Hi Joe,
And this is happening on a freshly booted instance (from
a previously existing cluster) using the same AMI? The order of execution
seems a bit odd, seeing Galaxy being removed before SGE is setup; SGE should
be the first thing that gets setup so I'm wondering...

If you log into the instance, what is in /etc/hosts? Does it match the
instance DNS?

And if you try executing that same command (cd /opt/sge; ./inst_sge -m -x
-auto /opt/sge/galaxyEC2.conf) by hand (as root), is any more info produced?
Also, qmaster log should be available under /opt/sge/ge6 (or something like
this) /default/spool/qmaster/ so please take a look there as well and see if
more info is available.



On Thu, Sep 22, 2011 at 12:46 AM, Joseph Hargitai <
joseph.hargi...@einstein.yu.edu> wrote:

>  the error is
>
> '
> [DEBUG] galaxy:139 2011-09-22 00:03:21,055:     Galaxy UI does not seem to
> be accessible.
> [DEBUG] master:1491 2011-09-22 00:03:21,055: S&S: SGE..Shut down;
> FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK;
> Galaxy..Starting;
> [DEBUG] root:354 2011-09-22 00:03:24,724: Managing services: []
> [INFO] galaxy:30 2011-09-22 00:03:24,724: Removing 'Galaxy' service
> [INFO] galaxy:122 2011-09-22 00:03:24,724: Shutting down Galaxy...
> [DEBUG] misc:511 2011-09-22 00:03:26,067: Successfully stopped Galaxy.
> [DEBUG] root:354 2011-09-22 00:03:33,936: Managing services: []
> [DEBUG] sge:61 2011-09-22 00:03:33,937: Unpacking SGE from
> '/opt/galaxy/pkg/ge6.2u5'
> [DEBUG] sge:76 2011-09-22 00:03:33,937: Cleaning '/opt/sge' directory.
> [DEBUG] sge:82 2011-09-22 00:03:34,117: Unpacking SGE to '/opt/sge'.
> [INFO] sge:96 2011-09-22 00:03:35,557: Configuring SGE...
> [DEBUG] sge:104 2011-09-22 00:03:35,558: Created SGE install template as
> file '/opt/sge/galaxyEC2.conf'
> [DEBUG] sge:112 2011-09-22 00:03:35,558: Setting up SGE.
> [ERROR] misc:514 2011-09-22 00:03:35,651: Setting up SGE did not go
> smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto
> /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359:
> 11: unexpected operator
> [: 359: 11: unexpected operator
> [: 359: 11: unexpected operator
> [: 359: 11: unexpected operator
> error resolving local host: can't resolve host name (h_errno =
> HOST_NOT_FOUND)
>
>
> j
>
>
>
>  ------------------------------
> *From:* Enis Afgan [afg...@gmail.com]
> *Sent:* Tuesday, September 13, 2011 4:20 AM
> *To:* Joseph Hargitai
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] cloud instance missing /opt/sge/default/common
> directory
>
>  Hi Joe,
> If you look in /mnt/cm/paster.log on the instance, are there any
> indications as to what went wrong? It should be toward the top of the log
> after the server gets started.
> SGE gets installed each time an instance is rebooted so simply rebooting it
> again may do the trick. You can also chose to manually remove/clean SGE
> before rebooting. To do so, you can follow the basic approach captured in
> this method:
> https://bitbucket.org/galaxy/cloudman/src/862d1087080f/cm/services/apps/sge.py#cl-26
>
>  Enis
>
> On Sun, Sep 11, 2011 at 12:05 AM, Joseph Hargitai <
> joseph.hargi...@einstein.yu.edu> wrote:
>
>>  Hi,
>>
>> Upon restarting a saved cloud instance I am missing:
>>
>> -bash: /opt/sge/default/common/settings.sh: No such file or directory
>> -bash: /opt/sge/default/common/settings.sh: No such file or directory
>>
>> all the other mounts are there and well preserved. Is this pulled from a
>> special place i may have not saved?
>>
>> The instance now does not boot beyond this point. Have login and admin
>> console access.
>>
>>
>> joe
>>
>>
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>
>
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