Greg; > I created a new Galaxy instance (probably around early July) with the > web launcher (https://biocloudcentral.herokuapp.com/launch). > > I've been coming back and re-using it since then. However for the > past week at least I haven't been able to launch new nodes. They show > up as red on the indicators, and below I've pasted the error messages.
BioCloudCentral updated to the latest Ubuntu release, 12.04, recently so I'd guess this is the source of your error. CloudMan required some changes to handle SGE compatibility with the updated libraries in 12.04. > (Could this be related to a new version of cloudman being released?) Did you upgrade your version of CloudMan? It should give you an option to 'Update CloudMan' in the upper panel on the cloud console page when it's out of date. Hopefully the updated CloudMan will take care of the issue, Brad > > This is the cluster status log from my last attempt: > > 15:55:02 - Retrieved file 'persistent_data.yaml' from bucket > 'cm-[redacted]' to 'pd.yaml'. > 15:55:02 - Master starting > 15:55:05 - Completed initial cluster configuration. > 15:55:25 - Prerequisites OK; starting service 'SGE' > 15:55:37 - Configuring SGE... > 15:55:37 - Setting up SGE did not go smoothly, running command 'cd > /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned > code '1' and following stderr: '' > 15:55:57 - Saved file 'persistent_data.yaml' to bucket 'cm-[redacted]' > 15:55:57 - Trouble comparing local (/mnt/cm/post_start_script) and > remote (post_start_script) file modified times: [Errno 2] No such file > or directory: '/mnt/cm/post_start_script' > 15:55:58 - Adding 2 instance(s)... > 15:57:32 - Instance 'i-56ba942e' reported alive > 15:57:33 - Successfully generated root user's public key. > 15:57:33 - Sent master public key to worker instance 'i-56ba942e'. > 15:57:47 - Adding instance 'i-56ba942e' as SGE administrative host. > 15:57:47 - Process encountered problems adding instance > 'i-56ba942e' as administrative host. Process returned code 2 > 15:57:47 - Adding instance 'i-56ba942e' to SGE execution host list. > 15:57:47 - Process encountered problems adding instance > 'i-56ba942e' as execution host. Process returned code 2 > 15:57:47 - Problems updating @allhosts aimed at adding > 'i-56ba942e', running command 'export SGE_ROOT=/opt/sge;. > $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf > -Mhgrp /tmp/ah_add_15_57_47' returned code '2' and following stderr: > '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' > 15:57:47 - Waiting on worker instance 'i-56ba942e' to configure itself... > 15:57:47 - Instance 'i-54ba942c' reported alive > 15:57:47 - Sent master public key to worker instance 'i-54ba942c'. > 15:58:01 - Adding instance 'i-54ba942c' as SGE administrative host. > 15:58:01 - Process encountered problems adding instance > 'i-54ba942c' as administrative host. Process returned code 2 > 15:58:01 - Adding instance 'i-54ba942c' to SGE execution host list. > 15:58:01 - Process encountered problems adding instance > 'i-54ba942c' as execution host. Process returned code 2 > 15:58:01 - Problems updating @allhosts aimed at adding > 'i-54ba942c', running command 'export SGE_ROOT=/opt/sge;. > $SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf > -Mhgrp /tmp/ah_add_15_58_01' returned code '2' and following stderr: > '/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh ' > 15:58:01 - Waiting on worker instance 'i-54ba942c' to configure itself... > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
