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-spec <#>

Excludes resources at submission (SLURM, TORQUE, and PBS)

 --ignore-memory-spec <#>

Excludes memory at submission (SLURM)

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.

BATCH_OPTIONS¶

MAKEFLOW_MAX_LOCAL_JOBS¶

MAKEFLOW_MAX_REMOTE_JOBS¶

Note that variables defined in your Makeflow are exported to the environment.

TCP_LOW_PORT¶

TCP_HIGH_PORT¶