
>> From: greg at r-hpc.com [mailto:greg at r-hpc.com] On Behalf Of Greg Keller
>> Sent: Wednesday, September 19, 2012 8:43 PM
>> To: beowulf at beowulf.org; Antti Korhonen
>> Subject: Re: [Beowulf] Cannot use more than two nodes on cluster
>>
>> I am going to bet $0.25 that SSH or TCP/IP is configured to allow the
>> master to get to the nodes without a password, but not from one
>> Compute to the other Compute.
>>
>> Test by sshing to Compute1, then from Compute1 to Compute2.   
>> Depending
>> on how you built the cluster, it's also possible there is iptables
>> running on the compute nodes but, my money is on the ssh keys need  
>> reconfiguring.
>> Let us know what you find.
>>
>> Cheers!
>> Greg
>>
>> Date: Wed, 19 Sep 2012 16:11:21 +0000
>> From: Antti Korhonen
>> <akorhonen at theranos.com<mailto:akorhonen at theranos.com>> Subject:
>> [Beowulf] Cannot use more than two nodes on cluster
>> To: "beowulf at beowulf.org<mailto:beowulf at beowulf.org>"
>> <beowulf at beowulf.org<mailto:beowulf at beowulf.org>> Message-ID:
>>
>> <B9D51F953BEE5C42BC2B503D288542992DD935FE at SRW004PA.theranos.local<mai 
>> l
>> to:B  
>> 9D51F953BEE5C42BC2B503D288542992DD935FE at SRW004PA.theranos.local>>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Hello
>>
>> I have a small Beowulf cluster (master and 3 slaves).
>> I can run jobs on any single nodes.
>> Running on two nodes sort of works, running jobs on master and 1  
>> slave
>> works. (all combos, master+slave1 or master+slave2 or master+slave3)
>> Running jobs on two slaves hangs.
>> Running jobs on master + any two slaves hangs.
>>
>> Would anybody have any troubleshooting tips?
>
> --
> *************************************************************
> Jörg Saßmannshausen
> University College London
> Department of Chemistry
> Gordon Street
> London
> WC1H 0AJ
>
> email: j.sassmannshausen at ucl.ac.uk
> web: http://sassy.formativ.net
>
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
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