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'
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 help@genome.edu.au as the default help mailing list for the GVL.
On Wed, Oct 14, 2015 at 11:31 PM, Aaron Darling aaron.darling@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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Thanks for the reply Enis,
I had some off-list discussion with Simon Gladman about this. Simon indicated it seems that OpenStack security groups are not propagating to worker nodes at startup. Manually configuring the worker node security group and then rebooting the master appears to be a workaround. Hopefully this is only a temporary issue, and obviously one that's specific to NeCTAR.
Cheers, -Aaron
On Thu, 2015-10-15 at 21:59 -0400, Enis Afgan wrote:
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 help@genome.edu.au as the default help mailing list for the GVL.
On Wed, Oct 14, 2015 at 11:31 PM, Aaron Darling aaron.darling@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 ______________________________________________________________ UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. 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