<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">OK, I have come around to this. Thanks!</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Dec 2, 2016 at 2:30 AM, Jacob Barhak <span dir="ltr"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">So Dylan,</p>
<p dir="ltr">It seems you are trying to bypass installation. I suggest avoiding shortcuts. </p>
<p dir="ltr">Using code in centralized storage also implies you need to make sure code is accessible. </p>
<p dir="ltr">If you install whatever you need on each node upon startup you should be good unless I am missing somethings. </p>
<p dir="ltr">In any case, getting back to basics and simplifying things may help. </p>
<p dir="ltr">Good luck. </p><span class="HOEnZb"><font color="#888888">
<p dir="ltr"> Jacob<br>
</p></font></span><div class="HOEnZb"><div class="h5">
<div class="gmail_extra"><br><div class="gmail_quote">On Dec 2, 2016 1:29 AM, "Dylan Kotliar" <<a href="mailto:dkotliar@broadinstitute.org" target="_blank">dkotliar@broadinstitute.org</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">Hi Jacob,</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">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:</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">export PATH="path_to_EBS_volume/bin/m<wbr>iniconda2/bin:$PATH"</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">source activate python2</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">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:</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"> for node in nodes:</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"> node.ssh.execute("source ~/.bashrc")</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">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.</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">Thanks,</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">Dylan</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><br></div></div></div><div class="gmail_extra"><div class="gmail_quote">On Thu, Dec 1, 2016 at 2:38 PM, Jacob Barhak <span dir="ltr"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p dir="ltr">So Dylan,</p>
<p dir="ltr">Did you install Ipython on all nodes? </p>
<p dir="ltr">It is the first thing that comes to mind. </p>
<p dir="ltr">There are plugins that come with starcluster to install other software through pip. Did you use one of there?</p>
<p dir="ltr">The third thing at comes to mind is using the Ipython plugin: </p>
<p dir="ltr"><a href="http://star.mit.edu/cluster/docs/latest/plugins/ipython.html#ipcluster-plugin" target="_blank">http://star.mit.edu/cluster/do<wbr>cs/latest/plugins/ipython.html<wbr>#ipcluster-plugin</a></p>
<p dir="ltr">It is hard to fully understand what you do, yet I hope on of these paths will be relevant towards a solution. </p>
<p dir="ltr"> Jacob</p>
<div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_-5499363289221940182m_2449955862102617883gmail-h5">On Nov 30, 2016 5:06 PM, "Dylan Kotliar" <<a href="mailto:dkotliar@broadinstitute.org" target="_blank">dkotliar@broadinstitute.org</a>> wrote:<br type="attribution"></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="m_-5499363289221940182m_2449955862102617883gmail-h5"><div dir="ltr"><div style="font-family:tahoma,sans-serif;font-size:small"><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">Hello all,</p><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">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.<br></p><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">Now I would like to use the ipcluster plugin to open ipython notebooks in the cluster. However, I get the error message:</p><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">Running plugin starcluster.plugins.ipcluster.<wbr>IPCluster !!! ERROR - Error occured while running plugin 'starcluster.plugins.ipcluster<wbr>.IPCluster': !!! ERROR - IPython is not installed!</p><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">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?</p><p style="margin:0px 0px 1em;padding:0px;border:0px;font-size:15px;clear:both;color:rgb(36,39,41);font-family:arial,"helvetica neue",helvetica,sans-serif">Thanks!</p></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="m_-5499363289221940182m_2449955862102617883gmail_signature"><div dir="ltr"><div><div dir="ltr"><div style="font-size:12.8px">Dylan Kotliar, </div><div style="font-size:12.8px">Harvard Medical School (HST) / Systems Biology PhD Program<div>MD/PhD candidate<div>Phone: <a href="tel:(732)%20379-0215" value="+17323790215" target="_blank">732-379-0215</a></div></div></div></div></div></div></div>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div style="font-size:12.8000001907349px">Dylan Kotliar, </div><div style="font-size:12.8000001907349px">Harvard Medical School (HST) / Systems Biology PhD Program<div>MD/PhD candidate<div>Phone: 732-379-0215</div></div></div></div></div></div></div>
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