Hi Brad,

I clicked terminate cluster and restarted it but it didn't seem to help.

Here's what's in S3:

Name    Size    Last Modified
cm.tar.gz       502.7 KB        Thu Jun 21 14:03:05 GMT-400 2012
cm.tar.gz_2012-07-24    502.7 KB        Tue Jul 24 14:21:20 GMT-400 2012
cm_boot.py      9.9 KB  Thu Jun 21 14:03:05 GMT-400 2012
persistent_data.yaml    170 bytes       Tue Jul 24 14:53:10 GMT-400 2012
post_start_script       0 bytes Wed Jun 27 15:06:02 GMT-400 2012
resistance.clusterName  0 bytes Thu Jun 21 13:52:27 GMT-400 2012

What do you think happened?  It appears to have downloaded a new
cm.tar.gz and added a date suffix to the name.

Should I delete cm.tar.gz and rename cm.tar.gz_2012-07-24 to cm.tar.gz?

-Greg


On Tue, Jul 24, 2012 at 9:45 PM, Brad Chapman <chapm...@50mail.com> wrote:
>
> Greg;
> Did you try rebooting or restarting the cluster? The error logs complain
> about SGE due to the original older CloudMan but it seems like cm.tar.gz
> got an update so will work going forward. You can double check by
> looking at your S3 console for the cm-yourinstance and seeing the date
> on the cm.tar.gz module.
>
> Hope this fixes it for you,
> Brad
>
>> 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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