Lehigh ISE / COR@L Lab Wiki

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====== COR@L User Guide ======

This page contains instructions and guidelines for COR@L users for accessing the resources available in the laboratory. These instructions are far from comprehensive but represent a basic guide for getting started. We hope you find these guidelines to be helpful on your path to becoming an expert on the tools you need in your research. Feel free to contact [[bsuresh@lehigh.edu|Suresh Bolusani]] if you have any questions or suggestions for additions to this page.

===== Getting Started with Linux =====

If you are new to Linux, then you may find the following links to be useful.

  * [[https://help.ubuntu.com/10.04/basic-commands/C/|Introduction to the command line in Ubuntu]]
  * [[http://www.tldp.org/LDP/intro-linux/html/|Introduction to Linux]]
  * [[http://www.lib.uchicago.edu/keith/tcl-course/emacs-tutorial.html|Introduction to Emacs]]
  * [[http://www.gnu.org/software/make/manual/make.html|Manual for GNU make]]

===== Logging into COR@L =====

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				<p>Every user with a COR@L account can access the machines listed <a href="https://coral.ie.lehigh.edu/wiki/doku.php/coral_lab#hardware">here</a> using her/his username and password.  However, if you are outside Lehigh’s network, then you need to connect to Lehigh VPN Concentrator or use the Lehigh Linux Jumphost - ssh.lehigh.edu. <a href="https://coral.ise.lehigh.edu/wiki/doku.php/tutorial:vpn">Please reference the Lehigh VPN Wiki page for guidance</a>. Once you are on the VPN or connected to the Jumphost you can connect to cluster directly from your host (vpn) or jumphost. The only host you should be connecting to for cluster work is <span style = "font-weight:bold">polyps.ie.lehigh.edu</span></p>
<h4> Linux users </h4>
<p>If you are a Linux user, then logging into COR@L is straightforward.  The following command uses ssh, which is typically available on standard Linux distributions:</p>
<pre><code>ssh username@machinename.ie.lehigh.edu</code></pre>
<p>Your COR@L username and password are the same for all machines.  COR@L uses NIS to manage passwords, so passwords can be at most 8 characters long.  Any extra characters will be ignored.  If you wish to change your password, then do not use the passwd command.  Use yppasswd instead.</p>
<h4> Windows users </h4>
<p>If you are using Windows and want to sign into a COR@L machine, then you need to install an ssh client first.  There are several free software options.  You can check <a href="http://en.wikipedia.org/wiki/Comparison_of_SSH_clients">Wikipedia</a> for more information about your choices.  A common free ssh client is PuTTY, which can be downloaded <a href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html">here</a>.  This ssh client is easy to use and it is well documented <a href="http://the.earth.li/~sgtatham/putty/0.60/htmldoc">here</a>. Another commonly used client is <a href="https://mobaxterm.mobatek.net">MobaXterm</a>.</p>
<p><a href="/coral-resources/coral-users">Back</a></p>
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===== Data Best Practices =====
The file server is backed up to an external hard drive adjacent to the storage node, but as a best practice to prevent against catastrophic loss of data, especially for data that you can not afford to lose, would be to duplicate your data on another host or resource. Lehigh University offers a few options for cloud storage:
  * [[https://confluence.cc.lehigh.edu/display/LKB/Google+Drive+-+an+Introduction|Google Drive]] - Available to all Lehigh University Faculty, Staff, and Students
  * [[https://lts.lehigh.edu/services/dropbox|Dropbox]] - Lehigh University offers Dropbox accounts that can be used for archival and project related work.


===== Compiling Programs =====
Eclipse is available on all machines. Use gcc to compile C programs, g++ to compile C++ programs, and f77 to compile Fortran programs. gdb may be used for debugging. valgrind may be used to check for memory leaks. [Purify/Quantify] are also available for checking memory leaks and for profiling.

