Lehigh ISE / COR@L Lab Wiki

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====== COR@L and COR@L Resources ======
===== Navigation =====

  * [[info:people|People]]
  * [[info:projects|Projects]]
  * [[info:datasets|Data Sets]]
  * [[info:tutorials|Tutorials]]
  * [[info:coral|Resources]]
  * [[info:user_guide|User Guide]]
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				<p>This site provides documentation and resources for the COR@L lab. This is a place where COR@L users can find guides on how to access and use the software available to them. All COR@L users have an account provided to them. Thus, in all of these resources, we assume that you already have a COR@L account. If you have any comments or suggestions, such as recommendations for additional resources to include on this site, please contact <a href="mailto:coral-admin-list@lehigh.edu">COR@L Admins</a>.</p>
<h3>Logging In</h3>
<p>You can log onto our servers using your Lehigh password. You need to be on the Lehigh network (either directly or via VPN) to access our servers. Alternately, you can access the system via the [[tutorial:vpn|Lehigh University Jumphost]].</p>
<h3>Servers Available</h3>
<p>We have the following servers in COR@L. Their purposes are explained next to them.</p>
<h4>coral.ie.lehigh.edu</h4>
<p>Web server of COR@L website. Hosts personal websites of users, MOPTA conference, INFORMS student chapter and some other sites related to the department.</p>
<h4>shark.ie.lehigh.edu</h4>
<p>Shark server manages various software licenses including AMPL license.</p>
<h4>polyps.ie.lehigh.edu</h4>
<p>Polyps is COR@L Lab’s cluster composed of 16 nodes (polyp1-polyp15, polyp30). It is our heavy duty cluster. Polyps has <a href="http://www.adaptivecomputing.com/products/torque" target="_parent">Torque</a> installed as a job scheduler. Torque aims to maximize resource utilization and high throughput by scheduling jobs submitted by users and allocating resources (CPU, memory) of Polyps to them. For a brief introduction to Torque see Software section. Long lasting experiments should be submitted to polyps through Torque. You can also check the load of Polyp nodes from <a href="http://polyps.ie.lehigh.edu/ganglia" target="_parent">ganglia</a> web interface.</p>
<p>You can check hardware section on COR@L website for more technical information about servers.</p>
<h3>Personal Websites</h3>
<p>If you are a professor or PhD student in IS&amp;E department and want a website on COR@L server, let your system admins know through e-mail. We can set up a WordPress page for you.</p>
<h3>Software available on COR@L</h3>
<h4>Operating System</h4>
<p>All servers run Debian 8.10 Jessie.</p>
<h4>Programming Languages, Compilers and Other Developer Tools</h4>
<p>We have C, C++, Fortran compilers available through GCC 4.7.2. GCC also implements shared memory parallel computing with OPENMP 3.1 standard. You can use GCC for your shared memory parallel computations on any polyp node. We also have MPICH2 implementation of MPI distributed parallel computing standard available on polyps.</p>
<p>Python 2.7 is installed on Polyps.</p>
<p>We have GNU Debugger (GDB) for debugging. Emacs and Vi is available as editors. Emacs comes with C/C++ and Python modes. We also have GNU make installed. Subversion and trac are also available. You can use your home directory and shark for setting Subversion repositories.</p>
<h4>Optimization/Numerical Software</h4>
<p>We have following optimization and numerical software available on polyps.</p>
<ul>
<li>CPLEX</li>
<li>COIN-OR Solvers</li>
<li>AMPL</li>
<li>GAMS</li>
<li>MOSEK</li>
<li>MINOS</li>
<li>GUROBI</li>
<li>SEDUMI</li>
<li>EXPRESS</li>
<li>MATLAB</li>
<li>SCIPY/NUMPY</li>
<li>IPOPT</li>
</ul>
<p>Please let your system admins know if any of the software fails. Do not forget to add the failing command or code.</p>
<p>Please let your system admins know if you need software that is not on the list. System admins do not decide the purchase of commercial software, but if it is freely available we will do our best to have it in COR@L Lab.</p>
<h3>User’s Responsibilities</h3>
<ul>
<li>Do not give your password to any other person. Do not let any other person to use COR@L Lab resources like friend, spouse etc. Your account is for your use only.</li>
<li>Do not store data that is not relevant to your academic studies, like personal pictures, videos, etc.</li>
<li>Do not use your account as a backup space.</li>
<li>Keep an eye on your disk usage (you can use “du” command, enter “du –help” for help).</li>
<li>Be very careful with experiments you are conducting. Make sure that your experiments do not write large output files or extremely many of them (like hundred thousands). Keep your output files reasonable. Try to anticipate the output before you run your code.</li>
<li>Keep an eye on your processes after you started them. Act if something seems wrong.</li>
<li>Do not forget to terminate processes that are not useful or will not yield results.</li>
<li>Keep an eye on resource use of your processes (CPU, memory etc.). If it uses excessive memory and starts using swap think about terminating it, if it is not reasonable to let it run then terminate it.</li>
<li>Choose a secure password.</li>
<li>Be careful with your Wordpress webpage. Do not leave comments section on. We get lots of spams if they leaved open.</li>
<li>Your files and user account will not be guaranteed to exist after 6 months of your graduation. We will keep it for 6 months for you to copy your files. After six months we will remove it.</li>
<li>There are two restrictions on processes in polyp1. First restriction is that a process is allowed to run only for 300 CPU time minutes. The second one is a process can use at most 10 Gb of memory. All long lasting experiments should be conducted through condor. You can see some guiding examples at directory “/scratch/coral_introduction” in polyp1. There are no restrictions in polyp2-12, they are only bounded by the hardware installed.</li>
<li>If you are not a PhD student in ISE department and have an account to use in one of the courses you take (like IE406) your account will be removed after two weeks the classes ended. You are supposed to copy your files in these two weeks.</li>
<li>Always protect your key pair with a passphrase when configuring Passwordless SSH.</li>
</ul>
<h3>Other Resources</h3>
<ul>
<li>If you are a COR@L user and are looking for guidelines on how to use lab resources, then visit the <a href="https://coral.ie.lehigh.edu/wiki/doku.php/info:user_guide"> COR@L users guide. </a></li>
<li>If you are a COR@L administrator, then visit the <a href="/coral-resources/coral-admin"> COR@L system administrator guide. </a></li>
<li>For a list of the hardware available in COR@L, visit the <a href="https://coral.ie.lehigh.edu/wiki/doku.php/coral_lab"> COR@L hardware list </a></li>
<li><a href="https://confluence.cc.lehigh.edu/display/hpc/SSH+public-key+authentication">SSH public-key authentication Setup Guide from LTS with Security Best Practices.</a> </li>
</ul>
						
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==== System Admins and Their Duties ====

You can find the list of system admins [[:coral_lab#administrators|here]]. System admins’ duty is to keep servers running and making sure that we have all the software required by users.
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