SciPy

Description
	SciPy is an Open Source library of scientific tools for Python providing a variety of high level science and engineering modules together as a single package. It includes support for statistics, optimization, numerical integration, linear algebra, Fourier transforms, signalp rocessing, image processing, genetic algorithms, ODE solvers and special functions
Site	Version (Latest: v0.7.1)	Notes
		Not currently available.

License

SciPy is open source software.

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)

The NGS provides a script

/usr/ngs/SCIPY

that will run 'python' with the Scipy libraries available. This will run the default version of SciPy where more than one version is available. To use version 0.6.0 explicitly, use SCIPY_0_6_0 instead.

• Submission Using the UI/WMS

  To submit an SciPy 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 scipy.jdl

  Type = "Job";
  JobType = "normal";
  Executable = "/usr/ngs/SCIPY"; 
  Arguments = "script.py"; 
  CpuNumber = 4; 
  StdOutput = "std.out"; 
  StdError = "std.err"; 
  Myproxyserver= "myproxy.ngs.ac.uk"; 
  InputSandbox = {"script.py"}; 
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/scipy"; 
  OutputSandbox = {"std.err","std.out"}; 
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/scipy"; 
  Requirements = (      
       member("NGS-UEE-SCIPY", other.GlueHostApplicationSoftwareRunTimeEnvironment) 
  );
  ShallowRetryCount = -1; 
      

• Submission Using Globus

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

  globus-url-copy -cd -rp file:///$PWD/script.py gsiftp://ngs.leeds.ac.uk/scipy/script.py 
    globusrun -b -r ngs.leeds.ac.uk/jobmanager-pbs '(executable=/usr/ngs/SCIPY) \
    (arguments="script.py")(jobtype=single)'
  or
    globus-job-run ngs.leeds.ac.uk/jobmanager-pbs -d scipy \ 
      /usr/ngs/SCIPY script.py  

Further Information

The SciPy website includes: 

• A full set of documentation
• A Getting started guide
•  A cookbook of useful SciPy scripts