Provided by: coop-computing-tools_7.0.22-1ubuntu1_amd64 
NAME
makeflow - workflow engine for executing distributed workflows
SYNOPSIS
makeflow [options] <dagfile>
DESCRIPTION
Makeflow is a workflow engine for distributed computing. It accepts a specification of a
large amount of work to be performed, and runs it on remote machines in parallel where
possible. In addition, Makeflow is fault-tolerant, so you can use it to coordinate very
large tasks that may run for days or weeks in the face of failures. Makeflow is designed
to be similar to Make, so if you can write a Makefile, then you can write a Makeflow.
You can run a Makeflow on your local machine to test it out. If you have a multi-core
machine, then you can run multiple tasks simultaneously. If you have a Condor pool or a
Sun Grid Engine batch system, then you can send your jobs there to run. If you don't
already have a batch system, Makeflow comes with a system called Work Queue that will let
you distribute the load across any collection of machines, large or small. Makeflow also
supports execution in a Docker container, regardless of the batch system used.
OPTIONS
When makeflow is ran without arguments, it will attempt to execute the workflow specified
by the Makeflow dagfile using the local execution engine.
Commands
-c, ----clean=<option>
Clean up: remove logfile and all targets. If option is one of [intermediates,
outputs, cache], only indicated files are removed.
-f, --summary-log=<file>
Write summary of workflow to file.
-h, --help
Show this help screen.
-m, --email=<email>
Email summary of workflow to address.
-v, --version
Show version string.
-X, --chdir=<directory>
Chdir to enable executing the Makefile in other directory.
Batch Options
-B, --batch-options=<options>
Add these options to all batch submit files.
-j, --max-local=<#>
Max number of local jobs to run at once. (default is # of cores)
-J, --max-remote=<#>
Max number of remote jobs to run at once. (default is 1000 for -Twq, 100 otherwise)
-l, --makeflow-log=<logfile>
Use this file for the makeflow log. (default is X.makeflowlog)
-L, --batch-log=<logfile>
Use this file for the batch system log. (default is X.<type>log)
-R, --retry
Automatically retry failed batch jobs up to 100 times.
-r, --retry-count=<n>
Automatically retry failed batch jobs up to n times.
--send-environment
Send all local environment variables in remote execution.
--wait-for-files-upto <#>
Wait for output files to be created upto this many seconds (e.g., to deal with NFS
semantics).
-S, --submission-timeout=<timeout>
Time to retry failed batch job submission. (default is 3600s)
-T, --batch-type=<type>
Batch system type: local, dryrun, condor, sge, pbs, torque, blue_waters, slurm,
moab, cluster, wq, amazon, mesos. (default is local)
--safe-submit-mode
Excludes resources at submission. (SLURM, TORQUE, and PBS)
--ignore-memory-spec
Excludes memory at submission. (SLURM)
--verbose-jobnames
Set the job name based on the command.
JSON/JX Options
--json
Interpret <dagfile> as a JSON format Makeflow.
--jx Evaluate JX expressions in <dagfile>. Implies --json.
--jx-args <args>
Read variable definitions from the JX file <args>.
--jx-define <VAL=EXPR>
Set the variable <VAL> to the JX expression <EXPR>.
--jx-context <ctx>
Deprecated.
Debugging Options
-d, --debug=<subsystem>
Enable debugging for this subsystem.
-o, --debug-file=<file>
Write debugging output to this file. By default, debugging is sent to stderr
(":stderr"). You may specify logs be sent to stdout (":stdout"), to the system
syslog (":syslog"), or to the systemd journal (":journal").
--verbose
Display runtime progress on stdout.
WorkQueue Options
-a, --advertise
Advertise the master information to a catalog server.
-C, --catalog-server=<catalog>
Set catalog server to <catalog>. Format: HOSTNAME:PORT
-F, --wq-fast-abort=<#>
WorkQueue fast abort multiplier. (default is deactivated)
-M, ---N=<project-name>
Set the project name to <project>.
-p, --port=<port>
Port number to use with WorkQueue. (default is 9123, 0=arbitrary)
-Z, --port-file=<file>
Select port at random and write it to this file. (default is disabled)
-P, --priority=<integer>
Priority. Higher the value, higher the priority.
-W, --wq-schedule=<mode>
WorkQueue scheduling algorithm. (time|files|fcfs)
-s, --password=<pwfile>
Password file for authenticating workers.
--disable-cache
Disable file caching (currently only Work Queue, default is false)
--work-queue-preferred-connection <connection>
Indicate preferred connection. Chose one of by_ip or by_hostname. (default is
by_ip)
Monitor Options
--monitor <dir>
Enable the resource monitor, and write the monitor logs to <dir>
--monitor-with-time-series
Enable monitor time series. (default is disabled)
--monitor-with-opened-files
Enable monitoring of openened files. (default is disabled)
--monitor-interval <#>
Set monitor interval to <#> seconds. (default 1 second)
--monitor-log-fmt <fmt>
Format for monitor logs. (default resource-rule-%06.6d, %d -> rule number)
--allocation <waste>
When monitoring is enabled, automatically assign resource allocations to tasks.
Makeflow will try to minimize waste or maximize throughput.
Umbrella Options
--umbrella-binary <filepath>
Umbrella binary for running every rule in a makeflow.
