[StarCluster] plugin shell help
Dan Tenenbaum
dtenenba at fhcrc.org
Sat Oct 30 14:45:48 EDT 2010
Keeping this on the list.
BTW, the new cluster.py has no syntax errors, so something else must be
happening.
Dan
On Sat, Oct 30, 2010 at 11:44 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Thanks. That gave me a different error, below.
> The first time this happened, I did:
> sudo easy_install iptools, but it is still happening.
>
> Dan
>
> $ starcluster shell
> Leopard libedit detected.
> 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))
>
> ---------------------------------------------------------------------------
> ImportError Traceback (most recent call last)
>
> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/EGG-INFO/scripts/starcluster
> in <module>()
> 3 __requires__ = 'StarCluster==0.91'
> 4 import pkg_resources
> ----> 5 pkg_resources.run_script('StarCluster==0.91', 'starcluster')
> 6
> 7
>
> /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.pyc
> in run_script(self, requires, script_name)
> 440 ns.clear()
> 441 ns['__name__'] = name
> --> 442 self.require(requires)[0].run_script(script_name, ns)
> 443
> 444
>
> /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.pyc
> in run_script(self, script_name, namespace)
> 1165 )
> 1166 script_code =
> compile(script_text,script_filename,'exec')
> -> 1167 exec script_code in namespace, namespace
> 1168
> 1169 def _has(self, path):
>
> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/EGG-INFO/scripts/starcluster
> in <module>()
> 1
> ----> 2 #!/usr/bin/python
>
> 3 # EASY-INSTALL-SCRIPT: 'StarCluster==0.91','starcluster'
>
> 4 __requires__ = 'StarCluster==0.91'
> 5 import pkg_resources
> 6 pkg_resources.run_script('StarCluster==0.91', 'starcluster')
>
> /Users/dante/.starcluster/build/bdist.macosx-10.6-universal/egg/starcluster/cli.py
> in <module>()
> 36
> 37
> ---> 38
> 39
> 40
>
> /Users/dante/.starcluster/build/bdist.macosx-10.6-universal/egg/starcluster/cluster.py
> in <module>()
> 10
> 11
> ---> 12
> 13
> 14
>
> ImportError: cannot import name iptools
>
>
> On Sat, Oct 30, 2010 at 11:38 AM, Marc Resnick <mresnick at mit.edu> wrote:
>
>> The version here
>>
>> http://github.com/jtriley/StarCluster/blob/experimental/starcluster/cluster.py
>> may have those bugs fixed, as I remember that one as well.
>>
>>
>> Marc
>>
>> On Sat, Oct 30, 2010 at 2:31 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> wrote:
>> > I already did that. ;)
>> > Now I'm getting another error:
>> > In [1]: cluster.run_plugin("shortreadplugin","myfirstcluster",cfg)
>> >>>> Using private key /Users/dante/.ec2/bioc-keypair.pem.rsa (rsa)
>> >
>> ---------------------------------------------------------------------------
>> > AttributeError Traceback (most recent call
>> last)
>> >
>> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/starcluster/cli.pyc
>> > in <module>()
>> > ----> 1
>> > 2
>> > 3
>> > 4
>> > 5
>> >
>> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/starcluster/cluster.pyc
>> > in run_plugin(plugin_name, cluster_tag, cfg)
>> > 175 plugins = {}
>> > 176 plugins[plugin_name] = plug
>> > --> 177 plugins = cl.load_plugins(plugins)
>> > 178 master = cl.master_node
>> > 179 for p in plugins:
>> >
>> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/starcluster/cluster.pyc
>> > in load_plugins(self, plugins)
>> > 314 plugs = []
>> > 315 for plugin in plugins:
>> > --> 316 setup_class = plugin.get('setup_class')
>> > 317 plugin_name = plugin.get('__name__')
>> > 318 mod_name = '.'.join(setup_class.split('.')[:-1])
>> > AttributeError: 'str' object has no attribute 'get'
>> > Hmm....
>> > Dan
>> >
>> > On Sat, Oct 30, 2010 at 11:27 AM, Marc Resnick <mresnick at mit.edu>
>> wrote:
>> >>
>> >> Yes, that's the bug I told Justin about this Summer... I think I
>> >> patched it, but he may have forgotten to pull from my fork.
>> >>
>> >> You can fix it by editing the run_plugin method, and replacing
>> >>
>> >> cl = get_cluster(cluster_tag)
>> >>
>> >> with
>> >>
>> >> cl = get_cluster(cluster_tag, cfg)
>> >>
>> >>
>> >>
>> >> Marc
>> >>
>> >>
>> >> On Sat, Oct 30, 2010 at 2:20 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> wrote:
>> >> > Hi Marc,
>> >> > I am running 0.91.
>> >> > I was doing a couple things wrong. I figured them out but I am still
>> >> > having
>> >> > this problem.
