{"id":91,"date":"2018-08-30T09:52:14","date_gmt":"2018-08-30T08:52:14","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=91"},"modified":"2025-07-15T09:34:36","modified_gmt":"2025-07-15T08:34:36","slug":"authorhelp","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/authorhelp\/","title":{"rendered":"Help for Authors"},"content":{"rendered":"

Adding \/ Editing a new Application Page<\/h2>\n

Use the template HTML code below to start a new application page after you’ve installed the app on the CSF.<\/p>\n

There are basically four things to do:<\/p>\n

    \n
  1. Write the main page content, pasting in the template HTML from below.<\/li>\n
  2. Set the Page Attributes –> Parent<\/em> (see right-hand-side panel) to Applications<\/em> or Compilers<\/em> or Libraries<\/em> or Tools<\/em> (to reflect the install area).<\/li>\n
  3. Add values for the Custom fields<\/em> (underneath the main editor panel) for RI_Cat<\/em> and RI_Summary<\/em> so that the app automatically appears in the A-Z list of apps<\/a> and the list of applications<\/a> or compilers<\/a> or libraries<\/a> or tools<\/a> pages (see each page for what values to set in the custom field to get an app to appear there).<\/li>\n
  4. Use the WordPress Menu Editor to add the page to the software — > applications<\/em> menu brick<\/em>.<\/li>\n<\/ol>\n

    Finding and Editing an Application’s Page<\/h3>\n
      \n
    1. If you are currently on the page you wish to edit, simply click on Edit Page<\/em> in the grey bar at the top.\n
    2. Otherwise, navigate to the required apps page using the site’s menus<\/li>\n
    3. In the grey WordPress bar click on “Edit Page”.<\/li>\n
    4. You will now be in the WordPress editor<\/li>\n<\/ol>\n

      Writing HTML<\/h3>\n

      WordPress does not use wiki-style markup. Instead you can use the “Visual” Editor for wysiwyg-style editing or use the “Text” Editor to write the usual HTML tags (look at the top-right of the edit box – there are two little tabs to switch between the different styles of editor). I prefer the “Text” editor so I can see exactly which tags are being used and where. <\/p>\n

      New Application Template Text<\/h4>\n

      Paste the following in to the editor<\/p>\n

      \r\n<h2>Overview<\/h2>\r\n\r\n<a href=\"\">APP<\/a> is a program to\r\n\r\nVersion N.M is installed on the CSF.\r\n\r\n<h2>Restrictions on use<\/h2>\r\n\r\nDetails of the licence, restrictions, links to licence docs etc\r\n\r\n<h2>Set up procedure<\/h2>\r\n\r\nWe now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.\r\n\r\nLoad one of the following modulefiles:\r\n\r\n<pre>\r\nmodule load apps\/path\/to\/module\/n.m\r\n<\/pre>\r\n\r\n<h2>Running the application<\/h2>\r\n\r\nPlease do not run XXX on the login node. Jobs should be submitted to the compute nodes via batch.\r\n\r\n<h3>Serial batch job submission<\/h3>\r\n\r\nCreate a batch submission script (which will load the modulefile in the jobscript), for example:\r\n\r\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p serial     # (or --partition=) Run on the nodes dedicated to 1-core jobs\r\n#SBATCH -t 4-0        # Wallclock time limit. 4-0 is 4 days. Max permitted is 7-0.\r\n\r\n# Start with a clean environment - modules are inherited from the login node by default.\r\nmodule purge\r\nmodule load apps\/path\/to\/module\/n.m\r\n\r\nAPP arg1 arg2\r\n<\/pre>\r\n\r\nSubmit the jobscript using: \r\n\r\n<pre>sbatch <em>scriptname<\/em><\/pre>\r\n\r\nwhere <em>scriptname<\/em> is the name of your jobscript.\r\n\r\n<h3>Parallel batch job submission<\/h3>\r\n\r\nIf the app is multicore capable, given an example parallel jobscript, including suitable partition\r\n\r\n<pre>\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore  # (or --partition=) Run on the AMD 168-core nodes\r\n#SBATCH -n 16         # (or --ntasks=) Number of cores to use.\r\n#SBATCH -t 4-0        # Wallclock time limit. 4-0 is 4 days. Max permitted is 7-0.\r\n\r\n# Start with a clean environment - modules are inherited from the login node by default.\r\nmodule purge\r\nmodule load apps\/path\/to\/module\/n.m\r\n\r\n# You must inform you app how many cores to use. $SLURM_NTASKS will be set to the -n number above.\r\nsomeApp.exe arg1 arg2\r\n# MPI is Slurm-aware so will use the correct number of cores.\r\nmpirun someApp.exe\r\n\r\n<\/pre>\r\n\r\nSubmit the jobscript using: \r\n\r\n<pre>sbatch <em>scriptname<\/em><\/pre>\r\n\r\nwhere <em>scriptname<\/em> is the name of your jobscript.\r\n\r\n<h2>Further info<\/h2>\r\n\r\n<ul>\r\n  <li><a href=\"\">APP website<\/a><\/li>\r\n<\/ul>\r\n\r\n<h2>Updates<\/h2>\r\n\r\nNone.\r\n\r\n<\/pre>\n
      HTML hints<\/h4>\n
      However, there are some rules to simplify things:<\/p>\n
      Links – we automatically add an icon to external links. There are two styles:<\/p>\n
        \n
      1. Icons on external links\n