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 starting13:05:25 - Completed initial cluster
configuration.13:05:33 - Starting service 'SGE'13:05:48 - Configuring
SGE...13:05:56 - Successfully setup SGE; configuring SGE13:05:57 - 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 1/513:05:59 - 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
application13:08:05
- 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
alive13:08:28 - 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 alive13:08:28 - Sent master public key to worker instance
'i-e26f0a8d'.13:08:33 - Instance 'i-e06f0a8f' reported alive13:08:33 - Sent
master public key to worker instance 'i-e06f0a8f'.13:08:33 - Adding instance
i-e46f0a8b to SGE Execution Host list13:08:44 - Successfully added instance
'i-e46f0a8b' to SGE13:08:44 - Waiting on worker instance 'i-e46f0a8b' to
configure itself...13:08:44 - Instance
'i-e26f0a8d' already in SGE's @allhosts13:08:44 - Waiting on worker instance
'i-e26f0a8d' to configure itself...13:08:45 - Instance 'i-e06f0a8f' already in
SGE's @allhosts13:08:45 - Waiting on worker instance 'i-e06f0a8f' to configure
itself...13:08:50 - Instance 'i-e46f0a8b' ready13:09:27 - 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 SGE22:38:18 -
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
SGE22:38:19 - 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 SGE22:38:41 - 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 alive22:41:02 - Sent master public key to worker instance
'i-fa096e95'.22:41:06 - Adding instance i-fa096e95 to SGE Execution Host
list22:41:17 - Successfully added instance 'i-fa096e95' to SGE22:41:17 -
Waiting on worker instance 'i-fa096e95' to configure itself...22:41:17 -
Instance 'i-fe096e91' reported alive22:41:17 - Sent master public key to worker
instance 'i-fe096e91'.22:41:22 - Adding instance i-fe096e91 to SGE Execution
Host list22:41:34 - Successfully added instance 'i-fe096e91' to SGE22:41:34 -
Waiting on worker instance 'i-fe096e91' to configure itself...22:41:34 -
Instance 'i-fa096e95' ready22:41:52 - Instance 'i-fe096e91' ready22:42:28 -
Instance 'i-fc096e93' reported alive22:42:28 - Sent master public key to worker
instance 'i-fc096e93'.22:42:38 - Adding instance i-fc096e93 to SGE Execution
Host list22:42:49 - Successfully added instance 'i-fc096e93'
to SGE22:42:49 - Waiting on worker instance 'i-fc096e93' to configure
itself...22:43:13 - Instance 'i-fc096e93' ready18:29:10 - Failure checking disk
usage. [Errno 12] Cannot allocate memory18:29:10 - Failure checking disk
usage. [Errno 12] Cannot allocate memory18:29:10 - Failure checking disk
usage. [Errno 12] Cannot allocate memory
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