Re: Using miniconda on EBS volume to run ipython notebook with ipcluster plugin on starcluster

From: Jacob Barhak <no email>
Date: Thu, 1 Dec 2016 13:38:06 -0600

So Dylan,

Did you install Ipython on all nodes?

It is the first thing that comes to mind.

There are plugins that come with starcluster to install other software
through pip. Did you use one of there?

The third thing at comes to mind is using the Ipython plugin:

http://star.mit.edu/cluster/docs/latest/plugins/ipython.html#ipcluster-plugin

It is hard to fully understand what you do, yet I hope on of these paths
will be relevant towards a solution.

        Jacob

On Nov 30, 2016 5:06 PM, "Dylan Kotliar" <dkotliar_at_broadinstitute.org>
wrote:

> Hello all,
>
> I am currently using Starcluster by mounting an EBS volume containing much
> of the software I want to use including python as version controlled by
> miniconda. I have written a plugin that copies necessary hidden files (e.g.
> .bashrc) to the home directory so that the environment is configured when I
> ssh to the master node and the python stored on the EBS volume is used by
> default.
>
> Now I would like to use the ipcluster plugin to open ipython notebooks in
> the cluster. However, I get the error message:
>
> Running plugin starcluster.plugins.ipcluster.IPCluster !!! ERROR - Error
> occured while running plugin 'starcluster.plugins.ipcluster.IPCluster':
> !!! ERROR - IPython is not installed!
>
> This must be because the ipcluster plugin is using the default version of
> python rather than my version controlled version. This is despite the fact
> that when I ssh to the cluster, the python in the environment is the
> correct one (the one on the EBS volume). Any suggestions on how to
> circumvent this?
>
> Thanks!
>
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Received on Thu Dec 01 2016 - 14:38:08 EST