Aha - so neither /tmp/cm/cm_boot.py.log nor /mnt/cm/paster.log exist, but the ec2autorun.log showed a reasonable error, I used a setup password beginning with an exclamation mark, which it seems not to like. I realised that I accidentally posted this to the list previously so don't worry about it being here I've killed that particular cluster. When I was trying different configurations, etc I also consistently used the same password format (which I will no longer use now I posted it to a public mail list like a moron).

I assume since ec2autorun is first in the bootstrap setup if it fails then so does everything else. I'll try it with a different password format - and get back to you (I have a meeting just now). But this looks like an issue with the password format to me...and possibly a bug in the script?

Best wishes,

Nick

[INFO] ec2autorun:57 2015-06-22 15:38:42,207: Getting user data from 'http://169.254.169.254/latest/user-data', attempt 0 [DEBUG] ec2autorun:61 2015-06-22 15:38:42,210: Saving user data in its original format to file '/tmp/cm/original_userData.yaml'
[DEBUG] ec2autorun:65 2015-06-22 15:38:42,211: Got user data
[INFO] ec2autorun:416 2015-06-22 15:38:42,211: Handling user data in YAML format.
Traceback (most recent call last):
  File "/usr/bin/ec2autorun.py", line 516, in <module>
    main()
  File "/usr/bin/ec2autorun.py", line 512, in main
    _parse_user_data(ud)
  File "/usr/bin/ec2autorun.py", line 504, in _parse_user_data
    _handle_yaml(ud)
  File "/usr/bin/ec2autorun.py", line 417, in _handle_yaml
    ud = _load_user_data(user_data)
  File "/usr/bin/ec2autorun.py", line 402, in _load_user_data
    ud = yaml.load(user_data)
File "/usr/lib/python2.7/dist-packages/yaml/__init__.py", line 71, in load
    return loader.get_single_data()
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 39, in get_single_data
    return self.construct_document(node)
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 48, in construct_document
    for dummy in generator:
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 398, in construct_yaml_map
    value = self.construct_mapping(node)
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 208, in construct_mapping
    return BaseConstructor.construct_mapping(self, node, deep=deep)
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 133, in construct_mapping
    value = self.construct_object(value_node, deep=deep)
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 88, in construct_object
    data = constructor(self, node)
File "/usr/lib/python2.7/dist-packages/yaml/constructor.py", line 414, in construct_undefined
    node.start_mark)
yaml.constructor.ConstructorError: could not determine a constructor for the tag '!galaxySATDEVZGK'
  in "<string>", line 4, column 13:
    freenxpass: !galaxySATDEVZGK


On 22/06/15 14:45, Enis Afgan wrote:
Hmm - /mnt definitely should not be empty. There's nothing unusual in the log you sent so could you please send me the one from the worker? It's in the same location (/mnt/cm/paster.log) If it's not there, please track the boot procedure logs as follows and can send those logs:
1. /usr/bin/ec2autorun.log
2. /tmp/cm/cm_boot.py.log
3. /mnt/cm/paster.log

Thanks,
Enis

On Fri, Jun 19, 2015 at 5:02 PM, Nicholas Dickens <nick.dick...@glasgow.ac.uk <mailto:nick.dick...@glasgow.ac.uk>> wrote:

    Thanks – I’ve attached the log. I just tried to start a worker and
    let it go to the first reboot and then copied this log.  I logged
    into the worker and it looks ok (dmesg, etc) the only noticable
    thing was /mnt is empty (just a lost+found directory) and I was
    expecting to see an nfs mount for galaxy export or something.  But
    I’m still finding my way round the system.  It may also have been
    the time in the reboot cycle that I was there.