===== Optimization Software =====
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				<p>Below is a list of the tools available for supporting optimization research at COR@L.</p>
<h4>Solvers:</h4>
<ul>
<li>COIN-OR</li>
<li>CPLEX</li>
<li>EXPRESS</li>
<li>GLPK</li>
<li>GUROBI</li>
<li>MOSEK</li>
</ul>
<h4>Modeling:</h4>
<ul>
<li>AMPL</li>
<li>GAMS</li>
<li>PULP</li>
</ul>
<p><a href="/coral-resources/coral-users">Back</a></p>
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===== Coin-all in mac =====
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				<p>This is a description of the steps followed to install coin-or on a OS X Mountain Lion using macports:</p>
<ol>
<li>Install macports, there is a nice installation guide in this <a href="http://www.macports.org/install.php">link</a></li>
<li>Install gcc47: To do this open a terminal and type “sudo port install gcc47″.</li>
<li>Install subversion: “sudo port install subversion”.</li>
<li>Download coin-all: svn co https://projects.coin-or.org/svn/CoinBinary/CoinAll/stable/1.6 coin-all</li>
<li>Move to directory coin-all and do “mkdir buildmac”</li>
<li>Download all the Third Party sources. Got to the ThirdParty folder and run the get script for: ASL, Blas, Lapack, Mumps, Metis, Glpk </li>
<li>Move to the directory buildmac</li>
<li>Run the configure script (This command is taken from <a href="https://projects.coin-or.org/Ipopt/wiki/Ipopt_on_Mac_OS_X">link</a>):<br>
../configure –disable-shared F77=gfortran-mp-4.7 FFLAGS=”-fexceptions -m64 -fbackslash” CFLAGS=”-fno-common -no-cpp-precomp -fexceptions -m64″ CXXFLAGS=”-fno-common -no-cpp-precomp -fexceptions -m64″<p></p>
</li><li>make tests (the DyLP test fails, rename the folder DyLP/test to DyLP/test.back if you want to run the other tests)</li>
<li>make install, remember that you need to use the option -prefix=/path/to/install if you want to specify a particular path to install the binaries</li>
</ol>
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===== Using Torque on COR@L =====
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PBS Torque is the batch queueing system on Cor@l. Torque is backed up by the Maui Scheduler. Please reference the Torque tutorial page. Condor has been retired.
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Check out the tutorial: [[:tutorial:torque]]
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===== Using CONDOR on COR@L =====

Also, check the main thread: [[:condor|CONDOR]]

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				<ul>
<li>To submit a job to the condor pool you need a condor.sub file similar to this one:<br>
<code>
#################################################################################<br>
# This line is important to get the license variables of mosek, cplex and others<br>
# This line is needed only once in the file<br>
getenv = TRUE <p></p>
<p># This is the standard universe, this should work fine with most of the tasks<br>
# This line is needed only once in the file<br>
Universe = vanilla  </p>
<p># This is where you specify the executable you want to use<br>
# Advice: absolute paths will ensure that you are using the file you want<br>
Executable = mosek</p>
<p># This is where you put the arguments for the executable<br>
arguments = -into r12c15k5i10.sol r12c15k5i10.mps</p>
<p># This tells condor where to place the outputs it can generate, they are really useful to identify<br>
# if there are problems with the job you are trying to run<br>
Output   = r12c15k5i10.out<br>
Error    = r12c15k5i10.err<br>
Log      = r12c15k5i10.log</p>
<p># This instruct condor to put the job in the queue<br>
queue</p>
<p># You can put as many jobs as you need repeating the same lines with different information<br>
# Notice that you don’t need to specify the executable again, unless you want to use a different<br>
# file</p>
<p>arguments = -into r12c15k5i15.sol r12c15k5i15.mps<br>
Output   = r12c15k5i10.out<br>
Error    = r12c15k5i10.err<br>
Log      = r12c15k5i10.log<br>
queue<br>
#######################################################################################################
</code>
</p></li>
<li> Once you have your condor file you can send it to the pool with the command “condor_submit condor.sub”</li>
<li> To check the status of the job you run “condor_q -global” and your username will appear under the column owner for the jobs you are currently running</li>
<li> To kill a job you use the command “condor_rm ID”, where ID is the number in the ID column of the output of condor_q associated with the job you want to remove. You can remove only those jobs you are the owner.</li>
</ul>
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