Hi Enis


1.       I first created the LVM on 2 new volumes.

2.       Mounted the LVM

3.       I stopped all services (SGE, PostgreSQL, Galaxy).

4.       Copied all data on filesystem /mnt/galaxyData to the LVM

5.       Umounted /mnt/galaxyData

6.       Mounted LVM to /mnt/galaxyData

7.       Started all services


As I mentioned in my previous posts all seems to be ok but I received a 


WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with
extension 'coverage', using datatype from /mnt/galaxyData/tmp/tmpGx9fsi.


while running the "Groom" tool.

I didn`t know what to do at that time and started "messing" around
removing tmp files, restarting SGE etc.

I later received the same error on a newly created Galaxy Cloudman
instance with normal (<1TB size) galaxyData filesystem.

Greg Von Kuster replied to me I had to remove a duplicate value in the
datatypes.conf.xml file.


Hello Yves,


You have one or more entries in your datatypes_conf.xml file for a
datatype named "coverage"  These should be eliminated from your
datatypes.conf.xml file because they are not valid datatypes (unless you
have added proprietary datatypes to your Galaxy instance with this
extension).  They were originally in the datatypes.conf.xml.sample file
for datatype indexers\, but datatype indexers have been eliminated from
the Galaxy framework because datatype converters do the same thing.


Greg Von Kuster


Currently I am running multiple Galaxy Cloudman instances to circumvent
the 1 TB limit.

If I find some time I will redo the exercise with the LVM.


Kind Regards


From: Enis Afgan [mailto:eaf...@emory.edu] 
Sent: Sunday, 19 February 2012 23:50
To: Wetzels, Yves [JRDBE Extern]
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy Cloudman - How to analyse > 1TB data ?


Hi Yves, 

When you create the LVM file system - are you composing it from the
volume that already contains the data (i.e., directory structure++
created by CloudMan) and then adding another volume into the LVM or
starting with 2 new, clean volumes? 

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




On Thu, Feb 16, 2012 at 7:37 PM, Wetzels, Yves [JRDBE Extern]
<ywet...@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

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,

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