[Starcluster] error when starting cluster
Damian Eads
eads at soe.ucsc.edu
Tue Apr 20 19:05:11 EDT 2010
I just added 6 instances to make the total 8 high cpu instances
(c1.xlarge). I rebooted the existing instances, restarted the cluster,
and the cluster started without any errors or warnings. I tried
running my code over 64 cores and after a while NFS fails.
[domU-12-31-38-04-A1-11:04233] [[651,0],3] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-04-A1-11:04233] [[651,0],3]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
[domU-12-31-38-04-A1-11:04233] [[651,0],3] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-04-A1-11:04233] [[651,0],3]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
[domU-12-31-38-04-A0-01:04255] [[651,0],2] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-01-61-81:02915] [[651,0],1]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
[domU-12-31-38-01-61-81:02915] [[651,0],1] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-01-61-81:02915] [[651,0],1]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
[domU-12-31-38-01-61-81:02915] [[651,0],1] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-01-61-81:02915] [[651,0],1]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
[domU-12-31-38-01-61-81:02915] [[651,0],1] routed:binomial: Connection
to lifeline [[651,0],0] lost
[domU-12-31-38-01-61-81:02915] [[651,0],1]->[[651,0],0]
mca_oob_tcp_msg_send_handler: writev failed: Bad file descriptor (9)
[sd = 9]
I then tried rebooting all the instances, detaching volumes, and
restarting the cluster but it hangs.
eads at street:~/work/repo/StarCluster$ starcluster start -x
--cluster-size 8 mycluster dtest
/tmp/qqq/lib/python2.6/site-packages/pycrypto-2.0.1-py2.6-linux-x86_64.egg/Crypto/Hash/SHA.py:6:
DeprecationWarning: the sha module is deprecated; use the hashlib
module instead
/tmp/qqq/lib/python2.6/site-packages/pycrypto-2.0.1-py2.6-linux-x86_64.egg/Crypto/Hash/MD5.py:6:
DeprecationWarning: the md5 module is deprecated; use hashlib instead
/var/lib/python-support/python2.6/IPython/Magic.py:38:
DeprecationWarning: the sets module is deprecated
from sets import Set
StarCluster - (http://web.mit.edu/starcluster)
Software Tools for Academics and Researchers (STAR)
Please submit bug reports to starcluster at mit.edu
>>> Validating cluster settings...
>>> Cluster settings are valid
>>> Starting cluster...
>>> Waiting for cluster to start...-
I know this output isn't very helpful. I'll see if I can reproduce the error.
Cheers,
Damian
On Tue, Apr 20, 2010 at 3:02 PM, Justin Riley <jtriley at mit.edu> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi Damian,
>
>> It worked, thanks very much for the prompt fix.
>
> Excellent, glad to hear that.
>
>> Tell me if you think this will work.
>
> Yep that should work although I don't believe you'll need to reboot the
> instances or even detach the volumes but it shouldn't hurt. The big
> thing is to make sure you have cluster_size consistent with how many
> running nodes are in the cluster's security group. So, you might need to
> do the following assuming your cluster template (mycluster) has
> cluster_size=8 and that there are actually 2 running instances:
>
> $ starcluster start -x --cluster-size 2 mycluster dtest
>
> Hope that helps,
>
> ~Justin
>
>
>
> On 04/20/2010 05:44 PM, Damian Eads wrote:
>> Hi Justin,
>>
>> It worked, thanks very much for the prompt fix. Before I received your
>> e-mail, I killed 6 of my 8 octcore instances to save money. Tell me if
>> you think this will work.
>>
>> 1. Through the AWS web console, detach currently used volumes.
>> 2. Manually reboot the instances currently running.
>> 3. Manually launch additional spot instances in the same
>> availability group as the ones currently running.
>> 4. Rerun starcluster start -x mycluster dtest
>>
>> Being able to restart the cluster without first terminating the
>> instances and then relaunching them will save money. Do you think this
>> will work? I don't mind doing it manually.
>>
>> Thanks a lot in advance!
>>
>> Damian
>>
>>
>> On Tue, Apr 20, 2010 at 2:16 PM, Justin Riley <jtriley at mit.edu> wrote:
>> Hi Damian,
>>
>> I believe I've fixed this in github. Could you pull and give it another
>> shot?
>>
>> Also, I've added support for master/node001/etc aliases to the sshnode
>> action. So, you should now be able to:
>>
>> $ starcluster sshnode mycluster master
>> $ starcluster sshnode mycluster node001
>> etc
>>
>> Please let me know if the latest github code fixes your problem below
>> and if you have any other issues.
>>
>> Thanks,
>>
>> ~Justin
>>
>> On 04/20/2010 04:38 PM, Damian Eads wrote:
>>>>> Hi Justin,
>>>>>
>>>>> I just did a git pull and got the following error when I tried
>>>>> creating my cluster. Ideas?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Damian
>>>>>
>>>>> eads at street:~/work/repo/StarCluster$ starcluster start -x mycluster dtest
>>>>> /tmp/qqq/lib/python2.6/site-packages/pycrypto-2.0.1-py2.6-linux-x86_64.egg/Crypto/Hash/SHA.py:6:
>>>>> DeprecationWarning: the sha module is deprecated; use the hashlib
>>>>> module instead
>>>>> /tmp/qqq/lib/python2.6/site-packages/pycrypto-2.0.1-py2.6-linux-x86_64.egg/Crypto/Hash/MD5.py:6:
>>>>> DeprecationWarning: the md5 module is deprecated; use hashlib instead
>>>>> /var/lib/python-support/python2.6/IPython/Magic.py:38:
>>>>> DeprecationWarning: the sets module is deprecated
>>>>> from sets import Set
>>>>> StarCluster - (http://web.mit.edu/starcluster)
>>>>> Software Tools for Academics and Researchers (STAR)
>>>>> Please submit bug reports to starcluster at mit.edu
>>>>>
>>>>>>>> Validating cluster settings...
