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  • 10:04, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Analytical Computation (content was: "<!--checked2016--> {{Template:Outdated}} ===<center>Defining Analytical Computation</center>=== <center>'''Nick Chepurniy, Ph.D.'''</center> <center>''' e-mail: nickc..." (and the only contributor was "Nickc"))
  • 10:04, 2 May 2019 Ppomorsk (Talk | contribs) deleted page RUNGE-KUTTA Tutorial (content was: "{{Template:Outdated}} ===<center> RUNGE-KUTTA for ORDINARY DIFFERENTIAL EQUATIONS </center>=== <center>'''Nick Chepurniy, Ph.D.'''</center> <center>''' e-mail: nickc@..." (and the only contributor was "Nickc"))
  • 10:03, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Digital Humanities (content was: "{{Template:Outdated}} = Introduction = This page is intended to serve as a community and information hub for our digital humanities users. It is our hope that interested users and staff share tips and tricks, information about what th...")
  • 10:03, 2 May 2019 Ppomorsk (Talk | contribs) deleted page A Big Bridge: High Performance Computing and the Humanities (content was: "{{Template:Outdated}} This is the abstract of a paper to be presented at the 2008 Congress of the Humanities and Social Sciences Authors: * Geoffrey Rockwell - Associate Professor, Department of Communication Studies and Multimedia, M...")
  • 10:03, 2 May 2019 Ppomorsk (Talk | contribs) deleted page ATLAS (content was: "<!--checked2016--> {{Template:Outdated}} {{Software |package_name=ATLAS |package_description=Automatically Tuned Linear Algebra Software |package_idnumber=3 }} <b><font color=red>IMPORTANT NOTICE:</font> ATLAS will removed from all SHAR...")
  • 10:03, 2 May 2019 Ppomorsk (Talk | contribs) deleted page GSL (content was: "{{Template:GrahamUpdate}} <!--checked2016--> {{Template:Outdated}} {{Software |package_name=GSL |package_description=Mathematical routines to C/C++ programmers |package_idnumber=31 }} ==Examples== ===Example 1: Random Numbers from a Po...")
  • 10:02, 2 May 2019 Ppomorsk (Talk | contribs) deleted page MPICH2 (content was: "<!--checked2016--> {{Template:Outdated}} {{Software |package_name=MPICH2 |package_description=To provide an MPI implementation |package_idnumber=52 }} Mpich2 is not installed on sharcnet please use openmpi instead. <br> <br> <b>Legacy Us...")
  • 10:02, 2 May 2019 Ppomorsk (Talk | contribs) deleted page SPAI (content was: "{{Template:Outdated}} [http://www.computational.unibas.ch/software/spai/spaidoc.html SPAI – SParse Approximate Inverse Preconditioner] (MPI) Warning: the above link is dead. You can still find the source file (v.3.2) in my home direc...")
  • 10:01, 2 May 2019 Ppomorsk (Talk | contribs) deleted page TORQUE (content was: "{{Software |package_name=TORQUE |package_description=Resource manager for SHARCNET clusters |package_idnumber=92 }} <b><U>NATIVE TORQUE COMMANDS (all T&M clusters)</..." (and the only contributor was "Isaac"))
  • 09:59, 2 May 2019 Ppomorsk (Talk | contribs) deleted page IPM (content was: "{{Template:GrahamUpdate}} {{Software |package_name=IPM |package_description=Profiling library for parallel codes |package_idnumber=125 }} =Introduction= IPM (Integrated Performance Monitoring) is a portable profiling infrastructure for...")
  • 09:59, 2 May 2019 Ppomorsk (Talk | contribs) deleted page PATHSCALE (content was: "{{Template:LegacyPage}} {{Software |package_name=Pathscale |package_description=the Pathscale Compiler Suite |package_idnumber=44 }} =Introduction= Pathscale is a compiler. Presently SHARCNET provides version 4 of the compiler. It u...")
