[Starcluster] failed installing Sun Grid Engine...

Wed Mar 17 13:35:36 EDT 2010

Hi Justin and Dan,
Sorry for all the trouble,  it's all my fault, it turned out that I used the
wrong AMI type. it worked like a charm after I changed that. I do have
another question though, I need to use GSL and gotoBLAS for my computation,
which I didn't find it installed on the cluster, I am thinking about
compiling these locally on my EBS volume and include the library in my code.
is there any other better way?
Thank you all guys for the help!
Chuan

On Wed, Mar 17, 2010 at 10:51 AM, Justin Riley <jtriley at mit.edu> wrote:

> Hi Chuan,
>
> Have you checked whether or not the EBS volume ever gets to an 'attached'
> state using either ElasticFox or the AWS web console?
>
> Also, you can run starcluster in debug mode by passing -d option:
>
> $ starcluster -d -s
>
> This will do the same thing as -s only with debug output enabled.
>
> Would you mind sending me that output? Please be careful about any
> sensitive
> data in the output if you cc this list.
>
> Thanks,
>
> ~Justin
>
>
> On Wednesday 17 March 2010 1:18:25 am chuan gao wrote:
> > Hi Justin and Dan,
> >
> > Sorry for the late reply cuz I was tied up on a few things.
> >
> > To Justin: I tried it without mount EBS and I still have that problem. I
> > believe it's related to this though cuz it happened at the last step of
> > configuring the cluster(all machines have been started by that time).
> >
> > To Dan: I did tried reinstall paramiko (not in debug mode though since I
> > didn't find out how to do so,) and the system said installed sucessfully.
> I
> > also tried starting the cluster outside the directory without success.
> >
> > I also tried the same thing on another machine which has ubuntu on it and
> I
> > got the same error. I am not the administrator to that machine but I
> guess
> > it should be ubuntu 9.04.
> >
> > any ideas?  thank you guys very much for handling this.
> >
> > Chuan
> >
> > On Tue, Mar 16, 2010 at 7:13 PM, Justin Riley <jtriley at mit.edu> wrote:
> > > Hi Chuan,
> > >
> > > Sorry to hear you're having issues with StarCluster. I just got back in
> > > town,
> > > sorry for the delayed response.
> > >
> > > Dan, as always, thanks for responding :D
> > >
> > > Could you try launching a cluster without using the EBS volume and let
> me
> > > know
> > > if it succeeds? Nicolas Pinto had a similar issue with StarCluster and
> I
> > > believe it only happened for him when using EBS.
> > >
> > > Thanks,
> > >
> > > ~Justin
> > >
> > > On Tuesday 16 March 2010 2:15:12 pm chuan gao wrote:
> > > > I am using the standard AMI
> > > > the OS is  ubuntu 9.10
> > > > yes. I can ssh into AMI with no problem. actually, the error occured
> at
> > >
> > > the
> > >
> > > > last step when it is configuring NFS. I checked the AMI on amazon and
> > >
> > > they
> > >
> > > > have been started. and my permanent volume has been mounted.
> > > > concerning the error,
> > > > build/bdist.linux-i686/egg/paramiko/sftp_client.py
> > > > I looked into directory StarCluster-0.90.1/build/bdist.linux-i686 and
> > > > nothing is there. should there be egg/paramiko/sftp_client.py ?
> > > > Thanks
> > > >
> > > > On Tue, Mar 16, 2010 at 1:46 PM, Dan Yamins <dyamins at gmail.com>
> wrote:
> > > > > Justin is on this list, so I'm sure he'll respond soon.
> > > > >
> > > > > Are you using the standard AMI, or one you built yourself?
> > > > >
> > > > > Also, what is your operating system and version?
> > > > >
> > > > > Also, can you ssh into instances of the AMI, independently of
> > > > > starcluster?
> > > > >
> > > > > On Tue, Mar 16, 2010 at 1:17 PM, chuan gao <aggie.gao at gmail.com>
> > >
> > > wrote:
> > > > >> Thanks Dan, I am pretty sure that I got paramiko installed
> > > > >> correctly. I'll work on it a bit more.
> > > > >> will Justin have a chance to look at this email list and try to
> > > > >> point out what could be the problem?
> > > > >>
> > > > >> On Tue, Mar 16, 2010 at 11:21 AM, Dan Yamins <dyamins at gmail.com>
> > >
> > > wrote:
> > > > >>> Hm.  I'm not sure what the problem is (your version is fine).
> > > > >>> Something is clearly wrong with either your paramiko installation
> > > > >>> or the way that starcluster is using it.
> > > > >>>
> > > > >>> Have you tried testing paramiko outside the context of
> starcluster?
> > > > >>> Try testing it for normal ssh usage.  If that fails, then you'll
> > > > >>> probably have identified the problem.   (I don't know if you just
> > > > >>> installed it, perhaps reinstallation would then help.)
> > > > >>>
> > > > >>> If paramiko works normally, then perhaps there's an argument that
> > > > >>> is being passed on line 109 of starcluster/ssh.py that is
> supposed
> > > > >>> to represent an existing file object, that somehow isn't being
> > > > >>> properly created (probably earlier in the ssh cycle).  In this
> > > > >>> case, Justin
> > >
> > > (the
> > >
> > > > >>> creator of starcluster) should probably be the one to address
> your
> > > > >>> problem.
> > > > >>>
> > > > >>> Dan
> > > > >>>
> > > > >>> On Tue, Mar 16, 2010 at 10:57 AM, chuan gao <aggie.gao at gmail.com
> >
> > >
> > > wrote:
> > > > >>>> paramiko-1.7.6-py2.6.egg
> > > > >>>> Thanks for replying.
> > > > >>>>
> > > > >>>> On Tue, Mar 16, 2010 at 9:02 AM, Dan Yamins <dyamins at gmail.com>
> > >
> > > wrote:
> > > > >>>>> On Tue, Mar 16, 2010 at 1:05 AM, chuan gao <
> aggie.gao at gmail.com
> > > >
> > > >wrote:
> > > > >>>>>> Here is the error message:
> > > > >>>>>> >>> Installing Sun Grid Engine...
> > > > >>>>>>
> > > > >>>>>> [SNIP]
> > > > >>>>>>
> > > > >>>>>>
> > > > >>>>>>   File "build/bdist.linux-i686/egg/paramiko/sftp_client.py",
> > > > >>>>>> line 675, in _read_response
> > > > >>>>>>   File "build/bdist.linux-i686/egg/paramiko/sftp_client.py",
> > > > >>>>>> line 701, in _convert_status
> > > > >>>>>> IOError: [Errno 2] No such file
> > > > >>>>>
> > > > >>>>> What version of paramiko do you have installed?
> > > > >>>>>
> > > > >>>>>
> > > > >>>>> _______________________________________________
> > > > >>>>> Starcluster mailing list
> > > > >>>>> Starcluster at mit.edu
> > > > >>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
> >
>
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