Hi Justin,<br>Sorry for the confusion, I used the wrong AMI IDs. stupid mistake that everybody can avoid by following the instructions. I saw it on the webpage but still went ahead and changed that because I want to use the fastest processor on amazon. :(<br>
thank you very much for the software, truly nice work.<br>Chuan<br><br><br><div class="gmail_quote">On Wed, Mar 17, 2010 at 1:51 PM, Justin Riley <span dir="ltr"><<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a>></span> wrote:<br>
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</div>Chuan,<br>
<br>
Responding to your other question concerning GSL and gotoBLAS:<br>
<br>
Installing these locally into a EBS volume is a perfectly reasonable<br>
solution. In fact, this is how I envisioned most people storing their<br>
software/data on StarCluster.<br>
<br>
The other way to do this is to launch an instance, install the software<br>
globally (using apt-get and/or source packages), and then rebundle the<br>
AMI. You could then tell starcluster to use this new AMI in your config<br>
file.<br>
<br>
I will add GSL to the next version of StarCluster's AMI. goto blas must<br>
be custom compiled. I'll have a look at this and if it's not too much<br>
work I'll consider adding it in.<br>
<br>
Hope that helps,<br>
<br>
~Justin<br>
<div class="im"><br>
On 03/17/2010 01:35 PM, chuan gao wrote:<br>
> Hi Justin and Dan,<br>
</div><div class="im">> Sorry for all the trouble, it's all my fault, it turned out that I used<br>
> the wrong AMI type. it worked like a charm after I changed that. I do<br>
> have another question though, I need to use GSL and gotoBLAS for my<br>
> computation, which I didn't find it installed on the cluster, I am<br>
> thinking about compiling these locally on my EBS volume and include the<br>
> library in my code. is there any other better way?<br>
> Thank you all guys for the help!<br>
> Chuan<br>
><br>
><br>
><br>
> On Wed, Mar 17, 2010 at 10:51 AM, Justin Riley <<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a><br>
</div><div><div></div><div class="h5">> <mailto:<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a>>> wrote:<br>
><br>
> Hi Chuan,<br>
><br>
> Have you checked whether or not the EBS volume ever gets to an<br>
> 'attached'<br>
> state using either ElasticFox or the AWS web console?<br>
><br>
> Also, you can run starcluster in debug mode by passing -d option:<br>
><br>
> $ starcluster -d -s<br>
><br>
> This will do the same thing as -s only with debug output enabled.<br>
><br>
> Would you mind sending me that output? Please be careful about any<br>
> sensitive<br>
> data in the output if you cc this list.<br>
><br>
> Thanks,<br>
><br>
> ~Justin<br>
><br>
><br>
> On Wednesday 17 March 2010 1:18:25 am chuan gao wrote:<br>
> > Hi Justin and Dan,<br>
> ><br>
> > Sorry for the late reply cuz I was tied up on a few things.<br>
> ><br>
> > To Justin: I tried it without mount EBS and I still have that<br>
> problem. I<br>
> > believe it's related to this though cuz it happened at the last<br>
> step of<br>
> > configuring the cluster(all machines have been started by that time).<br>
> ><br>
> > To Dan: I did tried reinstall paramiko (not in debug mode though<br>
> since I<br>
> > didn't find out how to do so,) and the system said installed<br>
> sucessfully. I<br>
> > also tried starting the cluster outside the directory without success.<br>
> ><br>
> > I also tried the same thing on another machine which has ubuntu on<br>
> it and I<br>
> > got the same error. I am not the administrator to that machine but<br>
> I guess<br>
> > it should be ubuntu 9.04.<br>
> ><br>
> > any ideas? thank you guys very much for handling this.<br>
> ><br>
> > Chuan<br>
> ><br>
> > On Tue, Mar 16, 2010 at 7:13 PM, Justin Riley <<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a><br>
</div></div><div><div></div><div class="h5">> <mailto:<a href="mailto:jtriley@mit.edu">jtriley@mit.edu</a>>> wrote:<br>
> > > Hi Chuan,<br>
> > ><br>
> > > Sorry to hear you're having issues with StarCluster. I just got<br>
> back in<br>
> > > town,<br>
> > > sorry for the delayed response.<br>
> > ><br>
> > > Dan, as always, thanks for responding :D<br>
> > ><br>
> > > Could you try launching a cluster without using the EBS volume<br>
> and let me<br>
> > > know<br>
> > > if it succeeds? Nicolas Pinto had a similar issue with<br>
> StarCluster and I<br>
> > > believe it only happened for him when using EBS.<br>
> > ><br>
> > > Thanks,<br>
> > ><br>
> > > ~Justin<br>
> > ><br>
> > > On Tuesday 16 March 2010 2:15:12 pm chuan gao wrote:<br>
> > > > I am using the standard AMI<br>
> > > > the OS is ubuntu 9.10<br>
> > > > yes. I can ssh into AMI with no problem. actually, the error<br>
> occured at<br>
> > ><br>
> > > the<br>
> > ><br>
> > > > last step when it is configuring NFS. I checked the AMI on<br>
> amazon and<br>
