From: Enis Afgan <eafgan@emory.edu>
Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
To: "Mike Dufault" <dufaultm@yahoo.com>
Cc: "Anton Nekrutenko" <anton@bx.psu.edu>, galaxy-user@bx.psu.edu
Date: Tuesday, April 12, 2011, 9:16 PM

Ahh, for some reason cloudman is thinking Galaxy is not 'running' but still 'starting' and has thus not enabled the given button. To access the analysis, in your browser, just delete the '/cloud' part of the URL and that should load Galaxy.

Sorry about the confusion,

Enis

On Tue, Apr 12, 2011 at 9:12 PM, Mike Dufault <dufaultm@yahoo.com> wrote:

Hi Enis, Thanks for looking into this. From the Galaxy Cloudman Console, I can see that it was restarted from the log (thanks), but the "Access Galaxy" choice is still grayed out and I don't know how to access the Analysis window. Is there a way back into my analysis? Thanks, Mike --- On Tue, 4/12/11, Enis Afgan <eafgan@emory.edu> wrote: From: Enis Afgan <eafgan@emory.edu> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!! To: "Mike Dufault" <dufaultm@yahoo.com> Cc: "Anton Nekrutenko" <anton@bx.psu.edu>, galaxy-user@bx.psu.edu Date: Tuesday, April 12, 2011, 8:55 PM Hi Mike,  Try accessing your Galaxy instance now. It should be ok. The link in your email contained the IP for your instance so I took the liberty of restarting Galaxy and that brought it back up. There seems to have been an issue with Galaxy accessing its database and that resulted in Galaxy crashing. We'll look into why that happened in the first place but should be ok now.  Let me know if you have any more trouble, Enis On Tue, Apr 12, 2011 at 2:49 PM, Mike Dufault <dufaultm@yahoo.com> wrote: Hello Galaxy Staff, My data has been running on the Amazon EC2 for just over 24hrs. I have not closed any windows and my Exome analysis made it all the way through to filter on Pile up. I have two tabs for this instance. One is the Galaxy Cloudman Console and the other is the tab where I perform the analysis, load data, history etc. Anyway, I went to add a step to the work flow and the screen "Welcome Galaxy to the Cloud" screen along with the information "There is no Galaxy instance running on this host, or the Galaxy instance is not responding. To manage Galaxy on this host, please use the Cloud Console." What happened??? When I go back to the Galaxy Cloudman Console, it shows that my instance is still running along with the four cores, the Cluster log is below. AWS also shows that my instance is running. Will the work flow finish? Can I get my data? How? I tried to re-access the analysis page by selecting "Access Galaxy" from the "Galaxy Cloudman Console" but it sends me to the same "Welcome page." Is there a way to get back into the analysis page? Please help!!! Thanks, Mike The cluster log shows: 13:05:24 - Master starting 13:05:25 - Completed initial cluster configuration. 13:05:33 - Starting service 'SGE' 13:05:48 - Configuring SGE... 13:05:56 - Successfully setup SGE; configuring SGE 13:05:57 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:05:57 - Saved file 'cm_boot.py' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:05:57 - Saved file 'cm.tar.gz' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:05:57 - Problem connecting to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3', attempt 1/5 13:05:59 - Saved file 'Fam122261.clusterName' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:06:24 - Initializing a 'Galaxy' cluster. 13:06:24 - Retrieved file 'snaps.yaml' from bucket 'cloudman' to 'cm_snaps.yaml'. 13:06:41 - Adding 3 instance(s)... 13:07:02 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:07:38 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:07:38 - Saved file 'universe_wsgi.ini.cloud' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:07:38 - Saved file 'tool_conf.xml.cloud' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:07:48 - Error mounting file system '/mnt/galaxyData' from '/dev/sdg3', running command '/bin/mount /dev/sdg3 /mnt/galaxyData' returned code '32' and following stderr: 'mount: you must specify the filesystem type ' 13:07:52 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:07:52 - Starting service 'Postgres' 13:07:52 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data' does not exist (yet?) 13:07:52 - Configuring PostgreSQL with a database for Galaxy... 13:08:05 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:08:05 - Starting service 'Galaxy' 13:08:05 - Galaxy daemon not running. 