Makeflow is a workflow engine that handles a large number of jobs. The following are characteristics of Makeflow.
Master/Workers paradigmThe master monitors and controls the workers while the workers complete the tasks. master monitors and controls the workers.
Parallel job executionJobs are executed in parallel as much as possible.
Fault tolerantIn case of failure, the jobs are continued from where they are stopped.
UNIX tool MakeThe syntax of Makeflow is similar to the popular UNIX tool Make. The Make rules are convenient in describing the job dependencies.
In this tutorial, we learn how to (1) use Makeflow and (2) detach the master process from the terminal.
It is convenient to start with the
tutorial command. In the command prompt, type
$ tutorial makeflow-quickstart # Copies input and script files to the directory tutorial-makeflow-quickstart
This will create a directory
tutorial-makeflow-quickstart. Inside the directory, you will see the following files
fibonacci.bash # A simple bash script that generates the Fibonacci sequence fibonacci.makeflow # Makeflow file submit_makeflow_to_local_condor.sh # Script to execute the makeflow file as a local condor job
fibonacci.makeflow is the makeflow file.
fibonacci.bash is a shell
script to generate Fibonacci sequence for a given integer. For example,
$ ./fibonacci.bash 6
would print Fibonacci sequence 1, 2, 3, 5, and 8.
Makeflow script and parent child relationship
The figure shows the graphical representation of
fibonacci.makeflow. It describes two independent jobs (Rules 1&2) followed by a dependent job (Rule 3). The syntax of the Makeflow file is based on Make rules.
Let us take a look at the Makeflow script,
$ cat fibonacci.makeflow # Rule 1 Outputfile = fib.10.out, Inputfile = fibonacci.bash fib.10.out: fibonacci.bash fibonacci.bash 10 > fib.10.out # Rule 2 Outputfile = fib.20.out, Inputfile = fibonacci.bash fib.20.out: fibonacci.bash fibonacci.bash 20 > fib.20.out # Rule 3 Local and depends on the output from Rules 1 and 2 fib.out: fib.10.out fib.20.out LOCAL paste fib.10.out fib.20.out > fib.out
In the above description, there are three Make rules. Rules 1 and 2 execute
fibonnaci.bash with input arguments 10 and 20, respectively. These two rules produce the output files fib.10.out and fib.20.out. Rules 1 and 2 are
independent, so they would run concurrently. Rule 3 waits for completion of Rules 1&2.
Executing Makeflow script as a local condor job.
We may execute Makeflow either as an interactive process or a detached process. It is a good practice to
run the master process in the detached mode rather than in an interactive mode. There are several ways
to detach the master process from the terminal, such as
tmux, and condor job as
Here we run the master process as a local job in condor universe with the shell
$ submit_makeflow_to_local_condor.sh fibonacci.makeflow Submitting job(s). 1 job(s) submitted to cluster 367027.
This shell command executes the makeflow file
fibonacci.makeflow as a local condor job. Further details on
condor local jobs are given in the section
Additional details on Makeflow execution: Interactive mode and detached mode at the end of this tutorial.
Check the job status
$ condor_q username -wide -- Submitter: login01.osgconnect.net : <18.104.22.168:21720> : login01.osgconnect.net ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 19150583.0 dbala 4/1 11:54 0+00:01:54 R 0 0.4 makeflow -T condor fibonacci.makeflow 19150584.0 dbala 4/1 11:54 0+00:00:40 I 0 0.0 condor.sh fibonacci.bash 20 > fib.20.out 19150585.0 dbala 4/1 11:54 0+00:00:20 I 0 0.0 condor.sh fibonacci.bash 10 > fib.10.out
The above output shows that the master is running and two workers are waiting in queue. The master process is a local condor job so it starts quickly. The worker jobs are distributed on OSG machines and they are waiting for resources. All jobs would complete in few minutes.
This tutorial explains the basics of Makeflow on the OSG with a toy example of generating fibonacci sequence. Next, check the examples on makeflow-R and makeflow-GROMACS that show how to run real applications on the OSG with Makeflow.
For technical questions about Makeflow, contact Cooperative Computing Lab (cclab). For general assistance or questions related to running the jobs on OSG, please email the OSG User Support team at firstname.lastname@example.org or visit the help desk and community forums.
Additional details on Makeflow execution: Interactive mode and detached mode
Makeflow runs in the interactive or detached mode. Interactive mode is is okay if the workflow finishes in few minutes. Often this is not the case. Therefore, it is a good practice to run the workflow in the detached mode.
To run fibonacci.makeflow in the interactive mode (takes only few minutes to complete), type
$ makeflow -T condor fibonacci.makeflow Total rules: 3 Starting execution of workflow: fibonacci.makeflow. fibonacci.bash 20 > fib.20.out fibonacci.bash 10 > fib.10.out paste fib.10.out fib.20.out > fib.out nothing left to do.
-T condor submits jobs to the condor batch system. The
nothing left to do means the workflow is completed.
To run fibonacci.makeflow in the detached mode on the OSG Connect, the condor local job is
highly recommended. The other options are
tmux. Here, we provide details
of the local condor job.
To run fibonacci.makeflow as a local condor job,
$ submit_makeflow_to_local_condor.sh fibonacci.makeflow
submit_makeflow_to_local_condor.sh creates a file
local_condor_makeflow.submit and submits
the job with the command
Let us take a look at the file
$ cat local_condor_makeflow.submit universe = local getenv = true executable = /usr/bin/makeflow arguments = -T condor fibonacci.makeflow log = local_condor.log queue
This is a job description file for HTCondor job schedular. The first line says that the job universe is local, so the
job would run on the login node itself. The executable for the job is
/usr/bin/makeflow with an argument
-T condor fibonacci.makeflow. The keyword
queue is the start button that submits the above three lines to the
HTCondor batch system.
This page was updated on Aug 24, 2019 at 19:00 from tutorials/tutorial-makeflow-quickstart/README.md.