> > ><br>
> > > they<br>
> > ><br>
> > > > have been started. and my permanent volume has been mounted.<br>
> > > > concerning the error,<br>
> > > > build/bdist.linux-i686/egg/paramiko/sftp_client.py<br>
> > > > I looked into directory<br>
> StarCluster-0.90.1/build/bdist.linux-i686 and<br>
> > > > nothing is there. should there be egg/paramiko/sftp_client.py ?<br>
> > > > Thanks<br>
> > > ><br>
> > > > On Tue, Mar 16, 2010 at 1:46 PM, Dan Yamins <<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a><br>
</div></div><div class="im">> <mailto:<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a>>> wrote:<br>
> > > > > Justin is on this list, so I'm sure he'll respond soon.<br>
> > > > ><br>
> > > > > Are you using the standard AMI, or one you built yourself?<br>
> > > > ><br>
> > > > > Also, what is your operating system and version?<br>
> > > > ><br>
> > > > > Also, can you ssh into instances of the AMI, independently of<br>
> > > > > starcluster?<br>
> > > > ><br>
> > > > > On Tue, Mar 16, 2010 at 1:17 PM, chuan gao<br>
</div>> <<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a> <mailto:<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a>>><br>
<div class="im">> > ><br>
> > > wrote:<br>
> > > > >> Thanks Dan, I am pretty sure that I got paramiko installed<br>
> > > > >> correctly. I'll work on it a bit more.<br>
> > > > >> will Justin have a chance to look at this email list and try to<br>
> > > > >> point out what could be the problem?<br>
> > > > >><br>
> > > > >> On Tue, Mar 16, 2010 at 11:21 AM, Dan Yamins<br>
</div>> <<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a> <mailto:<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a>>><br>
<div><div></div><div class="h5">> > ><br>
> > > wrote:<br>
> > > > >>> Hm. I'm not sure what the problem is (your version is fine).<br>
> > > > >>> Something is clearly wrong with either your paramiko<br>
> installation<br>
> > > > >>> or the way that starcluster is using it.<br>
> > > > >>><br>
> > > > >>> Have you tried testing paramiko outside the context of<br>
> starcluster?<br>
> > > > >>> Try testing it for normal ssh usage. If that fails, then<br>
> you'll<br>
> > > > >>> probably have identified the problem. (I don't know if<br>
> you just<br>
> > > > >>> installed it, perhaps reinstallation would then help.)<br>
> > > > >>><br>
> > > > >>> If paramiko works normally, then perhaps there's an<br>
> argument that<br>
> > > > >>> is being passed on line 109 of starcluster/ssh.py that is<br>
> supposed<br>
> > > > >>> to represent an existing file object, that somehow isn't being<br>
> > > > >>> properly created (probably earlier in the ssh cycle). In this<br>
> > > > >>> case, Justin<br>
> > ><br>
> > > (the<br>
> > ><br>
> > > > >>> creator of starcluster) should probably be the one to<br>
> address your<br>
> > > > >>> problem.<br>
> > > > >>><br>
> > > > >>> Dan<br>
> > > > >>><br>
> > > > >>> On Tue, Mar 16, 2010 at 10:57 AM, chuan gao<br>
</div></div>> <<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a> <mailto:<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a>>><br>
<div class="im">> > ><br>
> > > wrote:<br>
> > > > >>>> paramiko-1.7.6-py2.6.egg<br>
> > > > >>>> Thanks for replying.<br>
> > > > >>>><br>
> > > > >>>> On Tue, Mar 16, 2010 at 9:02 AM, Dan Yamins<br>
</div>> <<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a> <mailto:<a href="mailto:dyamins@gmail.com">dyamins@gmail.com</a>>><br>
<div class="im">> > ><br>
> > > wrote:<br>
> > > > >>>>> On Tue, Mar 16, 2010 at 1:05 AM, chuan gao<br>
</div>> <<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a> <mailto:<a href="mailto:aggie.gao@gmail.com">aggie.gao@gmail.com</a>><br>
<div class="im">> > > ><br>
> > > >wrote:<br>
> > > > >>>>>> Here is the error message:<br>
> > > > >>>>>> >>> Installing Sun Grid Engine...<br>
> > > > >>>>>><br>
> > > > >>>>>> [SNIP]<br>
> > > > >>>>>><br>
> > > > >>>>>><br>
> > > > >>>>>> File<br>
> "build/bdist.linux-i686/egg/paramiko/sftp_client.py",<br>
> > > > >>>>>> line 675, in _read_response<br>
> > > > >>>>>> File<br>
> "build/bdist.linux-i686/egg/paramiko/sftp_client.py",<br>
> > > > >>>>>> line 701, in _convert_status<br>
> > > > >>>>>> IOError: [Errno 2] No such file<br>
> > > > >>>>><br>
> > > > >>>>> What version of paramiko do you have installed?<br>
> > > > >>>>><br>
> > > > >>>>><br>
> > > > >>>>> _______________________________________________<br>
> > > > >>>>> Starcluster mailing list<br>
</div>> > > > >>>>> <a href="mailto:Starcluster@mit.edu">Starcluster@mit.edu</a> <mailto:<a href="mailto:Starcluster@mit.edu">Starcluster@mit.edu</a>><br>
<div class="im">> > > > >>>>> <a href="http://mailman.mit.edu/mailman/listinfo/starcluster" target="_blank">http://mailman.mit.edu/mailman/listinfo/starcluster</a><br>
> ><br>
><br>
><br>
<br>
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