>> >> > One thing I did wrong was have the
>> >> > plugins=shortreadplugin
>> >> > line under the global section; it needed to be under the
>> >> > [cluster smallcluster]
>> >> > section.
>> >> > When I start the cluster now, I can see the output from my plugin:
>> >> >>>> Running plugin shortreadplugin
>> >> >>>> about to echo
>> >> > But, when I run the shell and put in this command:
>> >> > cluster.run_plugin("shortreadplugin","myfirstcluster",cfg)
>> >> > I get the same error described below.
>> >> > Dan
>> >> >
>> >> > On Sat, Oct 30, 2010 at 11:11 AM, Marc Resnick <mresnick at mit.edu>
>> wrote:
>> >> >>
>> >> >> Hey Dan,
>> >> >>
>> >> >> Are you running the latest version? I saw that bug a few months ago,
>> I
>> >> >> thought I remember Justin fixing it.
>> >> >>
>> >> >>
>> >> >> Marc
>> >> >>
>> >> >> On Sat, Oct 30, 2010 at 2:00 PM, Dan Tenenbaum <dtenenba at fhcrc.org>
>> >> >> wrote:
>> >> >> > Hi,
>> >> >> > I am not much of a python programmer and I'm trying to figure out
>> the
>> >> >> > plugin
>> >> >> > system.
>> >> >> > I created a ~/.starcluster/plugins directory and put a file in it
>> >> >> > called
>> >> >> > shortread.py.
>> >> >> > Here are its contents:
>> >> >> >
>> >> >> > from starcluster.clustersetup import ClusterSetup
>> >> >> > from starcluster.logger import log
>> >> >> > class ShortReadPlugin(ClusterSetup):
>> >> >> > def __init__(self, arg1):
>> >> >> > self.arg1 = arg1
>> >> >> > log.info('arg1 = %s' % arg1)
>> >> >> > def run(self, nodes, master, user, user_shell, volumes):
>> >> >> > log.info("about to echo")
>> >> >> > master.ssh.execute("echo 'hey'")
>> >> >> > As you can see, it's just a test.
>> >> >> > In my config, I put this at the bottom:
>> >> >> > [plugin shortreadplugin]
>> >> >> > SETUP_CLASS = ShortReadPlugin
>> >> >> > arg1=foo
>> >> >> > And above in the [global] section I put:
>> >> >> > plugins=shortreadplugin
>> >> >> > I'm a bit confused about whether this is right because in your
>> >> >> > example:
>> >> >> > http://web.mit.edu/stardev/cluster/docs/plugins.html
>> >> >> > ...you have the SETUP_CLASS as ubuntu.PackageInstaller. I'm not
>> sure
>> >> >> > where
>> >> >> > the "ubuntu" fits into this. Is it like java where I need to have
>> a
>> >> >> > folder
>> >> >> > called ubuntu where the class resides?
>> >> >> > Anyway, I fired up my cluster and went to test this with
>> "starcluster
>> >> >> > shell"
>> >> >> > and got the following output:
>> >> >> > In [5]: cluster.run_plugin('shortreadplugin', 'myfirstcluster',
>> cfg)
>> >> >> >
>> >> >> >
>> >> >> >
>> ---------------------------------------------------------------------------
>> >> >> > TypeError Traceback (most recent
>> call
>> >> >> > last)
>> >> >> >
>> >> >> >
>> >> >> >
>> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/starcluster/cli.pyc
>> >> >> > in <module>()
>> >> >> > ----> 1
>> >> >> > 2
>> >> >> > 3
>> >> >> > 4
>> >> >> > 5
>> >> >> >
>> >> >> >
>> >> >> >
>> /Library/Python/2.6/site-packages/StarCluster-0.91-py2.6.egg/starcluster/cluster.pyc
>> >> >> > in run_plugin(plugin_name, cluster_tag, cfg)
>> >> >> > 170 def run_plugin(plugin_name, cluster_tag, cfg):
>> >> >> > 171 ec2 = cfg.get_easy_ec2()
>> >> >> > --> 172 cl = get_cluster(cluster_tag)
>> >> >> > 173 cl.load_receipt()
>> >> >> > 174 plug = cfg.get_plugin(plugin_name)
>> >> >> > TypeError: get_cluster() takes exactly 2 arguments (1 given)
>> >> >> >
>> >> >> > It's hard for me to understand what's happening here. I of course
>> am
>> >> >> > not
>> >> >> > calling get_cluster directly. Is there a bug in run_plugin() or is
>> >> >> > there
>> >> >> > something wrong in my setup, or both?
>> >> >> > Thanks
>> >> >> > Dan
>> >> >> >
>> >> >> > _______________________________________________
>> >> >> > StarCluster mailing list
>> >> >> > StarCluster at mit.edu
>> >> >> > http://mailman.mit.edu/mailman/listinfo/starcluster
>> >> >> >
>> >> >> >
>> >> >>
>> >> >
>> >> >
>> >>
>> >
>> >
>>
>>
>
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