>>>>>>>> Cluster settings are valid
>>>>>>>> Starting cluster...
>>>>>>>> Waiting for cluster to start...
>>>>>>>> The master node is ec2-174-129-172-124.compute-1.amazonaws.com
>>>>>>>> Attaching volume vol-c5e85dac to master node...
>>>>>>>> Setting up the cluster...
>>>>>>>> Mounting EBS volume vol-c5e85dac on /data...
>>>>> ssh.py:66 - WARNING - specified key does not end in either rsa or dsa,
>>>>> trying both
>>>>>>>> Using private key /home/eads/deadskey.pem (rsa)
>>>>> ERROR: An unexpected error occurred while tokenizing input
>>>>> The following traceback may be corrupted or invalid
>>>>> The error message is: ('EOF in multi-line statement', (405, 0))
>>>>>
>>>>> ---------------------------------------------------------------------------
>>>>> TypeError Traceback (most recent call last)
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/EGG-INFO/scripts/starcluster
>>>>> in <module>()
>>>>> 3 __requires__ = 'StarCluster==0.9999'
>>>>> 4 import pkg_resources
>>>>> ----> 5 pkg_resources.run_script('StarCluster==0.9999', 'starcluster')
>>>>> 6
>>>>> 7
>>>>>
>>>>> /usr/lib/python2.6/dist-packages/pkg_resources.pyc in run_script(self,
>>>>> requires, script_name)
>>>>> 446 ns.clear()
>>>>> 447 ns['__name__'] = name
>>>>> --> 448 self.require(requires)[0].run_script(script_name, ns)
>>>>> 449
>>>>> 450
>>>>>
>>>>> /usr/lib/python2.6/dist-packages/pkg_resources.pyc in run_script(self,
>>>>> script_name, namespace)
>>>>> 1171 )
>>>>> 1172 script_code = compile(script_text,script_filename,'exec')
>>>>> -> 1173 exec script_code in namespace, namespace
>>>>> 1174
>>>>> 1175 def _has(self, path):
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/EGG-INFO/scripts/starcluster
>>>>> in <module>()
>>>>> 4
>>>>> 5
>>>>> ----> 6
>>>>> 7
>>>>> 8
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/cli.pyc
>>>>> in main()
>>>>> 850 sys.exit(0)
>>>>> 851 try:
>>>>> --> 852 sc.execute(args)
>>>>> 853 except exception.BaseException,e:
>>>>> 854 log.error(e.msg)
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/cli.pyc
>>>>> in execute(self, args)
>>>>> 169 log.info('Cluster settings are valid')
>>>>> 170 if not self.opts.validate_only:
>>>>> --> 171 scluster.start(create=not self.opts.no_create)
>>>>> 172 if self.opts.login_master:
>>>>> 173 cluster.ssh_to_master(tag, self.cfg)
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/utils.pyc
>>>>> in wrapper(*arg, **kargs)
>>>>> 23 """Raw timing function """
>>>>> 24 time1 = time.time()
>>>>> ---> 25 res = func(*arg, **kargs)
>>>>> 26 time2 = time.time()
>>>>> 27 log.info('%s took %0.3f mins' % (func.func_name,
>>>>> (time2-time1)/60.0))
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/cluster.pyc
>>>>> in start(self, create)
>>>>> 476 self.nodes, self.master_node,
>>>>> 477 self.cluster_user, self.cluster_shell,
>>>>> --> 478 self.volumes
>>>>> 479 )
>>>>> 480 self.create_receipt()
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/clustersetup.pyc
>>>>> in run(self, nodes, master, user, user_shell, volumes)
>>>>> 312 self._volumes = volumes
>>>>> 313 self._setup_ebs_volume()
>>>>> --> 314 self._setup_cluster_user()
>>>>> 315 self._setup_scratch()
>>>>> 316 self._setup_etc_hosts()
>>>>>
>>>>> /tmp/qqq/lib/python2.6/site-packages/StarCluster-0.9999-py2.6.egg/starcluster/clustersetup.pyc
>>>>> in _setup_cluster_user(self)
>>>>> 67 max_uid = max(uid_db.keys())
>>>>> 68 max_gid = uid_db[max_uid][1]
>>>>> ---> 69 uid, gid = max_uid+1, max_gid+1
>>>>> 70
>>>>> 71 log.debug("Cluster user gid/uid: (%d, %d)" % (uid,gid))
>>>>>
>>>>> TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
>>>>> eads at street:~/work/repo/StarCluster$
>>>>> _______________________________________________
>>>>> Starcluster mailing list
>>>>> Starcluster at mit.edu
>>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>
>>>
>
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--
-----------------------------------------------------
Damian Eads Ph.D. Candidate
University of California Computer Science
1156 High Street Machine Learning Lab, E2-489
Santa Cruz, CA 95064 http://www.soe.ucsc.edu/~eads
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