Hi,

Correct. Same instance.

Slowly deteriorating even more - at first it had only SGE and Galaxy hung. Now when rebooting, only CM starts. No fs, postgres...

The knee-jerk reaction is to just start a brand new instance, but that would not help anyone who wants to use this AIM in the future for production.

I'll check your recommendation shortly.

j

From: Enis Afgan [eafgan@emory.edu]
Sent: Thursday, September 22, 2011 8:48 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,

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.hargitai@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 [afgane@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.hargitai@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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