[Starcluster] failed installing Sun Grid Engine...
Justin Riley
jtriley at MIT.EDU
Wed Mar 17 13:51:40 EDT 2010
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Chuan,
Responding to your other question concerning GSL and gotoBLAS:
Installing these locally into a EBS volume is a perfectly reasonable
solution. In fact, this is how I envisioned most people storing their
software/data on StarCluster.
The other way to do this is to launch an instance, install the software
globally (using apt-get and/or source packages), and then rebundle the
AMI. You could then tell starcluster to use this new AMI in your config
file.
I will add GSL to the next version of StarCluster's AMI. goto blas must
be custom compiled. I'll have a look at this and if it's not too much
work I'll consider adding it in.
Hope that helps,
~Justin
On 03/17/2010 01:35 PM, chuan gao wrote:
> 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
> <mailto: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
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:dyamins at gmail.com>>
> > >
> > > wrote:
> > > > >>>>> On Tue, Mar 16, 2010 at 1:05 AM, chuan gao
> <aggie.gao at gmail.com <mailto: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 <mailto:Starcluster at mit.edu>
> > > > >>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
> >
>
>
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