XSEDE 2013 SAGA Tutorial

Preparation

This tutorial is part of the XSEDE13 SAGA-BigJob Tutorial will use the TACC Virtual Machine (VM) repex1. Log-in via SSH using the username/password you received at the beginning of the tutorial:

ssh <username>@repex1.tacc.utexas.edu

Installation

Next, you need to install SAGA-Python in your user account on repex1. Since saga-python - as the name suggests - is written in Python, you can use virtualenv to create a local installation:

virtualenv $HOME/sagaenv
. $HOME/sagaenv/bin/activate

The SAGA-Python package on PyPi (Python Package Index) that we are using is called saga-python and can be installed via pip:

pip install saga-python

Code Example 1: Local Job Submission

Preparation

1. Take a look at the full example code on GitHub.

2. Create a new file in your home directory, copy & paste the code into it and save it, e.g., as saga_example_local.py.

Execution

Execute the Python script:

python saga_example_local.py

The output will look something like this:

Job ID    : None
Job State : New

...starting job...

Job ID    : [fork://localhost]-[31981]
Job State : Done

...waiting for job...

Job State : Done
Exitcode  : 0

Code Example 2: Remote Job Submission

Preparation

1. Take a look at the full example code on GitHub.

2. Create a new file in your home directory, copy & paste the code into it and save it, e.g., as saga_example_remote.py.

Execution

Execute the Python script:

python saga_example_remote.py

The output will look something like this:

Job ID    : None
Job State : New

...starting job...

Job ID    : [ssh://localhost]-[32704]
Job State : Done

...waiting for job...

Job State : Done
Exitcode  : 0

Discussion

If you want, try to replace ssh://localhost with another machine you have access to. Look for the saga.Context object in the code if you need to define specific login credentials. Look here for more information. For Stampede specific information look here.

SAGA-Python provides many other backend adaptors besides ssh and fork. Check out the adaptor section of the documentation if you want to learn more: http://saga-project.github.io/saga-python/doc/adaptors/saga.adaptor.index.html.

Code Example 3: Remote Job Submission + File Staging

Preparation

1. Take a look at the full example code on GitHub.

2. Create a new file in your home directory, copy & paste the code into it and save it, e.g., as saga_example_remote_staging.py.

Execution

Execute the Python script:

python saga_example_remote_staging.py

The output will look something like this:

Job ID    : None
Job State : New

...starting job...

Job ID    : [ssh://localhost]-[4319]
Job State : Done

...waiting for job...

Job State : Done
Exitcode  : 0

Staged out sftp://localhost/tmp/mysagajob-tutorial-00.stdout to file:///home/tutorial-00/ (size: 16 bytes)

You will find a .stdout file in your working directory that contains the output of your job.

Discussion

As in the previous example, you can replace ssh://localhost with another (remote) machine you have access to. This example shows you how to stage data out (i.e., back) automatically once the job is finished. Here is a link for more information.

Code Example 4: Sequentially Executing Many Tasks (Mandelbrot Set)

Mandelbrot Example http://saga-project.github.io/saga-python/doc/tutorial/part5.html