Maybe trying again and not messing with SGE at all would at least resolve the SGE issue. Namely, SGE is on the root file system so it should be fine as is. I'd suggest stopping Galaxy and PostgreSQL services (from the CloudMan Admin), from the CLI, unmount galaxyData file system and proceed to create the LVM. Mount the file system and ensure the directories and the data that were there are still there. The start back PostgreSQL and Galaxy services. See if it all comes up fine and try adding a worker node if it does.

Currently, CloudMan does not support composition of a file system from multiple volumes but I would think that as long as you did not restart the cluster and created the file system manually, things would work fine. I've been thinking about why you're seeing the described behavior and am not really sure so please let me know how the above process works out.

On Thu, Feb 16, 2012 at 7:37 PM, Wetzels, Yves [JRDBE Extern] <YWETZEL@its.jnj.com> wrote:

Hi Brad

I did not restart the master CloudMan node.
I only restarted the services (Galaxy, PostgreSQL and SGE).
I do not have these problems without creating the logical volume.

Kind Regards
Yves

Yves;
I'm hoping Enis can jump in here since he is more familiar with the
internals of CloudMan and may be able to offer better advice. I can tell
you what I see from your error messages.

> I used LVM2 to create the logical volume.

Does this involve stopping and restarting the master CloudMan node? The
error messages you are seeing look like SGE is missing or not properly
configured on the master node:

> 02/15/2012 11:22:08| main|domU-12-31-39-0A-62-12|E|error opening file
> "/opt/sge/default/common/./sched_configuration" for reading: No such
> file or directory
[...]
> DeniedByDrmException: code 17: error: no suitable queues

which is causing the job submission to fail since it can't find the SGE
cluster environment to submit to. The strange thing is that SGE is
present in /opt on the main EBS store, so I wouldn't expect your
modified /mnt/galaxyData volume to influence this.

Since starting worker nodes appears to be fine, I'd focus on the main
instance manipulations you are doing. Perhaps some of the setup causes
the problem without creating the logical volume? This could help narrow
down the issue and hopefully get you running again.

Hope this helps,
Brad

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