This guide is a tutorial for getting started programming with DRMAA. It is basically a one to one translation of the original in C for Grid Engine. It assumes that you already know what DRMAA is and that you have drmaa-python installed. If not, have a look at Installing. The following code segments are also included in the repository.
The following two code segments show the most basic DRMAA python binding program.
#!/usr/bin/env python
import drmaa
def main():
"""Create a drmaa session and exit"""
with drmaa.Session() as s:
print('A session was started successfully')
if __name__=='__main__':
main()The first thing to notice is that every call to a DRMAA function will return an error code. In this tutorial, we ignore all error codes.
Now let's look at the functions being called. First, on line 7, we initialise a
Session object by calling drmaa.Session(). The Session is
automatically initialized via initialize(), and it creates a session and starts
an event client listener thread. The session is used for organizing jobs
submitted through DRMAA, and the thread is used to receive updates from the
queue master about the state of jobs and the system in general. Once
initialize() has been called successfully, it is the responsibility of the
calling application to also call exit() before terminating, but since we're
using it as a context manager via the with statement, that will happene
automatically. If an application does not call exit() before terminating,
session state may be left behind in the user's home directory, and the queue
master may be left with a dead event client handle, which can decrease queue
master performance.
At the end of our program, exit() is called automatically when we leave the
with block. exit() cleans up the session and stops the event client
listener thread. Most other DRMAA functions must be called before exit().
Some functions, like getContact(), can be called after exit(), but these
functions only provide general information. Any function that does work, such as
runJob() or wait() must be called before exit() is called. If such a
function is called after exit() is called, it will return an error.
#!/usr/bin/env python
import drmaa
def main():
"""
Create a session, show that each session has an ID, use session ID to
disconnect, then reconnect. Finally, exit.
"""
s = drmaa.Session()
s.initialize()
print('A session was started successfully')
response = s.contact
print('session contact returns: %s' % response)
s.exit()
print('Exited from session')
s.initialize(response)
print('Session was restarted successfullly')
s.exit()
if __name__=='__main__':
main()This example is very similar to :ref:`Example 1 <example-1>`. The difference is
that it uses the Grid Engine feature of reconnectable sessions. The DRMAA
concept of a session is translated into a session tag in the Grid Engine job
structure. That means that every job knows to which session it belongs. With
reconnectable sessions, it's possible to initialize the DRMAA library to a
previous session, allowing the library access to that session's job list. The
only limitation, though, is that jobs which end between the calls to exit()
and init() will be lost, as the reconnecting session will no longer see
these jobs, and so won't know about them.
On line 13, we use the contact attribute to get the contact information for this
session. On line 15 we then exit the session. On line 18, we use the stored
contact information to reconnect to the previous session. Had we submitted jobs
before calling exit(), those jobs would now be available again for
operations such as wait() and synchronize(). Finally, on line 19 we exit
the session a second time.
The following code segments show how to use the DRMAA python binding to
submit a job to Grid Engine. It submits a small shell script (sleeper.sh)
which takes two arguments:
#!/bin/bash
echo "Hello world, the answer is $1"
sleep 3s
echo "$2 Bye world!"#!/usr/bin/env python
import drmaa
import os
def main():
"""
Submit a job.
Note, need file called sleeper.sh in current directory.
"""
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
jt.args = ['42', 'Simon says:']
jt.joinFiles=True
jobid = s.runJob(jt)
print('Your job has been submitted with ID %s' % jobid)
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()The beginning and end of this program are the same as the first example. What's
new is in lines 12--22. On line 12 we ask DRMAA to allocate a job template
for us. A job template is a structure used to store information about a job to
be submitted. The same template can be reused for multiple calls to runJob()
or runBulkJob().
On line 13 we set the remoteCommand attribute. This attribute tells DRMAA
where to find the program we want to run. Its value is the path to the
executable. The path can be either relative or absolute. If relative, it is
relative to the workingDirectory attribute, which if not set defaults to the
user's home directory. For more information on DRMAA attributes, please see the
attributes man page. Note that for this program to work, the script
sleeper.sh must be in the current directory.
On line 14 we set the args attribute. This attribute tells DRMAA what
arguments to pass to the executable.
On line 17 we submit the job with runJob(). DRMAA will place the ID assigned
to the job into the character array we passed to runJob(). The job is now
running as though submitted by qsub or bsub. At this point calling
exit() and/or terminating the program will have no effect on the job.
To clean things up, we delete the job template on line 21. This frees the memory DRMAA set aside for the job template, but has no effect on submitted jobs.
If instead of a single job we had wanted to submit an array job, we could have replaced the else on line 18 and 19 with the following:
jobid = s.runBulkJobs(jt, 1, 30, 2)
print('Your jobs have been submitted with IDs %s' % jobid)This code segment submits an array job with 15 tasks numbered 1, 3, 5, 7, etc.
An important difference to note is that runBulkJobs() returns the job ids in
a list. On the last line, we print all the job ids.
Now we're going to extend our example to include waiting for a job to finish.
#!/usr/bin/env python
import drmaa
import os
def main():
"""
Submit a job and wait for it to finish.
Note, need file called sleeper.sh in home directory.
