Hi Aaron,
Does the "AMQP Connection Failure:" error continue indefinitely?
It would be helpful to see the log files from the time a worker is being
added as well as the CloudMan logs from a worker node. It appears you're
launching GVL v3.04 however, the default is now 4.0.0. Have you tried
keeping the defaults?
PS
I'm cc'ing h...@genome.edu.au as the default help mailing list for the GVL.
On Wed, Oct 14, 2015 at 11:31 PM, Aaron Darling <aaron.darl...@uts.edu.au>
wrote:
> Hi all, I'm new to CloudMan, and trying to launch a cluster via GVL (3 or
> 4) on NeCTAR.
> I'm able to get a head node running without trouble via
> launch.genome.edu.au, but launching worker nodes from the CloudMan
> interface appears to fail. CloudMan reboots the worker repeatedly before
> giving up. I logged into the worker to inspect log files and found the
> following, but it's not obvious to me what to do next. Hope this is
> something simple?
>
>
> ubuntu@server-fbbd9a10-fb58-48d8-89cd-5ddd22821648:~$ cat
> /mnt/cm/paster.log
> Python version: (2, 7)
> Image configuration suports: {'apps': ['cloudman', 'galaxy']}
> 2015-10-15 14:15:24,973 DEBUG app:73 Initializing app
> 2015-10-15 14:15:24,973 DEBUG ec2:109 Gathering instance zone,
> attempt 0
> 2015-10-15 14:15:25,140 DEBUG ec2:115 Instance zone is 'NCI'
> 2015-10-15 14:15:25,140 DEBUG ec2:44 Gathering instance ami,
> attempt 0
> 2015-10-15 14:15:25,459 DEBUG app:76 Running on 'openstack'
> type of cloud in zone 'NCI' using image 'ami-00003484'.
> 2015-10-15 14:15:25,459 DEBUG app:98 Getting pd.yaml
> 2015-10-15 14:15:25,459 DEBUG openstack:99 Establishing a boto
> Swift connection.
> 2015-10-15 14:15:25,459 DEBUG openstack:109 Got boto Swift
> connection.
> 2015-10-15 14:15:26,112 DEBUG misc:578 Retrieved file
> 'persistent_data.yaml' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' on
> host 'swift.rc.nectar.org.au' to 'pd.yaml'.
> 2015-10-15 14:15:26,118 INFO app:119 Worker starting
> 2015-10-15 14:15:26,136 DEBUG ec2:76 Gathering instance id,
> attempt 0
> 2015-10-15 14:15:26,338 DEBUG ec2:82 Instance ID is
> 'i-0019a2fc'
> 2015-10-15 14:16:29,488 DEBUG comm:134 AMQP Connection
> Failure: [Errno 110] Connection timed out
> 2015-10-15 14:16:29,492 DEBUG base:57 Enabling 'root'
> controller, class: CM
> 2015-10-15 14:16:29,494 DEBUG buildapp:93 Enabling
> 'httpexceptions' middleware
> 2015-10-15 14:16:29,496 DEBUG buildapp:99 Enabling 'recursive'
> middleware
> 2015-10-15 14:16:29,499 DEBUG buildapp:119 Enabling 'print debug'
> middleware
> 2015-10-15 14:16:29,506 DEBUG buildapp:133 Enabling 'error'
> middleware
> 2015-10-15 14:16:29,507 DEBUG buildapp:143 Enabling 'config'
> middleware
> 2015-10-15 14:16:29,508 DEBUG buildapp:147 Enabling
> 'x-forwarded-host' middleware
> 2015-10-15 14:16:29,517 DEBUG misc:768 'cp /etc/hosts
> /etc/hosts.orig' command OK
> 2015-10-15 14:16:29,528 DEBUG misc:768 'cp /tmp/tmpuV3NTJ
> /etc/hosts' command OK
> Starting server in PID 2825.
> 2015-10-15 14:16:29,533 DEBUG misc:768 'chmod 644 /etc/hosts'
> command OK
> 2015-10-15 14:16:29,533 DEBUG worker:558 Trying to setup AMQP
> connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>'
> serving on 0.0.0.0:42284 view at http://127.0.0.1:42284
> 2015-10-15 14:17:32,656 DEBUG comm:134 AMQP Connection
> Failure: [Errno 110] Connection timed out
> 2015-10-15 14:17:32,656 DEBUG worker:558 Trying to setup AMQP
> connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>'
> 2015-10-15 14:18:35,760 DEBUG comm:134 AMQP Connection
> Failure: [Errno 110] Connection timed out
> 2015-10-15 14:18:35,760 DEBUG worker:558 Trying to setup AMQP
> connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>'
> 2015-10-15 14:19:38,864 DEBUG comm:134 AMQP Connection
> Failure: [Errno 110] Connection timed out
> 2015-10-15 14:19:38,864 DEBUG worker:558 Trying to setup AMQP
> connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>'
>
>
>
>
> ubuntu@server-fbbd9a10-fb58-48d8-89cd-5ddd22821648:~$ cat
> /tmp/cm/cm_boot.py.log
> 2015-10-15 14:23:43,713 DEBUG cm_boot:430 - virtual-burrito seems to be
> installed
> 2015-10-15 14:23:44,037 DEBUG cm_boot:25 - Successfully ran '/bin/bash
> -l -c 'VIRTUALENVWRAPPER_LOG_DIR=/tmp/; HOME=/home/ubuntu; .
