[Starcluster] Problems after rebundling / ssh keys?

Tue Feb 9 06:48:27 EST 2010

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:

/etc/rcS.d/S50ec2-ssh-host-key-gen

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 
(http://developer.amazonwebservices.com/connect/message.jspa?messageID=150389) 
suggest replacing the above script with this new version:

http://ec2ubuntu.googlecode.com/svn/trunk/etc/init.d/ec2-ssh-host-key-gen

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,
Cheers,
Rob

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>    1. Re: WebFeedback - cluster: Hi again I guess it s	better to
>       use this than email Here s ... [help.mit.edu #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 ... [help.mit.edu #1142117]
> To: rentzsch at biochem.ucl.ac.uk
> Cc: starcluster at mit.edu
> Message-ID: <201002011900.30417.jtriley at mit.edu>
> Content-Type: Text/Plain;  charset="utf-8"
>
> Hi Rob,
>
> If you wouldn't mind, I'd prefer to use the starcluster 
> (http://mailman.mit.edu/mailman/listinfo/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 rentzsch at biochem.ucl.ac.uk via RT 
> wrote:
>   
>> Mon Feb 01 12:26:55 2010: Request 1142117 was acted upon.
>> Transaction: Ticket created by rentzsch at biochem.ucl.ac.uk
>>        Queue: StarIssues
>>      Subject: WebFeedback - cluster: Hi again I guess it s better to use
>>  this than email Here s ... Owner: Nobody
>>   Requestors: rentzsch at biochem.ucl.ac.uk
>>       Status: new
>>  Ticket <URL: https://help.mit.edu/Ticket/Display.html?id=1142117 >
>>
>>
>>
>> Star WebFeedback
>> Time: Mon Feb  1 12:26:56 2010
>> Name: Rob
>> Project: cluster
>> Source: web
>> Report: Question
>> Email: rentzsch at biochem.ucl.ac.uk
>> 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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