  • 09:59, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Quantifying the Importance of Horizontal Gene Transfer for Bacterial Genome Evolution (content was: "This project was conducted in the first round of SHARCNET's dedicated programming support competition. It mainly concerned developing a program that reads in the sequences of all genes present o...")
  • 09:58, 2 May 2019 Ppomorsk (Talk | contribs) deleted page ROOT (content was: "{{Template:Outdated}} ===about=== [http://root.cern.ch/drupal/ ROOT] ''The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.'' ===instal...")
  • 09:58, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Unsupported Software Documentation (content was: "#REDIRECT Unsupported Software" (and the only contributor was "Roberpj"))
  • 09:57, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Software Resources (content was: "#REDIRECT Unsupported Software Documentation" (and the only contributor was "Merz"))
  • 09:56, 2 May 2019 Ppomorsk (Talk | contribs) deleted page UCSC Kent Utilities (content was: "{{Template:LegacyPage}} ==Overview== The "UCSC Kent Utilities" is a collection of utilities for performing genomics and related work that was used to build the web based [http://genome.ucsc.edu/cgi-bin/hgTracks?org=human UCSC Genome Bro...")
  • 09:54, 2 May 2019 Ppomorsk (Talk | contribs) deleted page MAFFT (content was: "{{Template:Outdated}} {{Template:LegacyPage}} '''Update November 2014''': These instructions were written for the older SHARCNET environment. It should be possible to build MAFFT for the present SHARCNET environment without any deviati...")
  • 09:54, 2 May 2019 Ppomorsk (Talk | contribs) deleted page LinBox (content was: "{{Template:Outdated}} {{Template:GrahamUpdate}} '''Update November 2014''': These instructions are from 2010 and were created for the SHARCNET environment at that time. It should be possible to install this software on the newer operat...")
  • 09:54, 2 May 2019 Ppomorsk (Talk | contribs) deleted page KmerGenie (content was: "=kmergenie-1.6741= Built successfully on orca under centos6.4 using the system GCC, see [https://www.sharcnet.ca/my/problems/ticket/23952 ticket 23952]. ssh orca.sharcnet.ca wget http://kmergenie.bx.psu.edu/kmergenie-1.6741.tar.gz t...")
  • 09:54, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Vi and vim configuration (content was: "This page is now included in the SHARCNET Vim Documentation page at: VIM#Configuration <!--checked2015-->")
  • 09:54, 2 May 2019 Ppomorsk (Talk | contribs) deleted page VIM (content was: "{{Software |package_name=VIM |package_description=Text editor |package_idnumber=100 }} =Introduction= The vim console text editor can be started by typing <i>vim</i>. A graphical version is also available on most Sharcnet systems: <...")
  • 09:53, 2 May 2019 Ppomorsk (Talk | contribs) deleted page OwnCloud (content was: "{{LegacyPage}} <div class="alert-info" style="margin-bottom: 10pt"> <div style="float:left; vertical-align:top; text-align: center; font-weight:bold; font-size: 3em; color: white; background-color: red; height: 0.8em; width: 1.2em; pad...")
  • 09:53, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Enzo (content was: "{{Template:Outdated}} =Introduction= Enzo is a parallel adaptive mesh refinement (AMR) grid-based code for simulating structure formation in the Universe. It..." (and the only contributor was "Razoumov"))
  • 09:52, 2 May 2019 Ppomorsk (Talk | contribs) deleted page HOOMD-blue (content was: "'''HOOMD-blue''' is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs. =Install from git= Tested on Compute Canada cluster "graham" November 2017 by <ppomorsk@sharcnet.ca> <br> modul...")
  • 09:52, 2 May 2019 Ppomorsk (Talk | contribs) deleted page BINUTILS (content was: "{{Template:Outdated}} {{Software |package_name=BINUTILS |package_description=A collection of programming tools for the manipulation of object code |package_idnumber=114 }} =Intrduction= To load the most recent binutils module do: <pre...")