13:08:05 - Galaxy service state changed from 'Starting' to 'Error' 13:08:05 - Setting up Galaxy application 13:08:05 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. 13:08:05 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. 13:08:05 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cloudman' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. 13:08:05 - Starting Galaxy... 13:08:09 - Galaxy service state changed from 'Error' to 'Starting' 13:08:09 - Saved file 'persistent_data.yaml' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:08:09 - Saved file 'tool_data_table_conf.xml.cloud' to bucket 'cm-a42f040c55e7519eb63bbaf269fa78d3' 13:08:28 - Instance 'i-e46f0a8b' reported alive 13:08:28 - Successfully generated root user's public key. 13:08:28 - Sent master public key to worker instance 'i-e46f0a8b'. 13:08:28 - Instance 'i-e26f0a8d' reported alive 13:08:28 - Sent master public key to worker instance 'i-e26f0a8d'. 13:08:33 - Instance 'i-e06f0a8f' reported alive 13:08:33 - Sent master public key to worker instance 'i-e06f0a8f'. 13:08:33 - Adding instance i-e46f0a8b to SGE Execution Host list 13:08:44 - Successfully added instance 'i-e46f0a8b' to SGE 13:08:44 - Waiting on worker instance 'i-e46f0a8b' to configure itself... 13:08:44 - Instance 'i-e26f0a8d' already in SGE's @allhosts 13:08:44 - Waiting on worker instance 'i-e26f0a8d' to configure itself... 13:08:45 - Instance 'i-e06f0a8f' already in SGE's @allhosts 13:08:45 - Waiting on worker instance 'i-e06f0a8f' to configure itself... 13:08:50 - Instance 'i-e46f0a8b' ready 13:09:27 - Galaxy service state changed from 'Starting' to 'Running' 22:38:18 - Found '3' idle instances; trying to remove '2' 22:38:18 - Specific termination of instance 'i-e26f0a8d' requested. 22:38:18 - Removing instance 'i-e26f0a8d' from SGE 22:38:18 - Successfully updated @allhosts to remove 'i-e26f0a8d' 22:38:19 - Terminating instance 'i-e26f0a8d' 22:38:19 - Initiated requested termination of instance. Terminating 'i-e26f0a8d'. 22:38:19 - Specific termination of instance 'i-e46f0a8b' requested. 22:38:19 - Removing instance 'i-e46f0a8b' from SGE 22:38:19 - Successfully initiated termination of instance 'i-e26f0a8d' 22:38:19 - Successfully updated @allhosts to remove 'i-e46f0a8b' 22:38:20 - Terminating instance 'i-e46f0a8b' 22:38:20 - Initiated requested termination of instance. Terminating 'i-e46f0a8b'. 22:38:20 - Initiated requested termination of instances. Terminating '2' instances. 22:38:20 - Successfully initiated termination of instance 'i-e46f0a8b' 22:38:41 - Found '1' idle instances; trying to remove '1' 22:38:41 - Specific termination of instance 'i-e06f0a8f' requested. 22:38:41 - Removing instance 'i-e06f0a8f' from SGE 22:38:41 - Successfully updated @allhosts to remove 'i-e06f0a8f' 22:38:42 - Initiated requested termination of instance. Terminating 'i-e06f0a8f'. 22:38:42 - Initiated requested termination of instances. Terminating '1' instances. 22:38:42 - Terminating instance 'i-e06f0a8f' 22:38:42 - Successfully initiated termination of instance 'i-e06f0a8f' 22:38:47 - Instance 'i-e26f0a8d' successfully terminated. 22:38:49 - Instance 'i-e46f0a8b' successfully terminated. 22:38:59 - Adding 3 instance(s)... 22:39:07 - Instance 'i-e06f0a8f' successfully terminated. 22:41:02 - Instance 'i-fa096e95' reported alive 22:41:02 - Sent master public key to worker instance 'i-fa096e95'. 22:41:06 - Adding instance i-fa096e95 to SGE Execution Host list 22:41:17 - Successfully added instance 'i-fa096e95' to SGE 22:41:17 - Waiting on worker instance 'i-fa096e95' to configure itself... 22:41:17 - Instance 'i-fe096e91' reported alive 22:41:17 - Sent master public key to worker instance 'i-fe096e91'. 22:41:22 - Adding instance i-fe096e91 to SGE Execution Host list 22:41:34 - Successfully added instance 'i-fe096e91' to SGE 22:41:34 - Waiting on worker instance 'i-fe096e91' to configure itself... 22:41:34 - Instance 'i-fa096e95' ready 22:41:52 - Instance 'i-fe096e91' ready 22:42:28 - Instance 'i-fc096e93' reported alive 22:42:28 - Sent master public key to worker instance 'i-fc096e93'. 22:42:38 - Adding instance i-fc096e93 to SGE Execution Host list 22:42:49 - Successfully added instance 'i-fc096e93' to SGE 22:42:49 - Waiting on worker instance 'i-fc096e93' to configure itself... 22:43:13 - Instance 'i-fc096e93' ready 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate memory 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate memory 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate memory ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:  http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/