    Best wishes,

    Nick
-- Nick Dickens
    DPhil BSc ARCS

    Bioinformatics Team Leader
    Wellcome Trust Centre for Molecular Parasitology
    B6-21 SGDB
    120 University Place
    Glasgow
    G12 8TA

    Tel: +44 141 330 8282 <tel:%2B44%20141%20330%208282>

    http://fb.me/WTCMPbix
    @WTCMPbix
    http://www.gla.ac.uk/researchinstitutes/iii/staff/nickdickens/
    
http://www.gla.ac.uk/researchinstitutes/iii/staff/jeremymottram/comparativegenomicsofleishmania/

    From: Enis Afgan <enis.af...@irb.hr <mailto:enis.af...@irb.hr>>
    Date: Friday, 19 June 2015 17:00
    To: Nick Dickens <nick.dick...@glasgow.ac.uk
    <mailto:nick.dick...@glasgow.ac.uk>>
    Cc: "galaxy-dev@lists.galaxyproject.org
    <mailto:galaxy-dev@lists.galaxyproject.org>"
    <galaxy-dev@lists.galaxyproject.org
    <mailto:galaxy-dev@lists.galaxyproject.org>>
    Subject: Re: [spam?] [galaxy-dev] Cloudman cluster not starting
    workers

    Hi Nick,
    Sorry to hear you're having trouble. I just tried a couple of
    scenarios and they all worked as expected (e.g., with and without
    elastic IPs, different instance types).

    The main CloudMan log is located in /mnt/cm/paster.log, on both
    master and worker instances (if you didn't download the ssh key
    from cloudlaunch, you can ssh with ubuntu username and the same
    password as provided on the cloudlaunch form). The log is also
    available from the UI if you go to Admin page and then click 'Show
    CloudMan log' under 'System controls'. If you can share that, we
    can hopefully figure out what's going on.

    Best,
    Enis

    On Wed, Jun 17, 2015 at 11:47 AM, Nicholas Dickens
    <nick.dick...@glasgow.ac.uk <mailto:nick.dick...@glasgow.ac.uk>>
    wrote:

        Hi All,

        First time post, as a quick intro, I’m have some reasonable
        experience with EC2 & AWS for developing our own pipelines,
        I’m comfortable in python and *nix flavours and I am
        developing a completely custom galaxy in AWS for members of
        the WTCMP, Glasgow.  In the meantime, I have thrown up a quick
        cloudman galaxy using the cloudstart and the cloudman 2.3 ami
        (ami-a7dbf6ce) in us-east-1. Auto–scaling didn’t seem to work
        so I’ve switched it off and added nodes manually, I tried
        various sizes including ‘same as master’ instances but they
        just don’t start – in the EC2 console I can see them and see
        them running. But they’re constantly pending in the /cloud
        interface and in the log they reboot 4 times and then
        terminate – apparently not responding "10:16:56 - Instance
        i-xxxxxx not responding after 4 reboots. Terminating instance".

        It’s out of the box, I editted the universe_wsgi.ini… file to
        disallow user registration and allow me to impersonate users
        but didn’t change anything else.  The only other configuration
        I’ve done is associate an elastic IP with the master instance
        so I can have a more static url for a couple of test users (if
        I need to destroy it and start again, etc).

        I’m new to the system so don’t know which logs are best to
        check…and am I missing something obvious?  It there a known
        bug when using elastic IPs? I’ve googled but with no joy.

        Thanks for your help and best wishes,

        Nick
-- Nick Dickens
        DPhil BSc ARCS

        Bioinformatics Team Leader
        Wellcome Trust Centre for Molecular Parasitology
        B6-21 SGDB
        120 University Place
        Glasgow
        G12 8TA

        Tel: +44 141 330 8282 <tel:%2B44%20141%20330%208282>

        http://fb.me/WTCMPbix
        @WTCMPbix
        http://www.gla.ac.uk/researchinstitutes/iii/staff/nickdickens/
        
http://www.gla.ac.uk/researchinstitutes/iii/staff/jeremymottram/comparativegenomicsofleishmania/


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--
Nick Dickens
DPhil BSc ARCS

Bioinformatics Team Leader
Wellcome Trust Centre for Molecular Parasitology
B6-21 SGDB
120 University Place
Glasgow
G12 8TA

Tel: +44 141 330 8282

http://fb.me/WTCMPbix
@WTCMPbix
http://www.gla.ac.uk/researchinstitutes/iii/staff/nickdickens/
http://www.gla.ac.uk/researchinstitutes/iii/staff/jeremymottram/comparativegenomicsofleishmania/

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