  • 09:52, 2 May 2019 Ppomorsk (Talk | contribs) deleted page COMPILE (content was: "<!--checked2016--> {{Template:Outdated}} {{Software |package_name=COMPILE |package_description=Provide "wrappers" that permit generic compilation |package_idnumber=129 }} compile is loaded by default in the SHARCNET user-environment/1.0...")
  • 09:52, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Cutadapt (content was: "{{template:LegacyPage}} read more about this package here: https://cutadapt.readthedocs.org/en/stable/ To install on kraken in my home directory I'd do: ssh kraken.sharcnet.ca module load python wget http://cutadapt.googlecode.com...")
  • 09:51, 2 May 2019 Ppomorsk (Talk | contribs) deleted page GRAPHVIZ (content was: "{{Template:GrahamUpdate}} {{Template:Outdated}} {{Software |package_name=GRAPHVIZ |package_description=Graph visualization software |package_idnumber=98 }} =Version Selection= Please refer to the documentation [http://www.graphviz.org/...")
  • 09:51, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Geneious (content was: "{{Template:LegacyPage}} This software was test installed for a group on the SHARCNET vdi-centos6 host in March 2015. There is a trial license which was not configured at the time. Please email help@sharcnet.ca if you need help setting...")
  • 09:50, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Glossary of Terms (content was: "{{Ancient|27402}} ===Barrier=== A synchronization point in parallel code where two or more threads must both reach before continuing. ===IDE=== Integrated Develop..." (and the only contributor was "Edward"))
  • 09:50, 2 May 2019 Ppomorsk (Talk | contribs) deleted page LDWRAPPER (content was: "{{LegacyPage}} <!--checked2016--> {{Software |package_name=LDWRAPPER |package_description=Wrapper for the sharcnet default centos6 module environment to ensure LD_RUN_PATH is used. |package_idnumber=165 }} =Introduction= The ldwrappe...")
  • 09:50, 2 May 2019 Ppomorsk (Talk | contribs) deleted page NCL (content was: "{{Template:GrahamUpdate}} {{Software |package_name=NCL |package_description=Visualization and analysis of molecular structures. |package_idnumber=183 }} =Introduction= Provides installation of NCL scripts from operating system reposit...")
  • 09:49, 2 May 2019 Ppomorsk (Talk | contribs) deleted page NOTEBOOK (content was: "This page has been superceeded by https://www.sharcnet.ca/help/index.php/JUPYTER" (and the only contributor was "Roberpj"))
  • 09:47, 2 May 2019 Ppomorsk (Talk | contribs) deleted page PORTLAND (content was: "#REDIRECT PGI" (and the only contributor was "Roberpj"))
  • 09:46, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Singular (content was: "{{Template:GrahamUpdate}} New instructions (December 2015) for orca, for git version of Singular module unload intel openmpi mkl module load gmp mpfr gcc cd /work/$USER mkdir SINGULAR cd SINGULAR wget http://www.mathematik.uni-k...")
  • 09:46, 2 May 2019 Ppomorsk (Talk | contribs) deleted page PyCUDA (content was: "<big>'''PyCUDA''' makes it possible to easily use CUDA inside Python code.</big> Documentation can be found on the [http://mathema.tician.de/software/pycuda pa..." (and the only contributor was "Ppomorsk"))
  • 09:46, 2 May 2019 Ppomorsk (Talk | contribs) deleted page PyOpenCL (content was: "<big>'''PyOpenCL''' makes it possible to easily use OpenCL inside Python code.</big> Documentation can be found on the [http://mathema.tician.de/software/pyopencl package webpage]. This package is not currently installed as SHARCNET-su...")
  • 09:44, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Unsupported Software (content was: "{{Template:LegacyPage}} =Unsupported Software= Package listed on this page are NOT included on the Officially [https://www.sharcnet.ca/my/software Supported] Sharcnet software page. __TOC__ ==User-Installed Packages== This table prov...")