--umbrella-log-prefix <filepath>
Umbrella log file prefix for running every rule in a makeflow. (default is
<makefilename>.umbrella.log)
--umbrella-mode <mode>
Umbrella execution mode for running every rule in a makeflow. (default is local)
--umbrella-spec <filepath>
Umbrella spec for running every rule in a makeflow.
Docker Support
--docker <image>
Run each task in the Docker container with this name. The image will be obtained
via "docker pull" if it is not already available.
--docker-tar <tar>
Run each task in the Docker container given by this tar file. The image will be
uploaded via "docker load" on each execution site.
Singularity Support
--singularity <image>
Run each task in the Singularity container with this name. The container will be
created from the passed in image.
Amazon Options
--amazon-credentials <path>
Specify path to Amazon credentials file. The credentials file should be in the
following JSON format:
{
"aws_access_key_id" : "AAABBBBCCCCDDD"
"aws_secret_access_key" : "AAABBBBCCCCDDDAAABBBBCCCCDDD"
}
--amazon-ami <image-id>
Specify an amazon machine image.
Mesos Options
--mesos-master <hostname>
Indicate the host name of preferred mesos master.
--mesos-path <filepath>
Indicate the path to mesos python2 site-packages.
--mesos-preload <library>
Indicate the linking libraries for running mesos..
Amazon Lambda Options
--lambda-config <path>
Path to the configuration file generated by makeflow_lambda_setup
Kubernetes Options
--k8s-image <docker_image>
Indicate the Docker image for running pods on Kubernetes cluster.
Mountfile Support
--mounts <mountfile>
Use this file as a mountlist. Every line of a mountfile can be used to specify the
source and target of each input dependency in the format of target source (Note
there should be a space between target and source.).
--cache <cache_dir>
Use this dir as the cache for file dependencies.
Archiving Options
--archive <path>
Archive results of workflow at the specified path (by default
/tmp/makeflow.archive.$UID) and use outputs of any archived jobs instead of re-
executing job
--archive-read <path>
Only check to see if jobs have been cached and use outputs if it has been
--archive-write <path>
Write only results of each job to the archiving directory at the specified path
Other Options
-A, --disable-afs-check
Disable the check for AFS. (experts only)
-z, --zero-length-error
Force failure on zero-length output files.
-g, --gc=<type>
Enable garbage collection. (ref_cnt|on_demand|all)
--gc-size <int>
Set disk size to trigger GC. (on_demand only)
-G, --gc-count=<int>
Set number of files to trigger GC. (ref_cnt only)
--wrapper <script>
Wrap all commands with this script. Each rule's original recipe is appended to
script or replaces the first occurrence of {} in script.
--wrapper-input <file>
Wrapper command requires this input file. This option may be specified more than
once, defining an array of inputs. Additionally, each job executing a recipe has a
unique integer identifier that replaces occurrences %% in file.
--wrapper-output <file>
Wrapper command requires this output file. This option may be specified more than
once, defining an array of outputs. Additionally, each job executing a recipe has a
unique integer identifier that replaces occurrences %% in file.
--enforcement
Use Parrot to restrict access to the given inputs/outputs.
--parrot <path>
Path to parrot_run executable on the host system.
--shared-fs <dir>
Assume the given directory is a shared filesystem accessible at all execution
sites.
DRYRUN MODE
When the batch system is set to -T <dryrun>, Makeflow runs as usual but does not actually
execute jobs or modify the system. This is useful to check that wrappers and substitutions
are applied as expected. In addition, Makeflow will write an equivalent shell script to
the batch system log specified by -L <logfile>. This script will run the commands in
serial that Makeflow would have run. This shell script format may be useful for archival
purposes, since it does not depend on Makeflow.
ENVIRONMENT VARIABLES
The following environment variables will affect the execution of your Makeflow:
BATCH_OPTIONS
This corresponds to the -B <options> parameter and will pass extra batch options to the
underlying execution engine.
MAKEFLOW_MAX_LOCAL_JOBS
This corresponds to the -j <#> parameter and will set the maximum number of local batch
jobs. If a -j <#> parameter is specified, the minimum of the argument and the environment
variable is used.
MAKEFLOW_MAX_REMOTE_JOBS
This corresponds to the -J <#> parameter and will set the maximum number of local batch
jobs. If a -J <#> parameter is specified, the minimum of the argument and the environment
variable is used.
Note that variables defined in your Makeflow are exported to the environment.
TCP_LOW_PORT
Inclusive low port in range used with -p 0.
TCP_HIGH_PORT
Inclusive high port in range used with -p 0.
EXIT STATUS
On success, returns zero. On failure, returns non-zero.
EXAMPLES
Run makeflow locally with debugging:
makeflow -d all Makeflow
Run makeflow on Condor will special requirements:
makeflow -T condor -B "requirements = MachineGroup == 'ccl'" Makeflow
Run makeflow with WorkQueue using named workers:
makeflow -T wq -a -N project.name Makeflow
Create a directory containing all of the dependencies required to run the specified
makeflow
makeflow -b bundle Makeflow
COPYRIGHT
The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright
(C) 2005-2015 The University of Notre Dame. This software is distributed under the GNU
General Public License. See the file COPYING for details.
SEE ALSO
• Cooperative Computing Tools Documentation
• Makeflow User Manual
• makeflow(1) makeflow_monitor(1) makeflow_analyze(1) makeflow_viz(1)
makeflow_graph_log(1) starch(1) makeflow_ec2_setup(1) makeflow_ec2_cleanup(1)