2.4. Part 4: Adding File Transfer

In this fourth part of the tutorial, we again build on the previous example and some code that copies our job’s output file back to the local machine. This is done using the saga.filesystem API package.

2.4.1. Prerequisites

This example assumes that you have SFTP access to the remote resource that you have used in the previous example. Again, this example assumes that you have a working public/private SSH key-pair and that you can sftp into your remote resource using those keys, i.e., your public key is in the ~/.ssh/authorized_hosts file on the remote machine. If you are not sure how this works, you might want to read about SSH and GSISSH first. Hands-On: Remote Job Submission with File Staging

Copy the code from the previous example 3 to a new file saga_example_remote_staging.py. Add the following code after the last print, right before the except statement:


Make sure that you adjust the paths to reflect your home directory on the remote machine.

outfilesource = 'sftp://gw68.quarry.iu.teragrid.org/users/oweidner/mysagajob.stdout'
outfiletarget = 'file://localhost/tmp/'
out = saga.filesystem.File(outfilesource, session=ses)

print("Staged out %s to %s (size: %s bytes)" % (outfilesource, outfiletarget, out.get_size()))

2.4.2. Run the Code

Save the file and execute it (make sure your virtualenv is activated):

python saga_example_remote.py

The output should look something like this:

Job ID    : None
Job State : New

...starting job...

Job ID    : [ssh://gw68.quarry.iu.teragrid.org]-[18533]
Job State : Done

...waiting for job...

Job State : Done
Exitcode  : 0

Staged out gw68.quarry.iu.teragrid.org/users/oweidner/mysagajob.stdout to file://localhost/tmp/ (size: 16 bytes)

2.4.3. Check the Output

Your output file should now be in /tmp/mysagajob.stdout and contain the string Hello from SAGA.

2.4.4. Coding URLs

URLs sftp://username:password@hostname:port//some/path and sftp://username:password@hostname:port/some/path (note the two // in the first URL) are supposed to be the same. However, SAGA may treat them diffently due some missing path normalization. URL should be coded with single ‘/’ or composed as follow:

remote_dir_url = saga.Url()
remote_dir_url.scheme = 'sftp'
remote_dir_url.username = username
remote_dir_url.username = $PASSWORD
remote_dir_url.host = hostname
remote_dir_url.port = port
remote_dir_url.path = '/some/path'