Command-line interface¶

Sub-commands¶

help	Show how to use this tool
list (ls)	List tasks in queue
submit	Submit task(s) to queue
resubmit	Resubmit done, failed or timed-out tasks
remove (rm)	Remove or cancel task(s)
info	Show detailed information about MyQueue or a task
workflow	Submit tasks from Python script or several scripts matching pattern
kick	Restart T and M tasks (timed-out and out-of-memory)
modify	Modify task(s)
init	Initialize new queue
sync	Make sure SLURM/LSF/PBS and MyQueue are in sync
completion	Set up tab-completion for Bash
config	Create config.py file
daemon	Interact with the background process

Help: Show how to use this tool¶

usage: mq help [-h] [cmd]

Show how to use this tool.

More help can be found here: https://myqueue.readthedocs.io/.

cmd:

Subcommand.

options:

-h, --help: show this help message and exit

List (ls): List tasks in queue¶

usage: mq list [-h] [-s qhrdFCTMaA] [-i ID] [-n NAME] [-e ERROR]: [-c ifnaIrAste] [-S c] [-C] [–not-recursive] [-v] [-q] [-T] [folder …]

List tasks in queue.

Only tasks in the chosen folder and its subfolders are shown.

Columns:

i: id
f: folder
n: name of task
a: arguments
I: info: "+<nargs>,*<repeats>,d<ndeps>"
r: resources
A: age
s: state
t: time
e: error message

Examples:

$ mq list -s rq  # show running and queued jobs
$ mq ls -s F abc/  # show failed jobs in abc/ folder

folder:

List tasks in this folder and its subfolders. Defaults to current folder. Use –not-recursive to exclude subfolders.

options:

-h, --help: show this help message and exit
-s qhrdFCTMaA, --states qhrdFCTMaA: Selection of states. First letters of “queued”, “hold”, “running”, “done”, “FAILED”, “CANCELED”, “TIMEOUT”, “MEMORY”, “all” and “ALL”.
-i ID, --id ID: Comma-separated list of task ID’s. Use “-i -” for reading ID’s from stdin (one ID per line; extra stuff after the ID will be ignored).
-n NAME, --name NAME: Select only tasks with names matching “NAME” (* and ? can be used).
-e ERROR, --error ERROR: Select only tasks with error message matching “ERROR” (* and ? can be used).
-c ifnaIrAste, --columns ifnaIrAste: Select columns to show. Use “-c a-” to remove the “a” column.
-S c, --sort c: Sort rows using column c, where c must be one of i, f, n, a, r, A, s, t or e. Use “-S c-” for a descending sort.
-C, --count: Just show the number of tasks.
--not-recursive: Do not list subfolders.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Submit: Submit task(s) to queue¶

usage: mq submit [-h] [-d DEPENDENCIES] [-n NAME] [–restart N]: [–max-tasks MAX_TASKS] [-R RESOURCES] [-w] [-X EXTRA_SCHEDULER_ARGS] [-z] [-v] [-q] [-T] task [folder …]

Submit task(s) to queue.

Example:

$ mq submit script.py -R 24:1d  # 24 cores for 1 day

task:

Task to submit.

folder:

Submit tasks in this folder. Defaults to current folder.

options:

-h, --help: show this help message and exit
-d DEPENDENCIES, --dependencies DEPENDENCIES: Comma-separated task names.
-n NAME, --name NAME: Name used for task.
--restart N: Restart N times if task times out or runs out of memory. Time-limit will be doubled for a timed out task and number of cores will be increased to the next number of nodes for a task that runs out of memory.
--max-tasks MAX_TASKS: Maximum number of tasks to submit.
-R RESOURCES, --resources RESOURCES: Examples: “8:1h”, 8 cores for 1 hour. Use “m” for minutes, “h” for hours and “d” for days. “16:1:30m”: 16 cores, 1 process, half an hour. “1:xeon40:5m”: 1 core on “xeon40” for 5 minutes.
-w, --workflow: Write <task-name>.state file when task has finished.
-X EXTRA_SCHEDULER_ARGS, --extra-scheduler-args EXTRA_SCHEDULER_ARGS: Extra arguments for scheudler. Example: -X bla-bla. For arguments that start with a dash, leave out the space: -X–gres=gpu:4 or -X=–gres=gpu:4. Can be used multiple times.
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Resubmit: Resubmit done, failed or timed-out tasks¶

usage: mq resubmit [-h] [–keep] [-R RESOURCES] [-w] [-X EXTRA_SCHEDULER_ARGS]: [-s qhrdFCTMaA] [-i ID] [-n NAME] [-e ERROR] [-z] [-v] [-q] [-T] [-r] [folder …]

Resubmit done, failed or timed-out tasks.

