Ubuntu 13.04 Amazon image for testing

[Brad Chapman]

Hi all;
We've been working on a new CloudBioLinux image based on Ubuntu 13.04
and put together an initial AMI for testing:

ami-72eb961b

This has a large collection of added software and updated libraries since
our last release. Thank you to everyone who contributed code,
suggestions and problem reports.

Feedback on being able to boot and use this AMI would be super helpful.
I've tried to resolve AMI issues that plagued us on 12.10, so would like
to confirm that this is easy to boot and use. The remaining todo items
before rolling out a new official release are:

- Ensure FreeNX connectivity works.
- Test compatibility with new CloudMan release (thanks Enis and Dannon).
- Identify any new packages to add or problems with existing packages.

Thanks again to all the CloudBioLinux contributors,
Brad

[Tony Travis]

On 05/07/13 17:14, Brad Chapman wrote:
> [...]

> - Ensure FreeNX connectivity works.

Hi, Brad.

I've proposed that Bio-Linux replaces FreeNX with x2go:

http://x2go.org

The writing is on the wall for FreeNX, and Canonical support x2go. I
gave a talk about this recently at the Debian-Med Sprint at Schenberg
near Kiel in Germany:

http://wiki.debian.org/DebianMed/Meeting/Kiel2013

I've used x2go quite a lot now, and it performs well. It also makes it
*simple* to mount SSHFS shares from your client on the server. I;ll try
it out on your 13.04 AMI and see how it works.

Bye,

Tony.
--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony....@abdn.ac.uk, skype:ajtravis

[Jianwu Wang]

Hi Brad,

   I just tested this ami. But I had some problems logging into the instances using my key file. Neither 'ubuntu' nor 'root' account works for me. I tried the same key and security group for an old CloudBioLinux image (ami-01df5068), which works for me.

Best wishes

Sincerely yours

Jianwu Wang, Ph.D.
http://users.sdsc.edu/~jianwu/

Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.

[Brad Chapman]

Jianwu;
Thanks much for testing this and apologies for the delay in getting this
fixed. I wanted to coordinate a new testing round with the updated
CloudMan release, thanks to Enis and Dannon's hard work.

I created a new testing AMI that should fix the keypair login issue by
upgrading the cloud-init and boto dependencies:

ami-cb5419a2

Please let us know if you run into any issues, I'd be happy to debug
more. If this is working, I'll plan to prepare a new clean CloudBioLinux
release with all of the latest package updates.

The AMI is also available as a choice on BioCloudCentral:

http://biocloudcentral.org

(under advanced startup options -> Image)

and works cleanly with the new CloudMan release based on my testing.

Thank you again for this useful feedback,
Brad

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[Jianwu Wang]

Hi Brad,

    Thanks a lot for your help. We are testing the new version. So far so good. :) As you may know, we are building bioKepler (http://www.biokepler.org) cloud images on top of CloudBioLinux. We have received a lot of help from you and Ntino. Thanks a lot for it. 

     I have a few questions on this new version. Would you please help on them? Thanks a lot.

    1) Where I can find the corresponding Openstack image for this CloudBioLinux version? I found a lot of files in https://s3.amazonaws.com/cloudbiolinuxvms. Not sure which one corresponds to ami-cb5419a2.

    2) I remember this version built on top of biolinux 7. Just want to confirm it.

Jianwu Wang  

--

Best wishes

Sincerely yours

Jianwu Wang

wangj...@gmail.com

[Brad Chapman]

Jianwu;

> Thanks a lot for your help. We are testing the new version. So far so
> good. :) As you may know, we are building bioKepler (
> http://www.biokepler.org) cloud images on top of CloudBioLinux. We have
> received a lot of help from you and Ntino. Thanks a lot for it.

Brilliant, glad that this one works cleanly for you. We've been doing
updates based on using CloudBioLinux for local installs, so will
hopefully push a new 13.04 release with all the updates soon you can
build off.

>
> I have a few questions on this new version. Would you please help on
> them? Thanks a lot.
>
> 1) Where I can find the corresponding Openstack image for this
> CloudBioLinux version? I found a lot of files in
> https://s3.amazonaws.com/cloudbiolinuxvms. Not sure which one corresponds
> to ami-cb5419a2.

I don't believe we have one yet. Ntino has been making these but not
sure what his time frame is on being able to create one with Ubuntu 13.04.

> 2) I remember this version built on top of biolinux 7. Just want to
> confirm it.

Yes, we use the latest and greatest Bio-Linux packages so it's
essentially all of the Bio-Linux packages that work cleanly on 13.04.

Thanks again,
Brad

[Jianwu Wang]

Hi Brad,

Got it. Thanks a lot for your information.

Ntino told me long time ago to get the image for virtualbox from
https://s3.amazonaws.com/cloudbiolinuxvms/vboxcloudbiolinux-11-25-2012.
I'm been building OpenStack images from it. If cloudbiolinux doesn't
have newer images for virtualbox/openstack, I'll keep using this one.

--
Best wishes

Sincerely yours

Jianwu Wang
wangj...@gmail.com