Makeflow is a workflow engine that handles a large number
of jobs. It is based on
Master/Workers paradigm. A master process monitors and controls the
workers while the workers complete the assigned tasks. Makeflow rules are easy to pick up since its syntax is
similar to UNIX tool
In this tutorial, we learn how to run a sequence of jobs with Makeflow. We consider an example of running molecular dynamics simulation of 1CTA dimer in water using GROMACS package. To learn the basics of Makeflow, check the previous tutorial on makeflow-quickstart.
It is convenient to start with the
tutorial command. In the command prompt, type
$ tutorial makeflow-gromacs
This will create a directory
tutorial-makeflow-gromacs. Inside the directory, you see following files
$ ls tutorial-makeflow-gromacs 1cta_nvt.tpr gromacs_linear.makeflow submit_makeflow_to_local_condor.sh
1cta_nvt.tpr is an input file for GROMACS in binary format,
gromacs_linear.makeflow is a Makeflow file, and
submit_makeflow_to_local_condor.sh is a shell script to execute makeflow as a local condor job.
Makeflow script to run sequence of MD simulations
As shown in Figure, there are four rules in
gromacs_linear.makeflow. The jobs run in a sequential fashion. Rule 1 is the parent of Rule 2, Rule 2 is the parent of Rule 3, and so on. Rules 1, 2, and 3 are MD simulations that would run
on OSG machines. Rule 4 runs locally and cleans up the files.
Execute Makeflow script as a local condor job
Now let us execute the workflow,
$ submit_makeflow_to_local_condor.sh gromacs_linear.makeflow
This shell command executes the makeflow file
gromacs_linear.makeflow as a local condor job.
Further details on the condor local jobs are given in the tutorial on makeflow-quickstart.
Check the job status
$ condor_q username -wide
When all the jobs finished, you will see
Output directory that contains GROMACS output files such
as .gro, .edr, .log files.
A closer look at the Makeflow script
Let us take a closer look at the Makelfow file
gromacs_linear.makeflow and understand how GROMACS commands are available on remote machines.
Using GROMACS from OASIS.
GROMACS is available in OASIS as a distributed module. We want to make sure
that OASIS is accessible on a remote machine. This is done via the key word
Makeflow. Let us take a look at the line in
BATCH_OPTIONS = requirements = CVMFS_oasis_opensciencegrid_org_REVISION >= 5428
which sets the HTCondor requirement that an updated version of OASIS is available on a remote OSG machine.
Executing GROMACS simulation
To use GROMACS on a remote machine, we added the requirement of OASIS availability
BATCH_OPTIONS. We also need to do
module load GROMACS before
executing the GROMACS commands. Let us take a look at Rule 1 in
# Rule 1. Outputfile = 1cta_nvt_mdrun1.cpt, Inputfile = 1cta_nvt.tpr (Executables from OASIS) 1cta_nvt_mdrun1.cpt: 1cta_nvt.tpr module load gromacs/5.0.5; gmx mdrun -ntmpi 1 -ntomp 1 -nt 1 -s 1cta_nvt.tpr -deffnm 1cta_nvt_mdrun1 -nsteps 100
In the above rule,
1cta_nvt_mdrun1.cpt is the output and
1cta_nvt.tpr is the input. There are two command
executions. The first command execution,
module load gromacs/5.0.5, loads GROMACS from OASIS. The next
command execution, runs the MD simulation using GROMACS command
The arguments ntmpi, ntomp and nt are related to number of mpi threads, number of
openMP threads and total number of threads, respectively. Check GROMACS manual to understand the details of all the arguments. The argument
nsteps controls the number
of MD steps. Here, we chose small number of steps (100) for a quick demonstration.
Rules 2 and 3 are similar to Rule 1, except they use the check point files. For example, the checkpoint
1cta_nvt_mdrun1.cpt is produced from Rule 1 and it is used as an input for Rule2. Similarly, the
1cta_nvt_mdrun2.cpt from Rule 2 is used by Rule 3.
Rule 4 is the last step in the workflow and is executed locally. It waits for other jobs to complete, moves
certain files to
Output directory, and stores the list of moved files in a file
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 email@example.com or visit the help desk and community forums.
This page was updated on Jun 18, 2019 at 18:00 from tutorials/tutorial-makeflow-gromacs/README.md.