Example:

$ mq resubmit -i 4321  # resubmit job with id=4321

folder:

Task-folder. Use –recursive (or -r) to include subfolders.

options:

-h, --help: show this help message and exit
--keep: Do not remove old tasks.
-R RESOURCES, --resources RESOURCES: Examples: “8:1h”, 8 cores for 1 hour. Use “m” for minutes, “h” for hours and “d” for days. “16:1:30m”: 16 cores, 1 process, half an hour. “1:xeon40:5m”: 1 core on “xeon40” for 5 minutes.
-w, --workflow: Write <task-name>.state file when task has finished.
-X EXTRA_SCHEDULER_ARGS, --extra-scheduler-args EXTRA_SCHEDULER_ARGS: Extra arguments for scheudler. Example: -X bla-bla. For arguments that start with a dash, leave out the space: -X–gres=gpu:4 or -X=–gres=gpu:4. Can be used multiple times.
-s qhrdFCTMaA, --states qhrdFCTMaA: Selection of states. First letters of “queued”, “hold”, “running”, “done”, “FAILED”, “CANCELED”, “TIMEOUT”, “MEMORY”, “all” and “ALL”.
-i ID, --id ID: Comma-separated list of task ID’s. Use “-i -” for reading ID’s from stdin (one ID per line; extra stuff after the ID will be ignored).
-n NAME, --name NAME: Select only tasks with names matching “NAME” (* and ? can be used).
-e ERROR, --error ERROR: Select only tasks with error message matching “ERROR” (* and ? can be used).
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.
-r, --recursive: Use also subfolders.

Remove (rm): Remove or cancel task(s)¶

usage: mq remove [-h] [-f] [-s qhrdFCTMaA] [-i ID] [-n NAME] [-e ERROR] [-z]: [-v] [-q] [-T] [-r] [folder …]

Remove or cancel task(s).

Examples:

$ mq remove -i 4321,4322  # remove jobs with ids 4321 and 4322
$ mq rm -s d . -r  # remove done jobs in this folder and its subfolders

folder:

Task-folder. Use –recursive (or -r) to include subfolders.

options:

-h, --help: show this help message and exit
-f, --force: Remove also workflow tasks.
-s qhrdFCTMaA, --states qhrdFCTMaA: Selection of states. First letters of “queued”, “hold”, “running”, “done”, “FAILED”, “CANCELED”, “TIMEOUT”, “MEMORY”, “all” and “ALL”.
-i ID, --id ID: Comma-separated list of task ID’s. Use “-i -” for reading ID’s from stdin (one ID per line; extra stuff after the ID will be ignored).
-n NAME, --name NAME: Select only tasks with names matching “NAME” (* and ? can be used).
-e ERROR, --error ERROR: Select only tasks with error message matching “ERROR” (* and ? can be used).
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.
-r, --recursive: Use also subfolders.

Info: Show detailed information about MyQueue or a task¶

usage: mq info [-h] [-v] [-q] [-T] [-i ID] [-A] [folder]

Show detailed information about MyQueue or a task.

Example:

$ mq info  # show information about MyQueue
$ mq info -i 12345  # show information about task with id=12345

folder:

Show information for queues in this folder and its subfolders. Defaults to current folder.

options:

-h, --help: show this help message and exit
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.
-i ID, --id ID: Show information about specific task.
-A, --all: Show information about all your queues.

Workflow: Submit tasks from Python script or several scripts matching pattern¶

usage: mq workflow [-h] [–max-tasks MAX_TASKS] [-f] [-t TARGETS] [-p]: [-a ARGUMENTS] [-z] [-v] [-q] [-T] script [folder …]

Submit tasks from Python script or several scripts matching pattern.

The script(s) must define a workflow() function as shown here:

$ cat flow.py
from myqueue.workflow import run
def workflow():
    with run(<task1>):
        run(<task2>)
$ mq workflow flow.py F1/ F2/  # submit tasks in F1 and F2 folders

script:

Submit tasks from workflow script.

folder:

Submit tasks in this folder. Defaults to current folder.

options:

-h, --help: show this help message and exit
--max-tasks MAX_TASKS: Maximum number of tasks to submit.
-f, --force: Submit also failed tasks.
-t TARGETS, --targets TARGETS: Comma-separated target names. Without any targets, all tasks will be submitted.
-p, --pattern: Use submit scripts matching “script” pattern in all subfolders.
-a ARGUMENTS, --arguments ARGUMENTS: Pass arguments to workflow() function. Example: “-a name=hello,n=5” will call workflow(name=’hello’, n=5).
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Kick: Restart T and M tasks (timed-out and out-of-memory)¶

usage: mq kick [-h] [-z] [-v] [-q] [-T] [folder]

Restart T and M tasks (timed-out and out-of-memory).

