[BioC] Bioconductor AMI Amazon EC2 help

[Dan Tenenbaum]

On Wed, Apr 20, 2011 at 1:46 PM, David Gibbs <gibbsd at ohsu.edu> wrote:
> Thanks Dan,
>
> I found my problem.  :)
>
> I was running with a security group that had no open ports *within* the group.
> I only had the SSH port open, so I could log in, and start up instances, but the instances couldn't
> communicate with each other.  A possible change to the bioconductor cloud AMI page is to
> explicitly state what the security group should look like.
>
> Thanks for your help.  I'm ready to do some computations!
>


Thanks Dave,

I'm sharing with the list in case this is helpful for anyone else.


I'll update the documentation as you suggest.
Dan



> -dave
>
>
> ________________________________________
> From: Dan Tenenbaum [dtenenba at fhcrc.org]
> Sent: Tuesday, April 19, 2011 10:00 PM
> To: David Gibbs
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] Bioconductor AMI Amazon EC2 help
>
> Hi David,
>
>
> On Tue, Apr 19, 2011 at 9:09 PM, David Gibbs <gibbsd at ohsu.edu> wrote:
>> Hi there,
>>
>> I'm a student working on a project with some Rmpi code that I would love to run on more nodes,
>> but I'm having trouble with the Bioconductor image.
>>
>> I'm following the directions for spinning up a cluster found here: http://www.bioconductor.org/help/bioconductor-cloud-ami/
>> Once I have the cluster up with 3 nodes, I run the mpiTest.R script... it gets to the spawning function, then hangs.
>> After about half an hour I killed it.  Anyone getting this to work?  Any hints?  See output below.  Thanks!
>>
>> ...
>> ...
>> Creating volume...
>> I, [2011-04-20T03:31:10.592881 #763]  INFO -- : New RightAws::Ec2 using shared connections mode
>> I, [2011-04-20T03:31:10.681741 #763]  INFO -- : Opening new HTTPS connection to ec2.amazonaws.com:443
>> warning: peer certificate won't be verified in this SSL session
>> Waiting for volume to be available...
>> .
>> Volume is available.
>> Created volume vol-d33fd5b8 in availability zone us-east-1d.
>>
>> ...
>> ...
>> # /usr/local/Rmpi/mpiutil -a xxx -s yyy -w 3 -n "my cluster" -t t1.micro -v vol-d33fd5b8
>> warning: peer certificate won't be verified in this SSL session
>> using device /dev/sdg...
>> waiting for volume to be attached....
>> .......Volume is attached.
>> waiting for workers to start...
>> .....................workers are up
>> Cluster started.
>> ...
>> ...
>> ...
>>> library(Rmpi)
>>>
>>> mpi.spawn.Rslaves(nslaves = nsl)
>> Warning: Permanently added 'worker002,10.215.117.28' (RSA) to the list of known hosts.
>> Warning: Permanently added 'worker003,10.96.55.43' (RSA) to the list of known hosts.
>> Warning: Permanently added 'worker001,10.206.198.16' (RSA) to the list of known hosts.
>> ^Cmpirun: killing job...
>>
>> --------------------------------------------------------------------------
>> mpirun was unable to cleanly terminate the daemons on the nodes shown
>> below. Additional manual cleanup may be required - please refer to
>> the "orte-clean" tool for assistance.
>> --------------------------------------------------------------------------
>> worker001 - daemon did not report back when launched
>> worker002 - daemon did not report back when launched
>> worker003 - daemon did not report back when launched
>>
>
> Sometimes it takes a few moments for the workers to be ready. Did you
> try the test script a few times?
> If it doesn't respond within a minute, try ^C and then try the test
> script again.
>
> I just tried it and it worked, but I had to try a couple of times
> before the workers were ready (didn't have to interrupt with ^C
> though). Once they were ready, I could run the test script multiple
> times.
>
> Thanks for your interest in the AMI. Let us know if you need further help.
> Dan
>
>>
>> Thanks very much!
>> David Gibbs
>> OHSU student
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>