Re: [galaxy-dev] My CloudMan EC2 instance won't start Galaxy
Hi Enis! Turns out I was using a too small instance type. Since I was just checking to see if I could set it up I was using t1.micro and some other larger one as well. Anyhow, when I tried today I made sure to use something more reasonable (m3.medium) and it fired up just fine. Thanks, Jim On Sun, Oct 26, 2014 at 7:12 AM, Enis Afgan afg...@gmail.com wrote: Hi Jim, How did you launch your instance? If you still have the instance up, could you please also forward the first ~200 lines of /mnt/cm/paster.log (deleting any identifiable info from the log). Sorry abou the trouble and thanks for reporting it, Enis On Sat, Oct 25, 2014 at 8:58 PM, Jim White jimwh...@uw.edu wrote: When I start CloudMan following the instructions at (https://wiki.galaxyproject.org/CloudMan) (ami-a7dbf6ce, Galaxy CloudMan 2.3) I get pretty far in the process but then Galaxy won't start because the EBS volumes are never mounted. The Volume console shows that the volumes get created based on the public snapshots but they never go to in use which suggest that the call to mount them isn't getting done for some reason. I probably will end up building my own CloudMan AMI (I'm mostly interested in HTCondor DAGman rather than Galaxy) but I figured you'd want to know about this issue. Thanks, Jim Admin Console:https://dl.dropboxusercontent.com/u/73840666/CloudMan%20Trouble/Admin%20Console.png EC2 Volumes:https://dl.dropboxusercontent.com/u/73840666/CloudMan%20Trouble/Volumes%20OK.png Logs: Cluster status log 13:22:17 - Master starting 13:22:18 - Successfully retrieved root user's public key from file. 13:22:18 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type. 13:22:22 - Migration service prerequisites OK; starting the service 13:22:22 - SGE service prerequisites OK; starting the service 13:22:28 - Setting up SGE... 13:22:36 - Initializing 'Galaxy' cluster type with storage type 'volume'. Please wait... 13:22:40 - For filesystem galaxy, unknown kind: galaxy 13:22:40 - For filesystem galaxyIndices, unknown kind: galaxyIndices 13:22:45 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:22:46 - Adding volume vol-9fe10c87 (FS object for galaxy)... 13:22:46 - Could not determine next available device from frozenset([]) 13:22:46 - Error adding file system service FS object for galaxy: 'NoneType' object is not iterable 13:22:46 - Adding volume vol-6ae10c72 (FS object for galaxyIndices)... 13:23:32 - Could not determine next available device from frozenset([]) 13:23:32 - Error adding file system service FS object for galaxyIndices: 'NoneType' object is not iterable 13:23:36 - Empty disk usage for FS transient_nfs 13:23:36 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:23:36 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:23:36 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:23:49 - Empty disk usage for FS transient_nfs 13:23:49 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:23:49 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:23:49 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:24:01 - Empty disk usage for FS transient_nfs 13:24:01 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:24:01 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:24:01 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:24:14 - Empty disk usage for FS transient_nfs 13:24:14 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:24:14 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 Admin Console log 2014-10-25 13:27:42,910 DEBUG master:2445 Monitor adding service 'Galaxy' 2014-10-25 13:27:42,910 DEBUG __init__:300 Galaxy service prerequisites are not yet satisfied, waiting for: [, , , , ]. Setting Galaxy service state to 'Unstarted' 2014-10-25 13:27:42,911 DEBUG master:2445 Monitor adding service 'GalaxyReports' 2014-10-25 13:27:42,911 DEBUG __init__:300 GalaxyReports service prerequisites are not yet satisfied, waiting for: []. Setting GalaxyReports service state to 'Unstarted' 2014-10-25 13:27:47,307 DEBUGsge:552 qstat: ['al...@ip-10-158-92-92.ec2.inte BIP 0/0/1 0.33 lx24-amd64 '] 2014-10-25 13:27:47,344 WARNING filesystem:518 Empty disk usage for FS transient_nfs 2014-10-25 13:27:47,366 ERROR filesystem:582 STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 2014-10-25 13:27:47,390 ERROR filesystem:582 STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 2014-10-25 13:27:47,391 WARNING postgres:199 PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 2014-10-25 13:27:47,404
