Re: StarCluster Digest, Vol 44, Issue 5

From: Rajat Banerjee <no email>
Date: Sun, 5 May 2013 13:48:13 -0400

Hi Sergio,
Sorry for the delayed response. Busy week at work. Adding starcluster alias
back, in case this helps other people in the future.

Like I said, I'm not sure why your instance is coming up with PDT in the
EC2 instance, since from what I remember it would always return UTC.

Is it possible for you to download the latest dev version if you haven't
tried that already?

http://star.mit.edu/cluster/docs/latest/contribute.html

Slightly different directions than the one you specified. Then, you can
modify this file:
starcluster/balancers/sge/__init__.py line 466
To replace UTC with PDT. Then run the ELB, and it'll run the latest code.
Let me know if that works, and we can file a bug and go through the formal
process of letting you switch the timezone. I'm guessing that you're pretty
familiar with python programming, but if you have more problems then feel
free to ask more questions.

Best,
Rajat


On Tue, Apr 30, 2013 at 2:07 PM, Sergio Mafra <sergiohmafra_at_gmail.com>wrote:

> Hi Rajat,
>
> Thanks so much for your kindness in order to find out where this error
> was. Nice!
>
> Itīs a little bit odd to understand what is causing that since Iīm using
> the SC Controller as an instance in the same zone (us-east-1d) as the
> cluster launched by it. So this should be in the same time format...???
>
> What I did was donwload the code directly from the GITīs site and compile
> it as described in
> http://star.mit.edu/cluster/docs/latest/installation.html
>
> ???
>
> All the best,
>
> Sergio
>
>
> On Tue, Apr 30, 2013 at 2:18 PM, Rajat Banerjee <rajatb_at_post.harvard.edu>wrote:
>
>> Sergio,
>> I looked at the code that is causing your problems. It's this line:
>>
>> return datetime.datetime.strptime(str, "%a %b %d %H:%M:%S UTC %Y")
>>
>> where 'str' is the output of the *remote* call to date. My mac returns
>> this:
>> rbanerjee:~/starcluster/StarCluster/starcluster/balancers/sge $ date
>> Tue Apr 30 13:12:44 EDT 2013
>>
>> Which looks like it would time format OK. One oddity is that your time
>> format is returning PDT when UTC is expected:
>>
>> ValueError: time data 'Tue Apr 30 07:01:35 PDT 2013' does not match
>> format '%a %b %d %H:%M:%S UTC %Y'
>>
>> Not sure what's causing the problems since it looks mostly right, but
>> feel free to tweak the time setting in the code in
>> starcluster/balancers/sge/__init__.py line 466 to make the pattern match
>> yours. Do you know why your time zone may be set differently than other AWS
>> instances we've used? Custom images?
>> Best,
>> Rajat
>>
>>
>>
>>
>> On Tue, Apr 30, 2013 at 12:43 PM, <starcluster-request_at_mit.edu> wrote:
>>
>>> Send StarCluster mailing list submissions to
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>>> To subscribe or unsubscribe via the World Wide Web, visit
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>>> When replying, please edit your Subject line so it is more specific
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>>> Today's Topics:
>>>
>>> 1. Unable to mount ebs volume (Jerry Lee, GW/US)
>>> 2. LoadBalance (Sergio Mafra)
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: "Jerry Lee, GW/US" <Jerry.Lee_at_genewiz.com>
>>> To: <starcluster_at_mit.edu>
>>> Cc:
>>> Date: Mon, 15 Apr 2013 17:11:38 -0500
>>> Subject: [StarCluster] Unable to mount ebs volume
>>>
>>> Hi,****
>>>
>>> ** **
>>>
>>> I am a beginner of using the StarCluster. I created a ebs volme via
>>> Amazon AWS and configure it on the config file to use it for my cluster,
>>> but no matter what I do, it doesn't automatically mount the ebs volume onto
>>> the cluster. Please help.****
>>>
>>> ** **
>>>
>>> [cluster jerrycluster]****
>>>
>>> EXTENDS = smallcluster****
>>>
>>> VOLUMES = testdata****
>>>
>>> ** **
>>>
>>> [volume testdata]****
>>>
>>> VOLUME_ID=vol-a0fe24f9****
>>>
>>> MOUNT_PATH=/data****
>>>
>>> ** **
>>>
>>> >>> Waiting for cluster to come up... (updating every 30s)****
>>>
>>> >>> Waiting for instances to activate...****
>>>
>>> >>> Waiting for all nodes to be in a 'running' state...****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Waiting for SSH to come up on all nodes...****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Waiting for cluster to come up took 1.847 mins****
>>>
>>> >>> The master node is ec2-54-234-229-206.compute-1.amazonaws.com****
>>>
>>> >>> Setting up the cluster...****
>>>
>>> >>> Configuring hostnames...****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Creating cluster user: None (uid: 1001, gid: 1001)****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Configuring scratch space for user(s): sgeadmin****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Configuring /etc/hosts on each node****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Starting NFS server on master****
