Software < Main

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---+ <a name="servers"></a>Software on Department Servers
---++ NLP Software
   * [[NlpSoftware][Software we have and comments about it]]
---++ Version Control
---++++ Subversion server (lemur.ling.washington.edu)
   * [[LemurHomePage][Introductory information and policies]] &lt;- read this one first
   * [[SVNBasicUsage][Basic usage]]
   * [[SVNAdvanced][More complicated tasks]]
   * [[https://lemur.ling.washington.edu/cgi-bin/svnpasswd.pl][Change your password]] 
      * _(If your browser prompts you with a certificate warning, you need to [[https://www.washington.edu/computing/ca/][install the UW root certificate]].)_
---++++ Using Git on the Cluster
   * [[GitSetup][Setting up a Git Repo]]
---++ [[HowToUseCondor][Condor]] - How to Run your Code on the Cluster

[[HowToUseCondor][Condor]] is the job management software installed on the department cluster.

Many programs we will implement in the CLMS program can cause a high system load on a machine. To make sure that the system does not lock up and become unavailable, we use [[HowToUseCondor][Condor]] to pass jobs off to other machines in the cluster, and queue jobs if all other machines are busy.

Please familiarize yourself with how to run jobs via condor with the [[HowToUseCondor][How to Use Condor]] page.
---++ Other Software on the Cluster

While general usage of software like git and python are detailed below, a few "gotchas" or suggestions for how to run these tools on the cluster are given here.
   * Java 
      * The default version of java on the cluster is jdk8 (1.8.0). 
         * Other versions are available in <span style="font-family:courier">/opt/jdk[7-9]</span>
   * Python 
      * The default version of python on the cluster is *2.7.5* 
         * In order to use python 3, be sure to use the <span style="font-family:courier">python3</span> command or a virtualenv.
      * Virtual Environments 
         * Virtual environments are extremely helpful for using third-party modules in your software that you would like to run on the cluster, without requiring that software be installed in the root install.
         * Refer to the [[PythonVirtualEnvironments][Virtual Environments]] wiki page for more.
---+ <a name="localsoftware"></a>Software for your Local Machine
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   * [[CommandlineTools][Installing commandline tools + package managers for OSX or Windows]]
   * Python 
      * [[PythonInstall][Installing Python (All Systems)]]
      * [[PythonTools][Recommended tools (IDEs, packages)]]
   * Git 
      * [[GitInstall][Installing Git (All Systems)]]
      * [[GitTools][Recommended Tools (GUIs, web services)]]
   * [[SSH]]
---++ Other Academic Software
   * Academic paper management 
      * [[https://www.mendeley.com/][Mendeley]]
      * [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=2ahUKEwjWwd2g2NbdAhV1FjQIHeKaB6QQFjAAegQIABAC&url=https://www.zotero.org/&usg=AOvVaw3WB2zTrYFysjM4IeX43tLS][Zotero]]
      * [[https://www.readcube.com/papers/][Papers]]
   * !LaTeX Writing Software 
      * [[https://www.texpad.com/][TeXPad]]
      * [[https://pages.uoregon.edu/koch/texshop/][TeXShop]]
---++ Other Helpful Development Software
   * SSH
      * [[https://mountainduck.io/][Mountain Duck]] (Paid) &mdash; *Mount* SSH (and more) connections in the file explorer on Mac/Windows
      * [[https://cyberduck.io/][Cyberduck]] (Free) &mdash; *Browse* SSH (and more) connections in a helpful GUI on Mac/Windows

---+ <a name="guides"></a>General Guides
---

There are plenty of well-written guides for how to use git, python, and other tools that we will be using in the CLMS program. A number are linked below. Be sure to refer to the [[#servers][section on software on the department servers above]] for specifics on running on the department servers.
   * [[GitVsSVN][Should I use Git or Subversion (SVN)?]]
   * Git tutorials 
      * [[https://rogerdudler.github.io/git-guide/][git - the simple guide]]
      * [[https://git-scm.com/book/en/v2/Getting-Started-About-Version-Control][git-scm - introductory book]]
      * [[https://services.github.com/on-demand/downloads/github-git-cheat-sheet.pdf][git cheat sheet]]
   * Python tutorials 
      * [[https://docs.python.org/3/tutorial/index.html][Python doc tutorial]]
      * [[https://python-packaging.readthedocs.io/en/latest/index.html][How to Package Python Projects for Distribution]]
Topic revision: r6 - 2018-09-26 - rgeorgi