<div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small">Hi Teddy,</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 reply. You are spot on about my use case--I am currently trying out many different python environment configurations and different cluster users will want to be managing their own environments. Updating package installation plugins would be one solution but I was trying out this solution instead. Up until this issue, it worked without a hitch. And thanks for the tip about appending the miniconda path to <span style="font-size:12.8px;font-family:arial,sans-serif">/etc/profile.d</span><span style="font-size:12.8px;font-family:arial,sans-serif"> this solved the problem!</span></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><span style="font-size:12.8px;font-family:arial,sans-serif"><br></span></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><span style="font-size:12.8px;font-family:arial,sans-serif">Best,</span></div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"><span style="font-size:12.8px;font-family:arial,sans-serif">Dylan</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Dec 5, 2016 at 12:24 PM, Teddy Thomas <span dir="ltr"><<a href="mailto:tthoma24@mit.edu" target="_blank">tthoma24@mit.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Dylan-<div><br></div><div>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. </div><div><br></div><div>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.</div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-Teddy</div></font></span><div><div class="h5"><div><br></div><div>On Dec 4, 2016, at 5:43 PM, Dylan Kotliar <<a href="mailto:dkotliar@broadinstitute.org" target="_blank">dkotliar@broadinstitute.org</a>> wrote:<div><blockquote type="cite"><br class="m_-2821681374423831428Apple-interchange-newline"><div><div dir="ltr" style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><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" style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div></div></blockquote><blockquote type="cite"><div><div class="gmail_extra" style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div class="gmail_quote">On Fri, Dec 2, 2016 at 2:30 AM, Jacob Barhak<span class="m_-2821681374423831428Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a><wbr>></span><span class="m_-2821681374423831428Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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.<span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr">Using code in centralized storage also implies you need to make sure code is accessible.<span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr">If you install whatever you need on each node upon startup you should be good unless I am missing somethings. <span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr">In any case, getting back to basics and simplifying things may help. <span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr">Good luck.<span class="m_-2821681374423831428Apple-converted-space"> </span></p><span class="m_-2821681374423831428HOEnZb"><font color="#888888"><p dir="ltr"> <span class="m_-2821681374423831428Apple-converted-space"> </span>Jacob<br></p></font></span><div class="m_-2821681374423831428HOEnZb"><div class="m_-2821681374423831428h5"><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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style: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"> <span class="m_-2821681374423831428Apple-converted-space"> </span>for node in nodes:</div><div class="gmail_default" style="font-family:tahoma,sans-serif;font-size:small"> <span class="m_-2821681374423831428Apple-converted-space"> </span>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 class="m_-2821681374423831428Apple-converted-space"> </span><span dir="ltr"><<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a><wbr>></span><span class="m_-2821681374423831428Apple-converted-space"> </span>wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><p dir="ltr">So Dylan,</p><p dir="ltr">Did you install Ipython on all nodes?<span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr">It is the first thing that comes to mind.<span class="m_-2821681374423831428Apple-converted-space"> </span></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:<span class="m_-2821681374423831428Apple-converted-space"> </span></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.<span class="m_-2821681374423831428Apple-converted-space"> </span></p><p dir="ltr"> <span class="m_-2821681374423831428Apple-converted-space"> </span>Jacob</p><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_-2821681374423831428m_-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-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><div class="m_-2821681374423831428m_-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><br></div></div>______________________________<wbr>_________________<br>StarCluster mailing list<br><a href="mailto:StarCluster@mit.edu" target="_blank">StarCluster@mit.edu</a><br><a href="http://mailman.mit.edu/mailman/listinfo/starcluster" rel="noreferrer" target="_blank">http://mailman.mit.edu/mailman<wbr>/listinfo/starcluster</a><br><br></blockquote></div></div></blockquote></div><br><br clear="all"><div><br></div>--<span class="m_-2821681374423831428Apple-converted-space"> </span><br><div class="m_-2821681374423831428m_-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:<span class="m_-2821681374423831428Apple-converted-space"> </span><a href="tel:(732)%20379-0215" value="+17323790215" target="_blank">732-379-0215</a></div></div></div></div></div></div></div></div></div></blockquote></div></div></div></div></blockquote></div><br><br clear="all"><div><br></div>--<span class="m_-2821681374423831428Apple-converted-space"> </span><br><div class="m_-2821681374423831428gmail_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: <a href="tel:(732)%20379-0215" value="+17323790215" target="_blank">732-379-0215</a></div></div></div></div></div></div></div></div><span style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">______________________________<wbr>_________________</span><br style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">StarCluster mailing list</span><br style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href="mailto:StarCluster@mit.edu" style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">StarCluster@mit.edu</a><br style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><a href="http://mailman.mit.edu/mailman/listinfo/starcluster" style="font-family:HelveticaNeue;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">http://mailman.mit.edu/<wbr>mailman/listinfo/starcluster</a></div></blockquote></div><br></div></div></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>
</div>