makeflow(1)

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.

-v,--version

Show version string.

-X,--chdir=<directory>

Chdir to enable executing the Makefile in other directory.

--argv=<file>

Use command line arguments from JSON file.

Workflow Handling

-a,--advertise

Advertise the manager information to a catalog server.

-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)

-m,--email=<email>

Email summary of workflow to address.

-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)

-R,--retry

Automatically retry failed batch jobs up to 100 times.

-r,--retry-count=<n>

Automatically retry failed batch jobs up to n times.

--local-cores=<#>

Max number of cores used for local execution.

--local-memory=<#>

Max amount of memory used for local execution.

--local-disk=<#>

Max amount of disk used for local execution.

OPTION_END

Batch Options

-B,--batch-options=<options>

Add these options to all batch submit files.

--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, wq, vine, uge, pbs, torque, slurm, moab, cluster, amazon. (default is local)

--safe-submit-mode

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

--ignore-memory-spec

Excludes memory at submission. (SLURM)

--batch-mem-type=<type>

Specify memory resource type. (SGE)

--working-dir=<dir|url>

Working directory for batch system.

--sandbox

Run task in sandbox using bash script and task directory.

--verbose-jobnames

Set the job name based on the command.

--keep-wrapper-stdout

Do not redirect to /dev/null the stdout file from the batch system.

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. See '--jx-args'.

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 to be sent to stdout (":stdout") instead.

--debug-rotate-max=<byte>

Rotate debug file once it reaches this size.

--verbose

Display runtime progress on stdout.

TaskVine and Work Queue Options

-C,--catalog-server=<catalog>

Set catalog server to <catalog>. Format: HOSTNAME:PORT

-F,--wq-fast-abort=<#>

WorkQueue fast abort multiplier. (default is deactivated)

-M,--project-name=<project>

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.

-t,--keepalive-timeout=<#>

Work Queue keepalive timeout (default: 30s)

-u,--keepalive-interval=<#>

Work Queue keepalive interval (default: 120s)

-W,--schedule=<mode>

WorkQueue scheduling algorithm. (time|files|fcfs)

--password=<pwfile>

Password file for authenticating workers.

--ssl-cert=<>

Set the SSL certificate file for encrypting connection.

--ssl-key=<>

Set the SSL certificate file for encrypting connection.

--cache-mode

Control worker caching mode. (never|workflow|forever)

--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=<dir>

Enable the resource monitor, and write the monitor logs to <dir>

--monitor-exe=<file>

Specify resource monitor executable.

--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=<n>

Set monitor interval to <n> seconds. (default 1 second)

--monitor-log-fmt=<fmt>

Format for monitor logs. (default resource-rule-%06.6d, %d -> rule number)

--monitor-measure-dir

Monitor measures the task's current execution directory size.

--allocation=<waste>

When monitoring is enabled, automatically assign resource allocations to tasks. Makeflow will try to minimize FCwasteFT or maximize FCthroughputFT.

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-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.

--docker-opt=<string>

Specify options to be used in DSingularityocker execution.

Singularity Support

--singularity=<image>

Run each task in the Singularity container with this name. The container will be created from the passed in image.

--singularity-opt=<string>

Specify options to be used in Singularity execution.

Amazon Options

--amazon-config=<path>

Path to Amazon EC2 configuration file generated by makeflow_ec2_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=<>

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-dir=<path>

Specify archive base directory.

--archive-read=<path>

Only check to see if jobs have been cached and use outputs if it has been

--archive-s3=<s3_bucket>

Base S3 Bucket name

--archive-s3-no-check=<s3_bucket>

Blind upload files to S3 bucket (No existence check in bucket).

--s3-hostname=<s3_hostname>

Base S3 hostname. Used for AWS S3.

--s3-keyid=<s3_key_id>

Access Key for cloud server. Used for AWS S3.

--s3-secretkey=<secret_key>

Secret Key for cloud server. Used for AWS S3.

VC3 Builder Options

--vc3-builder

Enable VC3 Builder

--vc3-exe=<file>

VC3 Builder executable location

--vc3-log=<file>

VC3 Builder log name

--vc3-options=<string>

VC3 Builder option string

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>

Path to parrot_run executable on the host system.

--env-replace-path=<path>

Path to env_replace executable on the host system.

--skip-file-check

Do not check for file existence before running.

--do-not-save-failed-output

Disable saving failed nodes to directory for later analysis.

--shared-fs=<dir>

Assume the given directory is a shared filesystem accessible at all execution sites.

-X,--change-directory=<dir>

Change to <dir> prior to executing the workflow.

-X,--change-directory=<dir>

Change to <dir> prior to executing the workflow.

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 FC-p 0FT.

TCP_HIGH_PORT

Inclusive high port in range used with FC-p 0FT.