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

From: Teddy Thomas <no email>
Date: Mon, 5 Dec 2016 12:24:15 -0500

Hi Dylan-

One way you could accomplish what you want would be to write a plugin that modifies /etc/profile.d, rather than just the local homedir, on your machines to include the EBS volume where you’ve included the software in your PATH variable. By default, the profile in /etc/profile.d or /etc/bashrc should be being sourced.

I don’t think Jacob’s impression is correct that what you wanted is considered “taking a shortcut.” I’m sure you have a use case for doing what you want the way you’re trying to. One use case I see for this is having a lot of different packages, and people needing to use different version of the packages simultaneously. In our use of starcluster, we’ve found that it gets painful to need to update plugins to install things with apt on starcluster.

-Teddy

On Dec 4, 2016, at 5:43 PM, Dylan Kotliar <dkotliar_at_broadinstitute.org> wrote:
>
> OK, I have come around to this. Thanks!
>
> On Fri, Dec 2, 2016 at 2:30 AM, Jacob Barhak <jacob.barhak_at_gmail.com <mailto:jacob.barhak_at_gmail.com>> wrote:
> So Dylan,
>
> It seems you are trying to bypass installation. I suggest avoiding shortcuts.
>
> Using code in centralized storage also implies you need to make sure code is accessible.
>
> If you install whatever you need on each node upon startup you should be good unless I am missing somethings.
>
> In any case, getting back to basics and simplifying things may help.
>
> Good luck.
>
> Jacob
>
>
> On Dec 2, 2016 1:29 AM, "Dylan Kotliar" <dkotliar_at_broadinstitute.org <mailto:dkotliar_at_broadinstitute.org>> wrote:
> Hi Jacob,
>
> Thanks for the response. Since IPython is installed on the EBS volume, it should be accessible by all nodes. The only issue is that the EBS volume needs to be on the python path at the time the plugin execute. I have gotten around this by having a .bashrc file with the lines:
>
> export PATH="path_to_EBS_volume/bin/miniconda2/bin:$PATH"
> source activate python2
>
> that gets copied to the root directory upon startup. However, this .bashrc file is not getting sourced prior to running the ipcluster plugin. I tried to address this by extending the IPCluster class to include the following in the run method:
>
> for node in nodes:
> node.ssh.execute("source ~/.bashrc")
>
> However, I still get the "!!! ERROR - IPython is not installed!" error. If I comment out the call to _check_ipython_installed, it fails further on with ipython not found.
>
> Thanks,
> Dylan
>
>
>
> On Thu, Dec 1, 2016 at 2:38 PM, Jacob Barhak <jacob.barhak_at_gmail.com <mailto:jacob.barhak_at_gmail.com>> wrote:
> 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 <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 <mailto: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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>
>
>
> --
> Dylan Kotliar,
> Harvard Medical School (HST) / Systems Biology PhD Program
> MD/PhD candidate
> Phone: 732-379-0215 <tel:(732)%20379-0215>
>
>
> --
> Dylan Kotliar,
> Harvard Medical School (HST) / Systems Biology PhD Program
> MD/PhD candidate
> Phone: 732-379-0215
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Received on Mon Dec 05 2016 - 12:24:20 EST