  • 09:44, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Trilinos (content was: "{{Template:Outdated}} ==Newest instructions (August 2013, problem ticket https://www.sharcnet.ca/my/problems/ticket/21268 )== * orca, Centos 6.4, default compiler (inte..." (and the only contributor was "Syam"))
  • 09:43, 2 May 2019 Ppomorsk (Talk | contribs) deleted page UMFPACK (content was: "{{stub}}<br> Instruction to build UMFPACK have been given in 'README_Jemmy' file under /work/jemmyhu/software/umfpack/install_packages")
  • 09:43, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Transition to CentOS 6 (content was: "{{LegacyPage}} As of September 2013 most SHARCNET core, speciality and contributed systems that were running CentOS 5 have been upgraded to CentOS 6. As part of this upgrade we reorganized the default software environment and provide...")
  • 09:43, 2 May 2019 Ppomorsk (Talk | contribs) deleted page WIEN2K (content was: "<!--checked2016--> {{Template:Outdated}} {{Template:LegacyPage}} {{Software |package_name=WIEN2K |package_description=DFT simulation |package_license= Not free, users must purchase license |package_url=www.wien2k.at |package_idnumber= |...")
  • 09:42, 2 May 2019 Ppomorsk (Talk | contribs) deleted page GAMESS US (content was: "==Run instruction for Gamess_US on bull for serial jobs only == 1) create a subdirectory gamess_scr in your /scratch directory cd /scratch/youid mkdir gamess_scr 2) for first time user, add the path to your .bash_profile file you...")
  • 09:42, 2 May 2019 Ppomorsk (Talk | contribs) deleted page GCC (content was: "{{Template:GrahamUpdate}} {{Software |package_name=GCC |package_description=GNU compiler collection |package_idnumber=20 }} =Introduction= '''GCC''' is a free, open-source, very widely used compiler. While at SHARCNET it is usually best...")
  • 09:42, 2 May 2019 Ppomorsk (Talk | contribs) deleted page GNU (content was: "{{Software |package_name=GNU |package_description=Selected packages from the GNU project |package_idnumber=136 }} =Introduction= Sharcnet installs commonly used GNU packages from http://www.gnu.org/software/#allgnupkgs. =Version Selec...")
  • 09:41, 2 May 2019 Ppomorsk (Talk | contribs) deleted page IMAGEMAGICK (content was: "<!--checked2016--> {{Template:Outdated}} {{Software |package_name=IMAGE MAGICK |package_description=Suite for the creation, modification and display of bitmap images |package_idnumber=119 }} <u>COMMANDS</u> <b>convert</b> between imag...")
  • 09:40, 2 May 2019 Ppomorsk (Talk | contribs) deleted page Iqaluk (content was: "{{System |cluster_name=iqaluk |target_usage=Large, tightly-coupled threaded jobs |system_idnumber=93 }} ==System Overview== {| class="wikitable" style="text-align:center" border="1" |- | Node Range || 1 |- | CPU Model || Intel Xeon X750...")
  • 09:39, 2 May 2019 Ppomorsk (Talk | contribs) deleted page PGI (content was: "{{GrahamUpdate}} {{Software |package_name=PGI |package_description=the Portland Group Compiler suite |package_idnumber=46 }} =Overview= '''Portland Group''' produces high-quality compilers that include certain unusual features, such as...")
  • 09:39, 2 May 2019 Ppomorsk (Talk | contribs) deleted page SLURM (content was: "'''SLURM''' (Simple Linux Utility for Resource Management) is a job scheduler. On SHARCNET it is currently in use on clusters: Graham, Copper, and Mosaic. (On Copper and Mosaic, users can use our legacy command ''sqsub'' to submit jobs...")
  • 09:39, 2 May 2019 Ppomorsk (Talk | contribs) deleted page SPRNG (content was: "{{Software |package_name=SPRNG |package_description=To develop, implement and test a scalable package for parallel pseudo random number generation |package_idnumber=50 }} If you are on a <b>cluster with modular install</b> (most of our c...")
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