Re: [galaxy-dev] My CloudMan EC2 instance won't start Galaxy
Hi Jim, How did you launch your instance? If you still have the instance up, could you please also forward the first ~200 lines of /mnt/cm/paster.log (deleting any identifiable info from the log). Sorry abou the trouble and thanks for reporting it, Enis On Sat, Oct 25, 2014 at 8:58 PM, Jim White jimwh...@uw.edu wrote: When I start CloudMan following the instructions at (https://wiki.galaxyproject.org/CloudMan) (ami-a7dbf6ce, Galaxy CloudMan 2.3) I get pretty far in the process but then Galaxy won't start because the EBS volumes are never mounted. The Volume console shows that the volumes get created based on the public snapshots but they never go to in use which suggest that the call to mount them isn't getting done for some reason. I probably will end up building my own CloudMan AMI (I'm mostly interested in HTCondor DAGman rather than Galaxy) but I figured you'd want to know about this issue. Thanks, Jim Admin Console:https://dl.dropboxusercontent.com/u/73840666/CloudMan%20Trouble/Admin%20Console.png EC2 Volumes:https://dl.dropboxusercontent.com/u/73840666/CloudMan%20Trouble/Volumes%20OK.png Logs: Cluster status log 13:22:17 - Master starting 13:22:18 - Successfully retrieved root user's public key from file. 13:22:18 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type. 13:22:22 - Migration service prerequisites OK; starting the service 13:22:22 - SGE service prerequisites OK; starting the service 13:22:28 - Setting up SGE... 13:22:36 - Initializing 'Galaxy' cluster type with storage type 'volume'. Please wait... 13:22:40 - For filesystem galaxy, unknown kind: galaxy 13:22:40 - For filesystem galaxyIndices, unknown kind: galaxyIndices 13:22:45 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:22:46 - Adding volume vol-9fe10c87 (FS object for galaxy)... 13:22:46 - Could not determine next available device from frozenset([]) 13:22:46 - Error adding file system service FS object for galaxy: 'NoneType' object is not iterable 13:22:46 - Adding volume vol-6ae10c72 (FS object for galaxyIndices)... 13:23:32 - Could not determine next available device from frozenset([]) 13:23:32 - Error adding file system service FS object for galaxyIndices: 'NoneType' object is not iterable 13:23:36 - Empty disk usage for FS transient_nfs 13:23:36 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:23:36 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:23:36 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:23:49 - Empty disk usage for FS transient_nfs 13:23:49 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:23:49 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:23:49 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:24:01 - Empty disk usage for FS transient_nfs 13:24:01 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:24:01 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 13:24:01 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 13:24:14 - Empty disk usage for FS transient_nfs 13:24:14 - STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 13:24:14 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 Admin Console log 2014-10-25 13:27:42,910 DEBUG master:2445 Monitor adding service 'Galaxy' 2014-10-25 13:27:42,910 DEBUG __init__:300 Galaxy service prerequisites are not yet satisfied, waiting for: [, , , , ]. Setting Galaxy service state to 'Unstarted' 2014-10-25 13:27:42,911 DEBUG master:2445 Monitor adding service 'GalaxyReports' 2014-10-25 13:27:42,911 DEBUG __init__:300 GalaxyReports service prerequisites are not yet satisfied, waiting for: []. Setting GalaxyReports service state to 'Unstarted' 2014-10-25 13:27:47,307 DEBUGsge:552 qstat: ['al...@ip-10-158-92-92.ec2.inte BIP 0/0/1 0.33 lx24-amd64 '] 2014-10-25 13:27:47,344 WARNING filesystem:518 Empty disk usage for FS transient_nfs 2014-10-25 13:27:47,366 ERROR filesystem:582 STATUS CHECK: File system named 'galaxy' is not mounted. Error code 0 2014-10-25 13:27:47,390 ERROR filesystem:582 STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0 2014-10-25 13:27:47,391 WARNING postgres:199 PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?) 2014-10-25 13:27:47,404 DEBUG master:2534 SS: Migration..Completed; SGE..OK; FS object for transient_nfs..OK; PSS..Unstarted; FS object for galaxy..Error; FS object for galaxyIndices..Error; Postgres..Unstarted; ProFTPd..Unstarted; Galaxy..Unstarted; GalaxyReports..Unstarted; 2014-10-25 13:27:47,404 DEBUG master:2445 Monitor adding service 'PSS' 2014-10-25 13:27:47,404 DEBUG
