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GNU Parallel

GNU Parallel is a free, open-source tool for running shell commands and scripts in parallel and sequence on a single node.

A workflow pattern with the following characteristics is a good match for GNU parallel:

  • Individual tasks do not use MPI or multiple nodes.
  • Contains many similar tasks with no execution order requirements or data dependencies.

Strengths of GNU Parallel:

  • No user installation or configuration
  • No databases or persistent manager process
  • Easily scales to a very large number of tasks
  • Easily scales to multiple nodes
  • Efficient use of scheduler resources

Disadvantages of GNU Parallel:

  • Doesn't easily balance work amongst multiple nodes
  • User is required to do careful organization of input and output files
  • Scaling up requires consideration of system I/O performance
  • Modest familiarity with bash scripting recommended

How to use GNU Parallel at NERSC

In this first example, seq is used to generate four lines of input, which is piped into parallel. Those four input lines cause parallel to run four tasks in total. Then the command each task will run is passed to parallel, in this case, echo and its arguments. The {} in the command sets a location where individual input line content will be substituted inside each task command.

Basic example
elvis@cori04:~> module load parallel
elvis@cori04:~> seq 1 4 | parallel echo "Hello world {}!"
Hello world 1!
Hello world 2!
Hello world 3!
Hello world 4!
elvis@cori04:~>

The next necessary concept is how to submit substantial tasks and input files to parallel. This example shows how input data created with sequential file names can be passed to parallel using bash commands and pipes:

Sequentially named input files for each task

elvis@nid00050:~/work> ls
input01.dat  input02.dat  input03.dat  input04.dat  input05.dat
input06.dat  input07.dat  input08.dat  input09.dat  input10.dat
elvis@nid00050:~/work> seq -w 1 10 | parallel task_command.sh input{}.dat
This example occurs in an salloc session. Though parallel is great for automating mundane repetitive tasks like creating many directories or parsing lots of log files, tasks which use a substantial amount of compute resources still need to be run on Slurm allocated compute nodes and not on shared login nodes.

A second approach places all task inputs into the same directory and uses the find command to build the file listing all their paths:

Using find to build an input file list
elvis@nid00050:~/work> find -type f | grep dat | sort > input.txt
elvis@nid00050:~/work> cat input.txt | parallel task_command.sh {}
I/O Performance Pitfalls at Large Scale

If work requires large numbers (more than 1000) of tasks and input files then some extra precautions should be taken to avoid I/O scaling bottlenecks.

Use subdirectories to prevent a single folder from containing more than 1000 files or directories.

At larger scale it is more important to use higher performance file systems such as Cori Lustre or the Burst Buffer to read and write data.

If all of your tasks are reading the same files then you can increase performance by making multiple copies of those files and assigning different tasks to read different copies.

Running Many Tasks Inside a Single Node Allocation

This Slurm batch script will request one KNL node in the regular QOS and then run parallel on that node. The parallel command runs up six tasks of task_command.sh at a time, one for each line in the file list_of_inputs.txt. If the input file contains more than six lines then the additional tasks will wait until earlier tasks finish and space is available for them. Each input line string becomes an argument to its task script.

single_node_many_task_with_parallel.sh
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --Nodes=1
#SBATCH --constraint=knl

module load parallel

srun parallel --jobs 6 task_command.sh argument_{} < input.txt 

This arrangement is a great alternative to submitting many individual jobs or a task array to the shared Slurm QOS. Current scheduling policy only allows two jobs per user to gain priority at a time; a single job running many tasks will spend less time waiting in queue than many jobs each running a single task. Also, this work pattern requires much less interaction with the Slurm controller, which makes it less likely to cause or be impacted by the Slurm controller experiencing heavy load.

Many Tasks Inside a Multiple Node Allocation

Demonstrated using two scripts: a batch submission to Slurm and a payload script containing the parallel and task commands.

This batch submission will request two KNL nodes, then the srun will run two instances of payload.sh with the $1 argument containing the task input list.

multiple_nodes_many_tasks_parallel.sh
#!/bin/bash
#SBATCH --qos=regular
#SBATCH --Nodes=2
#SBATCH --constraint=knl
#SBATCH --ntasks-per-node 1

srun --no-kill --ntasks=2 --wait=0 payload.sh $1 

The --no-kill argument will keep the slurm allocation running if any of the allocated nodes fail during the job. The --wait=0 argument prevents the job from terminating the other payload instances when the first one finishes.

The payload script uses environment variables set by Slurm inside a job to distinguish each instance of parallel, and then round-robin distributes input tasks to them using awk.

payload.sh
#!/bin/bash
module load parallel
if [[ -z "${SLURM_NODEID}" ]]; then
    echo "need \$SLURM_NODEID set"
    exit
fi
if [[ -z "${SLURM_NNODES}" ]]; then
    echo "need \$SLURM_NNODES set"
    exit
fi
cat $1 |                                               \
awk -v NNODE="$SLURM_NNODES" -v NODEID="$SLURM_NODEID" \
'NR % NNODE == NODEID' |                               \
parallel task.sh {}

The conditional statements make sure the Slurm environment variables we need are in place. $SLURM_NNODES holds the total number of nodes in the job and $SLURM_NODEID holds the unique ID number of this node. The awk command uses the line number of each input and the two environment variables to implement round-robin assignments of tasks to nodes. An advantage of this method is the number of nodes requested by the job can be freely changed without needing to adjust the task-to-node assignment logic.

GNU parallel includes a feature to distribute tasks to multiple machines using ssh connections. Though this allows work to balance between multiple nodes, our testing suggests that scaling is much less effective and it would be better to use a different task manager. More detail about this finding is available upon request.

Resuming Unfinished or Retrying Failed Tasks

If any tasks in a GNU parallel instance return a non-zero exit code, the parallel will also return non-zero. Parallel can be configured to use a job log file which tracks failed or incomplete tasks so that they can be resumed or retried.

Add --resume-failed --joblog logfile.txt to the list of parallel arguments and the state of tasks will be recorded. When that parallel instance is rerun with the exact same command line, it will skip any tasks that are already complete and re-run any tasks which failed. When using joblog it is good practice to use the available Slurm environment variables to distinguish files for each instance of parallel.

It is very important that the input file and command line arguments not be modified between runs and that only one instance of parallel per log file run at a time.

Note that the --retries n parallel argument seems like it should allow an instance of parallel to retry a failed task, but actually, this feature only works when using the --sshlogin feature.