> /home/ubuntu/.venvburrito/startup.sh; lsvirtualenv | grep CM''
> 2015-10-15 14:23:44,037 DEBUG cm_boot:433 - 'CM' virtualenv found
> 2015-10-15 14:23:44,049 DEBUG cm_boot:493 - Fixing /etc/hosts on NeCTAR
> 2015-10-15 14:23:44,930 INFO cm_boot:244 - << Starting nginx >>
> 2015-10-15 14:23:44,931 DEBUG cm_boot:169 - Reconfiguring nginx conf
> 2015-10-15 14:23:44,931 INFO cm_boot:286 - Attempting to configure
> max_client_body_size in /usr/nginx/conf/nginx.conf
> 2015-10-15 14:23:44,934 DEBUG cm_boot:25 - Successfully ran 'cp
> /usr/nginx/conf/nginx.conf /tmp/cm/original_nginx.conf'
> 2015-10-15 14:23:44,936 DEBUG cm_boot:25 - Successfully ran 'uniq
> /tmp/cm/original_nginx.conf > /usr/nginx/conf/nginx.conf'
> 2015-10-15 14:23:44,937 DEBUG cm_boot:25 - Successfully ran 'grep
> 'client_max_body_size' /usr/nginx/conf/nginx.conf'
> 2015-10-15 14:23:44,938 DEBUG cm_boot:265 - Creating tmp dir for nginx
> /mnt/galaxy/upload_store
> 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/local/sbin/nginx
> 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/local/sbin/nginx is
> file: False; it's executable: False
> 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/local/bin/nginx
> 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/local/bin/nginx is file:
> False; it's executable: False
> 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/bin/nginx
> 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/bin/nginx is file:
> False; it's executable: False
> 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/sbin/nginx
> 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/sbin/nginx is file:
> False; it's executable: False
> 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /sbin/nginx
> 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /sbin/nginx is file: False;
> it's executable: False
> 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /bin/nginx
> 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /bin/nginx is file: False;
> it's executable: False
> 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /usr/sbin/nginx
> 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /usr/sbin/nginx is file:
> False; it's executable: False
> 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /usr/nginx/sbin/nginx
> 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /usr/nginx/sbin/nginx is
> file: True; it's executable: True
> 2015-10-15 14:23:44,939 DEBUG cm_boot:270 - Using '/usr/nginx/sbin/nginx'
> as the nginx executable
> 2015-10-15 14:23:44,946 ERROR cm_boot:31 - Error running 'ps xa | grep
> nginx | grep -v grep'. Process returned code '1' and following stderr: ''
> 2015-10-15 14:23:44,964 DEBUG cm_boot:25 - Successfully ran
> '/usr/nginx/sbin/nginx'
> 2015-10-15 14:23:44,966 DEBUG cm_boot:25 - Successfully ran 'rm -rf
> /mnt/galaxy/upload_store'
> 2015-10-15 14:23:44,966 DEBUG cm_boot:281 - Deleting tmp dir for nginx
> /mnt/galaxy/upload_store
> 2015-10-15 14:23:44,966 INFO cm_boot:339 - << Downloading CloudMan >>
> 2015-10-15 14:23:44,966 DEBUG cm_boot:43 - Checking existence of
> directory '/mnt/cm'
> 2015-10-15 14:23:44,966 DEBUG cm_boot:52 - Directory '/mnt/cm' exists.
> 2015-10-15 14:23:44,966 DEBUG cm_boot:344 - Using user-provided default
> bucket: cloudman-gvl-304
> 2015-10-15 14:23:44,966 INFO cm_boot:324 - Connecting to a custom Object
> Store
> 2015-10-15 14:23:44,967 DEBUG cm_boot:333 - Got boto S3 connection:
> S3Connection:swift.rc.nectar.org.au
> 2015-10-15 14:23:44,967 DEBUG cm_boot:210 - Checking if key 'cm.tar.gz'
> exists in bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d'
> 2015-10-15 14:23:45,276 INFO cm_boot:356 - CloudMan found in cluster
> bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d'.
> 2015-10-15 14:23:45,276 DEBUG cm_boot:190 - Getting file cm.tar.gz from
> bucket cm-45b53bf5024e962bd27e15fd81fcc07d
> 2015-10-15 14:23:45,276 DEBUG cm_boot:194 - Attempting to retrieve file
> 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d'
> 2015-10-15 14:23:45,726 INFO cm_boot:197 - Successfully retrieved file
> 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' via
> connection 'swift.rc.nectar.org.au' to '/mnt/cm/cm.tar.gz'
> 2015-10-15 14:23:45,727 DEBUG cm_boot:388 - Getting metadata 'revision'
> for file 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d'
>
>
>
> --
> Aaron E. Darling, Ph.D.
> Associate Professor, ithree institute
> University of Technology Sydney
> Australia
> http://darlinglab.org
> twitter: @koadman
>
>
>
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