It is there:

data_filesystems:
  galaxyData:
  - size: 200
    vol_id: vol-5b059a30
services:
- service: SGE
- service: Postgres
- service: Galaxy
static_filesystems:
- filesystem: galaxyIndices
  size: 700
  snap_id: !!python/unicode 'snap-5b030634'
- filesystem: galaxyTools
  size: 2
  snap_id: !!python/unicode 'snap-7dad9712'


________________________________
From: Enis Afgan [eaf...@emory.edu]
Sent: Monday, September 26, 2011 8:52 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common 
directory

Are you continuously running this instance and just restarting it or do you 
start a clean instance each time?
I'd suggest ensuring the persistent_data.yaml in your cluster's bucket is 
correct (see below), terminating this instance, and starting a new one with the 
same user data as used for this cluster. That way you should get a clean (i.e., 
standardized) start and that is something that should follow the process 
correctly.

persistent_data.yaml contains the data required to reestablish an existing 
cluster and must follow the following format but contain proper values 
(especially if you customized your cluster via custom snapshots). This file is 
in your cluster's bucket on S3 so you can download it, check it, and upload if 
anything was changed or got out of sync.

data_filesystems:
  galaxyData:
  - size: 50
    vol_id: vol-909342f8
services:
- service: SGE
- service: Postgres
- service: Galaxy
static_filesystems:
- filesystem: galaxyIndices
  size: 700
  snap_id: !!python/unicode 'snap-5b030634'
- filesystem: galaxyTools
  size: 2
  snap_id: !!python/unicode 'snap-1688b978'



On Fri, Sep 23, 2011 at 1:09 PM, Joseph Hargitai 
<joseph.hargi...@einstein.yu.edu<mailto:joseph.hargi...@einstein.yu.edu>> wrote:
Hi,

the mount is no longer there:

ubuntu@ip-10-68-42-15:~$ more /etc/hosts
127.0.0.1 localhost

# The following lines are desirable for IPv6 capable hosts
::1 ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters
ff02::3 ip6-allhosts
ubuntu@ip-10-68-42-15:~$ df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/sda1              15G  9.5G  5.6G  63% /
devtmpfs              7.3G  128K  7.3G   1% /dev
none                  7.6G     0  7.6G   0% /dev/shm
none                  7.6G   96K  7.6G   1% /var/run
none                  7.6G     0  7.6G   0% /var/lock
none                  7.6G     0  7.6G   0% /lib/init/rw
/dev/sdb              414G  201M  393G   1% /mnt
ubuntu@ip-10-68-42-15:~$ cd /mnt
ubuntu@ip-10-68-42-15:/mnt$ ls
cm  lost+found



ubuntu@ip-10-68-42-15:/mnt$ more /etc/fstab
# /etc/fstab: static file system information.
# <file system>                                 <mount point>   <type>  <options
>       <dump>  <pass>
proc                                            /proc           proc    nodev,no
exec,nosuid 0       0
/dev/sda1                                       /               xfs     defaults
        0       0
/dev/sdb    /mnt    auto    defaults,nobootwait,comment=cloudconfig    0
0


________________________________
From: Enis Afgan [eaf...@emory.edu<mailto:eaf...@emory.edu>]
Sent: Thursday, September 22, 2011 8:48 AM

To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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.hargi...@einstein.yu.edu<mailto: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<mailto:afg...@gmail.com>]
Sent: Tuesday, September 13, 2011 4:20 AM
To: Joseph Hargitai
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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<mailto: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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