Thanks for the reply, Brad.

I tried clicking "update cloudman" but it now says "there was an error
updating cloudman".

Here are the contents of the Cluster status log but I'm not sure what
the error is:

    18:06:43 - Retrieved file 'persistent_data.yaml' from bucket
'cm-xxx' to 'pd.yaml'.
    18:06:43 - Master starting
    18:06:44 - Completed initial cluster configuration.
    18:07:04 - Prerequisites OK; starting service 'SGE'
    18:07:24 - Configuring SGE...
    18:07:24 - 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: ''
    18:07:38 - Saved file 'persistent_data.yaml' to bucket 'cm-xxx'
    18:07:38 - 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'
    18:09:23 - Updating CloudMan application source file in cluster's
bucket 'cm-xxx'. It will be automatically available the next this
cluster is instantiated.

Thanks again,

Greg


On Mon, Jul 23, 2012 at 3:49 PM, Brad Chapman <chapm...@50mail.com> wrote:
>
> 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 it's out of date.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...
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