StarCluster - Mailing List Archive

Re: Error running custom AMI

From: Joseph <Kyeong>
Date: Sat, 31 Dec 2011 20:58:48 +0000

Hi Justin,

First of all, I do wish you a Happy & Fruitful New Year!

Now I am trying to catch up with the great progress you and others
have made since our last discussion on the large cluster.

As for the creation of the custom image via "ebsimage", however,
although I have been testing with several different kinds, I haven't
got any success.

Below is the list of images I've been playing with so far (with the SC
ver. 0.92.1):

>>> Your registered images:

32bit Images:

64bit Images:
[0] ami-9dce1af4 us-east-1 starcluster-hnrl-ubuntu-10.04-x86_64 (EBS)
[1] ami-03cd196a us-east-1 starcluster-hnrl-ubuntu-11.10-x86_64 (EBS)
[2] ami-b5c91ddc us-east-1 starcluster-test-ubuntu-10.04-x86_64 (EBS)
[3] ami-2857a641 us-east-1 hnrl-starcluster-image

total images: 4

Except the last one (s3-backed; ubuntu 10.04), I cannot even start a
1-node cluster with all those three EBS-backed images; it simply hangs
forever at SSH setup (i.e., "Waiting for SSH to come up on all
nodes..."). This is quite strange because the 3rd ([2]) and the 4th
([3]) images above are in fact identical one except the differences in
storing (i.e., EBS vs S3).

I have had no problem with the good-old S3-backed images, which I
created early this year, but I have no clue what to do with the
EBS-backed ones.

Note that I followed the manual (i.e., procedure for a 1-node
imagehost) in creating the EBS-backed images.

BTW, the reason I do not attach the debugging log is that it actually
does not give any useful information that the StarCluster is simply
waiting for the SSH to come up.

Kyeong Soo (Joseph) Kim, Ph.D.
Senior Lecturer in Networking
Room 112, Digital Technium
Multidisciplinary Nanotechnology Centre, College of Engineering
Swansea University, Singleton Park, Swansea SA2 8PP, Wales UK
- TEL: +44 (0)1792 602024
- (group)
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On Sat, Dec 31, 2011 at 8:35 PM, Justin Riley <> wrote:
> Hash: SHA1
> FYI, I meant to say "ebsimage/s3image" commands instead of the
> deprecated "createimage" command...old habits die hard :D
> ~Justin
> On 12/31/2011 03:33 PM, Justin Riley wrote:
>> Hi Paolo,
>> StarCluster comes with a set of base 32bit/64bit AMIs as you've
>> seen/used. These AMIs are tuned for use with StarCluster and any
>> AMI you wish to use with StarCluster must be configured similarly
>> in order to be used with StarCluster.
>> The two most important requirements are:
>> 1. root ssh logins must be permitted (this is what's currently
>> causing your "Garbage Packet" error in your logs...) 2. NFS must be
>> installed and the NFS start-up script in /etc/init.d must be linked
>> to /etc/init.d/nfs
>> StarCluster also expects that /opt/sge6-fresh contains a binary
>> build of SGE/OGS in order to configure SGE/OGS at runtime. You can
>> disable SGE/OGS support by setting disable_queue=True in your
>> cluster templates if you do not require SGE/OGS and would like to
>> skip this requirement.
>> You can see all of the gory details involved with building a
>> StarCluster AMI in the AMI "Cookbooks" in the StarCluster wiki:
>> The majority of the steps in the guides are related to installing
>> custom ATLAS/numpy/scipy/OpenMPI/etc which you can skip if you do
>> not require.
>> With that said, the recommended way to create a custom AMI for use
>> with StarCluster is to launch a single instance of one of the
>> StarCluster AMIs, configure to your liking, and then use
>> StarCluster's 'createimage' command to build your custom AMI:
>>  This approach avoids having to fiddle anything but your packages
>> and customizations and lets StarCluster do the rest.
>> ~Justin
>> On 10/10/2011 08:20 AM, Paolo Di Tommaso wrote:
>>> Dear StarCluster Team,
>>> I'm evaluating your tool.
>>> I had no problem starting a small cluster with the default
>>> configuration. But when I tried to use a custom AMI (no more than
>>> a Basic 64-bit Amazon Linux AMI, with few other custom tools). I
>>> get the error message below.
>>> Is there any special configuration in order to use custom AMI
>>> images?
>>> By the way your tool is amazing!
>>> Thank you,
>>> Paolo Di Tommaso Software Engineer Comparative Bioinformatics
>>> Group Centre de Regulacio Genomica (CRG) Dr. Aiguader, 88 08003
>>> Barcelona, Spain
>> _______________________________________________ StarCluster mailing
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Received on Sat Dec 31 2011 - 15:58:50 EST
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