The queue is kicked automatically every ten minutes - so you don’t have to do it manually.

folder:

Kick tasks in this folder and its subfolders. Defaults to current folder.

options:

-h, --help: show this help message and exit
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Modify: Modify task(s)¶

usage: mq modify [-h] [-E STATES] [-N NEW_STATE] [-s qhrdFCTMaA] [-i ID]: [-n NAME] [-e ERROR] [-z] [-v] [-q] [-T] [-r] [folder …]

Modify task(s).

The following state changes are allowed: h->q or q->h.

folder:

Task-folder. Use –recursive (or -r) to include subfolders.

options:

-h, --help: show this help message and exit
-E STATES, --email STATES: Send email when state changes to one of the specified states (one or more of the letters: rdFCTMA).
-N NEW_STATE, --new-state NEW_STATE: New state (one of the letters: qhrdFCTM).
-s qhrdFCTMaA, --states qhrdFCTMaA: Selection of states. First letters of “queued”, “hold”, “running”, “done”, “FAILED”, “CANCELED”, “TIMEOUT”, “MEMORY”, “all” and “ALL”.
-i ID, --id ID: Comma-separated list of task ID’s. Use “-i -” for reading ID’s from stdin (one ID per line; extra stuff after the ID will be ignored).
-n NAME, --name NAME: Select only tasks with names matching “NAME” (* and ? can be used).
-e ERROR, --error ERROR: Select only tasks with error message matching “ERROR” (* and ? can be used).
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.
-r, --recursive: Use also subfolders.

Init: Initialize new queue¶

usage: mq init [-h] [-z] [-v] [-q] [-T]

Initialize new queue.

This will create a .myqueue/ folder in your current working directory and copy ~/.myqueue/config.py into it.

options:

-h, --help: show this help message and exit
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Sync: Make sure SLURM/LSF/PBS and MyQueue are in sync¶

usage: mq sync [-h] [-z] [-v] [-q] [-T] [folder]

Make sure SLURM/LSF/PBS and MyQueue are in sync.

Remove tasks that SLURM/LSF/PBS doesn’t know about. Also removes a task if its corresponding folder no longer exists.

folder:

Sync tasks in this folder and its subfolders. Defaults to current folder.

options:

-h, --help: show this help message and exit
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Completion: Set up tab-completion for Bash¶

usage: mq completion [-h] [-v] [-q] [-T]

Set up tab-completion for Bash.

Do this:

$ mq completion >> ~/.bashrc

options:

-h, --help: show this help message and exit
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Config: Create config.py file¶

usage: mq config [-h] [-Q QUEUE_NAME] [–in-place] [-z] [-v] [-q] [-T]: [{local,slurm,pbs,lsf}]

Create config.py file.

This tool will try to guess your configuration. Some hand editing afterwards will most likely be needed. Read more about config.py file here:

https://myqueue.readthedocs.io/en/latest/configuration.html

Example:

$ mq config -Q hpc lsf

{local,slurm,pbs,lsf}:

Name of scheduler. Will be guessed if not supplied.

options:

-h, --help: show this help message and exit
-Q QUEUE_NAME, --queue-name QUEUE_NAME: Name of queue. May be needed.
--in-place: Overwrite ~/.myqueue/config.py file.
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Daemon: Interact with the background process¶

usage: mq daemon [-h] [-z] [-v] [-q] [-T] {start,stop,status} [folder]

Interact with the background process.

Manage daemon for sending notifications, restarting, holding and releasing tasks.

{start,stop,status}:

Start, stop or check status.

folder:

Pick daemon process corresponding to this folder. Defaults to current folder.

options:

-h, --help: show this help message and exit
-z, --dry-run: Show what will happen without doing anything.
-v, --verbose: More output.
-q, --quiet: Less output.
-T, --traceback: Show full traceback.

Command-line interface¶

Sub-commands¶

Help: Show how to use this tool¶

List (ls): List tasks in queue¶

Submit: Submit task(s) to queue¶

Resubmit: Resubmit done, failed or timed-out tasks¶

Remove (rm): Remove or cancel task(s)¶

Info: Show detailed information about MyQueue or a task¶

Workflow: Submit tasks from Python script or several scripts matching pattern¶

Kick: Restart T and M tasks (timed-out and out-of-memory)¶

Modify: Modify task(s)¶

Init: Initialize new queue¶

Sync: Make sure SLURM/LSF/PBS and MyQueue are in sync¶

Completion: Set up tab-completion for Bash¶

Config: Create config.py file¶

Daemon: Interact with the background process¶

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