Grython is a Java package that contains both the Grisu client library and a version of the Jython interpreter. Basically, it allows you to access all the convenience (Java) methods and objects of the Grisu client library via Python syntax.
Beware, you can't run this package in a native Python environment. So, if you want to write a python script that relies on 3rd party modules which don't run in Jython (for example because they are written in C), you're (most likely) out of luck.
- Sun Java (version >= 6)
- (recommended) the NeSI-tools installer package: Windows, Mac OS X or cross-OS (make sure you check the 'grython' option and put [install_dir]/bin in you system path)
- or (for advanced users/developers) the Grisu jython jar: grython-binary.jar
- Javadoc for the Grisu client library whose classes/methods can be used from jython: javadoc
- Script examples can be found here: grython examples
- More examples (but pure Java): grisu examples
- Grisu wiki: https://github.com/grisu/grisu/wiki
grython is started like so (if you used the NeSI tools installer package and adjusted your path):
grython [-b <backend>] [<script-name>.py]
or, alternatively:
java -jar grython-binary.jar [-b backend] [<script-name>.py]
To play around with it, we can use an interactive jython console or run a script (see below)
On your first run (or whenever your session credential expires), you will be asked for login information. For the sake of testing, use those temporary ones:
username: [email protected]
password: grisudemo
Also, we are login into the test backend (alias: testbed):
grython -b testbed --login
[1] Institution login
[2] Institution login (using: 'The University of Auckland')
[3] Certificate login
[4] MyProxy login
[0] Exit
Please choose your login type: 4
Please enter your username [grisudemo]: [email protected]
Please enter password: *********
Jython 2.5.2 (Release_2_5_2:7206, Mar 2 2011, 23:12:06)
[OpenJDK 64-Bit Server VM (Sun Microsystems Inc.)] on java1.6.0_24
Type "help", "copyright", "credits" or "license" for more information.
>>>
The '--login' option forces authentication, otherwise, if you already have an existing credential it'll re-use that, which is quite handy for scripting. If you want to use our production system, just ommit the '-b testbed' options. And, once you got started, don't use the '--login' option.
Login is done whenever grython can't find a valid session information (an x509 proxy in $HOME/.grid/grid.proxy) without you having to do anything. To get the object holding the session, you need to import it:
from grisu.Grython import serviceInterface as si
Now you can get access to information and resources you are allowed to use. Have a look at the javadoc for the ServiceInterface class to get an idea which methods are available: link. Let's for example get some information about the dn (distinguised name -- your internal username):
>>> si.getDN()
u'DC=nz,DC=org,DC=bestgrid,DC=slcs,O=The University of Auckland,CN=Markus Binsteiner _bK32o4Lh58A3vo9kKBcoKrJ7ZY'
Or, we can get some information about the backend we are connected to:
>>> si.getInterfaceInfo('VERSION')
u'0.5.4'
>>> si.getInterfaceInfo('HOSTNAME')
u'compute.services.bestgrid.org / 130.216.161.32'
Now, let's do something useful and submit a job:
>>> from grisu.frontend.model.job import GrisuJob
>>> job = GrisuJob(si)
>>> job.setJobname("grython_demo_job")
>>> job.setCommandline("echo \"Hello World\"")
>>> job.createJob()
u'grython_demo_job'
>>> job.submitJob()
u'submission_task_grython_demo_job_1353884813463'
# now we wait for the job to finish, which shouldn't take long...
>>> job.waitForJobToFinish(10)
True
# and get the output of the job:
>>> job.getStdOutContent()
u'Hello World\n'
Of course, the interactive console is not really practical for your day-to-day workflows. You most definitely want to write scripts. Here's a simple example of how to run a submission workflow using a script (code also here).
Copy and paste the following code into a file called diffJob.py:
#! /usr/bin/grython -b testbed
'''
A simple job submission to show how to submit a job with input files.
Created on 26/11/2012
@author: Markus Binsteiner
'''
from grisu.Grython import serviceInterface as si
from grisu.frontend.model.job import GrisuJob
from grisu.model import FileManager
import sys
print 'Parsing commandline arguments...'
file1url = sys.argv[1]
file1Name = FileManager.getFilename(file1url)
file2url = sys.argv[2]
file2Name = FileManager.getFilename(file2url);
print 'Creating job...'
# create the job object
job = GrisuJob(si);
# set a unique jobname
job.setTimestampJobname("diff_job")
print 'Set jobname to: '+ job.getJobname()
# set the commandline that needs to be executed
job.setCommandline('diff ' + file1Name+ ' ' + file2Name)
job.addInputFileUrl(file1url);
job.addInputFileUrl(file2url);
# create the job on the backend
job.createJob()
print 'Submitting job...'
# submit the job
job.submitJob()
print 'Waiting for the job to finish...'
# this waits until the job is finished. Checks every 10 seconds (which would be too often for a real job)
job.waitForJobToFinish(10)
print 'Job finished. Status: '+job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
print "Stdout: " + job.getStdOutContent()
# download and cache the jobs' stderr and display it's content
print "Stderr: " + job.getStdErrContent()
# kill and clean the job on the backend
job.kill(True)
# don't forget to exit properly. this cleans up possible existing threads/executors
sys.exit()
Also, create two textfiles called testfile1.txt and testfile2.txt with slightly different content (in your current working directory).
Exit the interactive console, if open:
>>> quit()
Now, let's start the workflow:
grython -b testbed --login diffJob.py testfile1.txt testfile2.txt
Parsing commandline arguments...
Creating job...
Set jobname to: diff_job_2012.11.26_12.21.29.288
Submitting job...
Waiting for the job to finish...
Job finished. Status: Done
Stdout: 1c1
< This is testfile 1.
---
> This is testfile 2.
Stderr: