Application Documentation Template

Description
	Include a brief description of the application
Site	Version (Latest: v1.2)	Notes
Site name eg ngs.rl.ac.uk	v1.2 (v1.1, v1.0)	Some notes about versions
Site name eg ngs.oerc.ox.ac.uk	v1.1 (v1.0)	Some notes about versions
Once you have installed the application (and it's publishing via the GLUE tags) and created the application page, check that the url is on the category page (eg /appslications/chemistry) and hence appears in the correct category on the /applications page.

On this page:

1. License
2. Running on the NGS (general)
   • Submission using the UI-WMS
   • Submission using the NGS portal
   • Submission using Globus
   • Version Specific Information
3. Compilation Information
4. Further Information

License

Include the licensing information here.

• * Is it open source software or commercial?
• * Do users need their own license to use it?
• * Do they need to register with the application authors before using it?
• * Do they need to inform the NGS support centre of their registration?

Include a statement such as below.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.

Running the Application on the NGS (General)

General info on running the application such as the environment required. An example job should be shown and described, using first WMS , then the NGS portal, then Globus and finally local batch submission (only if its not possible to launch from the grid for som reason). Site specific information also needs to go here.

• Submission Using the UI/WMS

  To submit an ABC job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a abc.jdl

  Type = "Job";
  JobType = "mpich";
  #JobType = "normal";
  Executable = "/usr/ngs/ABC"; 
  Arguments = "-i input.in"; 
  CpuNumber = 4; 
  StdOutput = "std.out"; 
  StdError = "std.err"; 
  Myproxyserver= "myproxy.ngs.ac.uk"; 
  InputSandbox = {"input.in"}; 
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/abc"; 
  OutputSandbox = {"std.err","output","std.out"}; 
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/abc"; 
  Requirements = (      
       member("NGS-UEE-ABC", other.GlueHostApplicationSoftwareRunTimeEnvironment) #
  );
  Rank = other.GlueCEStateFreeCPUs;
  ShallowRetryCount = -1;

• NGS Web Portal Submission

  After logging in to the NGS portal, select the "Abc" template under the " Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  Eg To submit an ABC job use the following command (one line. You should not include the backslashes):

  globus-url-copy -cd -rp file:///$PWD/input.file gsiftp://ngs.rl.ac.uk/apps/abc/examples/in.file
  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf '(executable=/usr/ngs/ABC) \
  (arguments="job=MyJobName" "input=in.file")(jobtype=single)'
  or
  globus-job-run ngs.leeds.ac.uk/jobmanager-pbs -d povtest \
    /usr/ngs/ABC -i input.file
  globus-url-copy -rp gsiftp://ngs.leeds.ac.uk/abc/output.file file:///$PWD/output.file
   
   

  • This runs the default version. To run 1.2 use ABC_1_2 instead of ABC.

   

• Running the Application on the NGS (version specific)

  Version-specific information about running the application, i.e. newer versions and parallel versions. Example jobs should be described, using Globus submission.

Compilation Information

If relevant to the application, include here what was used to compile it and the bug fixes in place.

Further Information

Anything else the user needs to know should go here i.e.:

• links to application website
• links to user documentation
• links to mailing lists