"""
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
jt.args = ['42', 'Simon says:']
jt.joinFiles = True
jobid = s.runJob(jt)
print('Your job has been submitted with ID %s' % jobid)
retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER)
print('Job: {0} finished with status {1}'.format(retval.jobId, retval.hasExited))
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()This example is very similar to :ref:`Example 2 <example-2>` except for line
21. On line 21 we call wait() to wait for the job to end. We have to give
wait() both the ID of the job for which we want to wait, and also how long
we are willing to wait for the job to finish. This could be a number of
seconds, or it could be either TIMEOUT_WAIT_FOREVER or TIMEOUT_NO_WAIT.
wait() returns a JobInfo tuple, which has the following attributes:
jobId, hasExited, hasSignal, terminatedSignal, hasCoreDump,
wasAborted, exitStatus, and resourceUsage. jobId is
particularly useful if we passed in JOB_IDS_SESSION_ANY as the ID argument
for wait(), because without it we would have no way of knowing which job it
actually waited for. Lastly, we print out the job ID and the exit status on
line 22.
An alternative to wait() when working with multiple jobs, such as jobs
submitted by runBulkJobs() or multiple calls to runJob() is
synchronize(). synchronize() waits for a set of jobs to finish. To use
synchronize(), we could replace lines 18--22 with the following:
joblist = s.runBulkJobs(jt, 1, 30, 2)
print('Your jobs have been submitted with IDs %s' % joblist)
s.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, True)With the switch to runBulkJobs() we now have several jobs for which to wait.
On line 20, instead of calling wait(), we call synchronize().
synchronize() takes only three interesting parameters. The first is the list
of string IDs for which to wait. If the special ID, JOB_IDS_SESSION_ALL,
appears in the array, synchronize() will wait for all jobs submitted via
DRMAA during this session (i.e., since initialize() was called). The second
is how long to wait for all the jobs in the list to finish. This is the same as
the timeout parameter for wait(). The third is whether this call to
synchronize() should clean up after the job. After a job completes, it
leaves behind accounting information, such as exit status and usage, until
either wait() or synchronize() with dispose set to True is
called. It is the responsibility of the application to make sure one of these
two functions is called for every job. Not doing so creates a memory leak. Note
that calling synchronize() with dispose set to true flushes all accounting
information for all jobs in the list. If you want to use synchronize() and
still recover the accounting information, set dispose to False and call
wait() for each job. To do this in :ref:`Example 3 <example-3>`, we would
replace lines 18--22 with the following:
joblist = s.runBulkJobs(jt, 1, 30, 2)
print('Your jobs have been submitted with IDs %s' % joblist)
s.synchronize(joblist, drmaa.Session.TIMEOUT_WAIT_FOREVER, False)
for curjob in joblist:
print('Collecting job ' + curjob)
retval = s.wait(curjob, drmaa.Session.TIMEOUT_WAIT_FOREVER)
print('Job: {0} finished with status {1}'.format(retval.jobId,
retval.hasExited))What's different is that on line 21 we set dispose to False, and then on
lines 22--26 we wait once for each job, printing the exit status and usage
information as we did in :ref:`Example 3 <example-3>`.
We pass joblist to synchronize() to wait for each job specifically.
Otherwise, the wait() could end up waiting for a job submitted after the
call to synchronize().
Now let's look at an example of how to control a job from DRMAA:
#!/usr/bin/env python
import drmaa
import os
def main():
"""Submit a job, then kill it.
Note, need file called sleeper.sh in home directory.
"""
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
jt.args = ['42', 'Simon says:']
jt.joinFiles = True
jobid = s.runJob(jt)
print('Your job has been submitted with ID %s' % jobid)
# options are: SUSPEND, RESUME, HOLD, RELEASE, TERMINATE
s.control(jobid, drmaa.JobControlAction.TERMINATE)
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()This example is very similar to :ref:`Example 2 <example-2>` except for line
20. On line 20 we use control() to delete the job we just submitted. Aside
from deleting the job, we could have also used control() to suspend,
resume, hold, or release it.
Note that control() can be used to control jobs not submitted through DRMAA.
Any valid SGE job ID could be passed to control() as the ID of the job to
delete.
Here's an example of using DRMAA to query the status of a job:
#!/usr/bin/env python
import drmaa
import time
import os
def main():
"""
Submit a job, and check its progress.
Note, need file called sleeper.sh in home directory.
"""
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.path.join(os.getcwd(), 'sleeper.sh')
jt.args = ['42', 'Simon says:']
jt.joinFiles=True
jobid = s.runJob(jt)
print('Your job has been submitted with ID %s' % jobid)
# Who needs a case statement when you have dictionaries?
decodestatus = {drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
drmaa.JobState.RUNNING: 'job is running',
drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
drmaa.JobState.DONE: 'job finished normally',
drmaa.JobState.FAILED: 'job finished, but failed'}
for ix in range(10):
print('Checking %s of 10 times' % ix)
print decodestatus(s.jobStatus(jobid))
time.sleep(5)
print('Cleaning up')
s.deleteJobTemplate(jt)
if __name__=='__main__':
main()Again, this example is very similar to :ref:`Example 2 <example-2>`, this time
with the exception of lines 22--40. On line 36, we use jobStatus() to get
the status of the job. Line 43 determine what the job status is and report it.
Lastly, let's look at how to query the DRMAA library for information about the DRMS and the DRMAA implementation itself:
#!/usr/bin/env python
import drmaa
def main():
""" Query the system. """
with drmaa.Session() as s:
print('A DRMAA object was created')
print('Supported contact strings: %s' % s.contact)
print('Supported DRM systems: %s' % s.drmsInfo)
print('Supported DRMAA implementations: %s' % s.drmaaImplementation)
print('Version %s' % s.version)
print('Exiting')
if __name__=='__main__':
main()On line 9, we get the contact string list. This is the list of contact strings that will be understood by this DRMAA instance. Normally on of these strings is used to select to which DRM this DRMAA instance should be bound. On line 10, we get the list of supported DRM systems. On line 11, we get the list of supported DRMAA implementations. On line 12, we get the version number of the DRMAA C binding specification supported by this DRMAA implementation.