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<p class="MsoNormal">All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Just chiming in here. Admitedly, Rstudio is the only app we have running internally (and I’m the power user on it).
<o:p></o:p></p>
<p class="MsoNormal">We are not using Singularity for Rstudio Server here.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Slightly related, is there a script or tool that can help me identify versions of all the infrastructure components? I feel like there should be one, or maybe there is one and I didn’t read properly …<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Kevin<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:12.0pt">--<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Kevin Manalo, PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Senior Software Engineer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Maryland Advanced Research Computing Center (MARCC)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt">Johns Hopkins University<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt"><a href="mailto:kmanalo@jhu.edu"><span style="color:#0563C1">kmanalo@jhu.edu</span></a> | 410-516-7392<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">OOD-users <ood-users-bounces@lists.osc.edu> on behalf of "Nicklas, Jeremy" <jnicklas@osc.edu><br>
<b>Reply-To: </b>User support mailing list for Open OnDemand <ood-users@lists.osc.edu><br>
<b>Date: </b>Tuesday, February 27, 2018 at 8:51 AM<br>
<b>To: </b>User support mailing list for Open OnDemand <ood-users@lists.osc.edu><br>
<b>Subject: </b>Re: [OOD-users] R Server<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">Hi Shawn,
<o:p></o:p></span></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">> So far I get "no implicit conversion of Hash into Array" when submitting the job.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">If you copied the source from OSC's "bc_osc_rstudio_server" Interactive App:<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">https://github.com/OSC/bc_osc_rstudio_server/<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">then it sounds like your "submit.yml.erb" might have PBS/Torque specific references in it (this is what OSC uses).
You should probably copy your "submit.yml.erb" that you used in your Jupyter app.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">> Has anyone managed to get R Server working?<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">A couple centers have got RStudio Server working, although caution should be taken if you use OSC's "bc_osc_rstudio_server"
Interactive App as it takes advantage of some features in the latest Dashboard app that aren't present in the OnDemand 1.2 release.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">That leaves you with three options:<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">1. Manually update the Dashboard code from the GitHub repo, or wait until OnDemand 1.3 release in March<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">2. Volunteer to install the beta RPM we are currently developing<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">3. Modify the "bc_osc_rstudio_server" app so it works with the current Dashboard<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"> - I believe this means replacing "$(find_port ${host})" with just "$(find_port)" in the template files<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"> - Also, removing the "template/after.sh.erb" since it calls "wait_until_port_used" which doesn't exist yet<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">Also, you will need to install the dependencies on the compute nodes (see README.md). I believe both HPC centers went
the route of using a Singularity image.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Verdana",sans-serif;color:black">--
</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#555555;background:white">Jeremy Nicklas</span></b></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#555555;background:white">Web and Interface App Engineer</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#555555"><br>
</span></span><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://osc.edu/"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#CF102D;background:white;text-decoration:none">Ohio
Supercomputer Center (OSC)</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#555555"><br>
<span style="background:white">A member of the </span></span></span><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://oh-tech.org/"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#CF102D;text-decoration:none">Ohio
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<span style="background:white">Learn more about OSC at </span></span></span><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://osc.edu/"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:9.0pt;font-family:"Verdana",sans-serif;color:#CF102D;text-decoration:none">https://osc.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black"><o:p></o:p></span></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">From:</span></b></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif;color:black">
OOD-users [ood-users-bounces@lists.osc.edu] on behalf of Shawn Doughty [shawn.doughty@tufts.edu]<br>
<b>Sent:</b> Monday, February 26, 2018 8:56 PM<br>
<b>To:</b> User support mailing list for Open OnDemand<br>
<b>Subject:</b> [OOD-users] R Server</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Hi,<o:p></o:p></span></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">Has anyone managed to get R Server working? I know it is not officially supported until
the next release... We have jupyter and jupyterlab working with pilot users (way cool!) and they are now clamoring to test R Server... and Matlab.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">So far I get "no implicit conversion of Hash into Array" when submitting the job.<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><br clear="all">
<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p> </o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">--
<o:p></o:p></span></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica;color:black">Shawn G. Doughty<br>
Senior Research Technology Specialist</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black">, Research Technology<br>
</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica;color:black">Tufts Technology Services (TTS)</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><br>
16 Dearborn Road<br>
Somerville, MA 02144</span></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica;color:black"><br>
617-627-5462<br>
</span></span><span style="mso-bookmark:_MailOriginalBody"></span><a href="https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f" target="_blank"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica">http://it.tufts.edu/</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"></span><span style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><o:p></o:p></span></p>
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