>>>
>>> >>> Configuring NFS exports path(s):****
>>>
>>> /home****
>>>
>>> >>> Mounting all NFS export path(s) on 1 worker node(s)****
>>>
>>> 1/1 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Setting up NFS took 0.073 mins****
>>>
>>> >>> Configuring passwordless ssh for root****
>>>
>>> >>> Configuring passwordless ssh for sgeadmin****
>>>
>>> >>> Shutting down threads...****
>>>
>>> 20/20 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Configuring SGE...****
>>>
>>> >>> Configuring NFS exports path(s):****
>>>
>>> /opt/sge6****
>>>
>>> >>> Mounting all NFS export path(s) on 1 worker node(s)****
>>>
>>> 1/1 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Setting up NFS took 0.020 mins****
>>>
>>> >>> Installing Sun Grid Engine...****
>>>
>>> 1/1 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Creating SGE parallel environment 'orte'****
>>>
>>> 2/2 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Adding parallel environment 'orte' to queue 'all.q'****
>>>
>>> >>> Shutting down threads...****
>>>
>>> 20/20 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> 100%****
>>>
>>> >>> Configuring cluster took 1.325 mins****
>>>
>>> >>> Starting cluster took 3.197 mins****
>>>
>>> ** **
>>>
>>> ** **
>>>
>>> Thanks,****
>>>
>>> ** **
>>>
>>> Jerry Lee****
>>>
>>> ** **
>>>
>>> Jerry Lee****
>>>
>>> Assistant Manager of Global Infrastructure****
>>>
>>> GENEWIZ Inc.****
>>>
>>> 40 Cragwood Road. Suite 201****
>>>
>>> South Plainfield, NJ 07080****
>>>
>>> Phone: 908-222-0711 ext. 3379****
>>>
>>> Fax: 908-333-4511 ****
>>>
>>> jerry.lee_at_genewiz.com****
>>>
>>> www.genewiz.com****
>>>
>>> ****
>>>
>>> This electronic message, including its attachments, is confidential and
>>> proprietary and is solely for the intended recipient. If you are not the
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>>> ** **
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Sergio Mafra <sergiohmafra_at_gmail.com>
>>> To: "starcluster_at_mit.edu" <starcluster_at_mit.edu>
>>> Cc:
>>> Date: Tue, 30 Apr 2013 11:05:45 -0300
>>> Subject: [StarCluster] LoadBalance
>>> Hi fellows,
>>>
>>> Iīm testing StarCluster version 0.999 and so far so good.
>>> one thing that isnīt working is loadbalance. This is what I get:
>>>
>>> ubuntu_at_domU-12-31-39-02-19-36:~$ starcluster loadbalance newcam
>>> StarCluster - (http://star.mit.edu/cluster) (v. 0.9999)
>>> Software Tools for Academics and Researchers (STAR)
>>> Please submit bug reports to starcluster_at_mit.edu
>>>
>>> >>> Starting load balancer (Use ctrl-c to exit)
>>> Maximum cluster size: 3
>>> Minimum cluster size: 1
>>> Cluster growth rate: 1 nodes/iteration
>>>
>>> *** WARNING - Failed to retrieve stats (1/5):
>>> Traceback (most recent call last):
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/balancers/sge/__init__.py",
>>> line 515, in get_stats
>>> self.stat = self._get_stats()
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/balancers/sge/__init__.py",
>>> line 487, in _get_stats
>>> now = self.get_remote_time()
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/balancers/sge/__init__.py",
>>> line 466, in get_remote_time
>>> return datetime.datetime.strptime(str, "%a %b %d %H:%M:%S UTC %Y")
>>> File "/usr/lib/python2.7/_strptime.py", line 325, in _strptime
>>> (data_string, format))
>>> ValueError: time data 'Tue Apr 30 07:01:35 PDT 2013' does not match
>>> format '%a %b %d %H:%M:%S UTC %Y'
>>> *** WARNING - Retrying in 60s
>>> ^CTraceback (most recent call last):
>>> File "/usr/local/bin/starcluster", line 9, in <module>
>>> load_entry_point('StarCluster==0.9999', 'console_scripts',
>>> 'starcluster')()
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/cli.py",
>>> line 313, in main
>>> StarClusterCLI().main()
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/cli.py",
>>> line 257, in main
>>> sc.execute(args)
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/commands/loadbalance.py",
>>> line 90, in execute
>>> lb.run(cluster)
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/balancers/sge/__init__.py",
>>> line 576, in run
>>> self.get_stats()
>>> File "<string>", line 2, in get_stats
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/utils.py",
>>> line 92, in wrap_f
>>> res = func(*arg, **kargs)
>>> File
>>> "/usr/local/lib/python2.7/dist-packages/StarCluster-0.9999-py2.7.egg/starcluster/balancers/sge/__init__.py",
>>> line 521, in get_stats
>>> time.sleep(self.polling_interval)
>>>
>>> Any ideas?
>>>
>>> All Best,
>>>
>>> Sergio
>>>
>>> _______________________________________________
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>>> StarCluster_at_mit.edu
>>> http://mailman.mit.edu/mailman/listinfo/starcluster
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>>>
>>
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>
Received on Sun May 05 2013 - 13:48:34 EDT