StarCluster - Mailing List Archive

Re: [Starcluster] Problems after rebundling / ssh keys?

From: Robert Rentzsch <no email>
Date: Tue, 09 Feb 2010 11:48:27 +0000

Hi Justin,

did you ever run into SGE problems after rebundling, i.e. commands
hanging, probably because of SSH troubles? I followed the normal
rebundling guidelines and the new instances come up but their logs contain:

/etc/init.d/rc: 390: /etc/rcS.d/S50ec2-ssh-host-key-gen: Permission denied

I googled a bit and it's down to Eric Hammond's original AMI (the one
the StarCluster one is based on) having this 'clever' script:


which is set to make itself un-executable (chmod -x) after the very
first instantiation of an AMI. Could this be the cause for the SGE
commands not working anymore (hanging) after rebundling? I think it must
be since a bit of fiddling (sourcing the above script 'manually' and
then ./sge_master makes the commands not hang anymore but it also
doesn't fix things on the running instance).

Some people
suggest replacing the above script with this new version:

or chmod +x the old script before rebundling

But before I go through the whole rebundling process again just to
replace this script I'd like to get your opinion on whether this causes
my problems? I'm afraid I myself know too little about this whole keys
business in conjunction with SGE.

Hope you can help,
Rob wrote:
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> 1. Re: WebFeedback - cluster: Hi again I guess it s better to
> use this than email Here s ... [ #1142117] (Justin Riley)
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 1 Feb 2010 19:00:30 -0500
> From: Justin Riley <jtriley_at_MIT.EDU>
> Subject: Re: [Starcluster] WebFeedback - cluster: Hi again I guess it
> s better to use this than email Here s ... [ #1142117]
> To:
> Cc:
> Message-ID: <>
> Content-Type: Text/Plain; charset="utf-8"
> Hi Rob,
> If you wouldn't mind, I'd prefer to use the starcluster
> ( mailing list for
> reporting any issues/questions you might have in the future.
> Concerning your question, I'm guessing you mean is there a way to download the
> StarHPC AMI as a standalone virtual machine image? If so, I know that you can
> download the individual virtual machine files from S3 (ie the parts of the
> volume created by ec2-bundle-vol and the likes) but I've never tried to unpack
> them and get the vm running within a local Xen installation.
> This is not to say it couldn't be done, but I certainly don't have any
> experience with this. Regardless, the amount of money you'd save not storing a
> 10GB AMI on S3 you'd likely spend on the data transfer into S3 every time you
> wanted to launch the AMI. Furthermore, the process of transferring the image
> to s3, registering the AMI, and then launching the instance would make for an
> insanely long boot time. Honestly, I don't see the benefit.
> I typically do things the old fashioned way (launch instance, customize,
> rebundle) and also utilize EBS for housing research/application data and also
> applications themselves. Amazon allows you to create EBS volumes up to 1TB
> each. You can then mount these volumes to the instance. Starcluster supports
> this btw and nfs's the mounted EBS volume to all the nodes. Have a look at the
> docs if you're interested in using this.
> Interestingly enough, EC2 recently added support for booting from an EBS
> volume which opens up the amount of data that can be stored on an instance/AMI
> (up to 1TB). This feature is not available in the current stable version of
> StarCluster. Needless to say, I'll be experimenting with this in the very near
> future.
> Hope that helps,
> ~Justin
> On Monday 01 February 2010 12:26:56 pm via RT
> wrote:
>> Mon Feb 01 12:26:55 2010: Request 1142117 was acted upon.
>> Transaction: Ticket created by
>> Queue: StarIssues
>> Subject: WebFeedback - cluster: Hi again I guess it s better to use
>> this than email Here s ... Owner: Nobody
>> Requestors:
>> Status: new
>> Ticket <URL: >
>> Star WebFeedback
>> Time: Mon Feb 1 12:26:56 2010
>> Name: Rob
>> Project: cluster
>> Source: web
>> Report: Question
>> Email:
>> Subscribe: on
>> Note: Hi again,
>> I guess it's better to use this than email?
>> Here's a more general question: is the unbundled StarCluster AMI available
>> from somewhere or will be? I might want to customize the AMI a bit
>> (software and maybe even some input data since I think an AMI can be 10
>> Gigs = using that could save S3 space?) and be able to to this 'offline'
>> i.e. mount it on my local machine.
>> Don't worry if not, I'll try to do it the 'online' way then
>> (edit&rebundle).
>> Cheers,
>> Rob
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> End of Starcluster Digest, Vol 6, Issue 2
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Received on Tue Feb 09 2010 - 06:48:33 EST
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