Hi guys, I'm running into a problem with updating a
completely squeaky clean fresh cloudman install using the current
ami-da58aab3
Once it is up and running, I have SSHed in and made sure the sample files
in run.sh are complete.
I hit the update button, and 3 or 4 minutes later when the daemon tries to
restart, I get status= error.
Is anyone else having this issue?? The only threads and posts I have found
are from a year ago, and the line is in my run.sh.
The ultimate goal of all this was just so that I could have a cufflinks
version that is not 0.5.

Thanks for any help anyone can provide.

Brian


Here are the logs:

paster.log:


/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
  from csamtools import *
python path is:
/mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
/mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
/mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading
references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded
reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg
successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database version 114
tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643
psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
line 37, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 54, in __init__
    verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
  File 
"/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py",
line 145, in verify_tools
    raise Exception( msg )
Exception:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Console Log:

   - 02:46:56 - Removing 'Galaxy' service
   - 02:46:56 - Shutting down Galaxy...
   - 02:47:25 - Starting Galaxy...
   - 02:47:25 - Galaxy service state changed from 'Shut down' to 'Starting'
   - 02:47:26 - Saved file 'persistent_data.yaml' to bucket
   'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
   - 02:48:28 - Galaxy daemon not running.
   - 02:48:28 - Galaxy service state changed from 'Starting' to 'Error'
   - 02:48:29 - Saved file 'persistent_data.yaml' to bucket
   'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
   - 02:49:30 - Galaxy daemon not running.

pgSQL.log:


LOG:  database system was shut down at 2013-03-15 02:11:48 UTC
LOG:  autovacuum launcher started
LOG:  database system is ready to accept connections
ERROR:  relation "page_revision" does not exist
STATEMENT:  ALTER TABLE page ADD CONSTRAINT page_latest_revision_id_fk
FOREIGN KEY(latest_revision_id) REFERENCES page_revision (id)
ERROR:  relation "visualization_revision" does not exist
STATEMENT:  ALTER TABLE visualization ADD CONSTRAINT
visualization_latest_revision_id_fk FOREIGN KEY(latest_revision_id)
REFERENCES visualization_revision (id)
LOG:  unexpected EOF on client connection

SGE log:

03/15/2013 01:12:20|  main|ip-10-149-20-174|I|read job database with 0
entries in 0 seconds
03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
"/opt/sge/default/common/./sched_configuration" for reading: No such
file or directory
03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
"/opt/sge/default/spool/qmaster/./sharetree" for reading: No such file
or directory
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster hard descriptor
limit is set to 8192
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster soft descriptor
limit is set to 8192
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will use max.
8172 file descriptors for communication
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will accept max.
99 dynamic event clients
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|starting up GE 6.2u5 (lx24-amd64)
03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open job sequence
number file "jobseqnum": for reading: No such file or directory --
guessing next number
03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open ar sequence
number file "arseqnum": for reading: No such file or directory --
guessing next number
03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
"ip-10-149-20-174.ec2.internal" already exists
03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
"ip-10-149-20-174.ec2.internal" already exists
03/15/2013 02:46:57|listen|ip-10-149-20-174|E|commlib error: got read
error (closing "ip-10-149-20-174.ec2.internal/drmaa/416")


-- 
Brian Lin
cont...@brian-lin.com
brian....@tufts.edu
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