abirun.py

This script allows the user to submit the calculations contained in the AbiPy Flow (for further detail, consult the TaskManager documentation).

$ abirun.py --help
usage: abirun.py [-h] [-V]
                 [flowdir]
                 {single,rapid,scheduler,batch,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,panel,new_manager,tail,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,group,diff,networkx,graphviz,listext}
                 ...

positional arguments:
  flowdir               File or directory containing the ABINIT
                        flow/work/task. If not given, the flow in the current
                        workdir is selected.

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit

subcommands:
  Valid subcommands

  {single,rapid,scheduler,batch,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,panel,new_manager,tail,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,group,diff,networkx,graphviz,listext}
                        sub-command help
    single              Run single task and exit.
    rapid               Run all tasks in rapidfire mode.
    scheduler           Run all tasks with a Python scheduler. Requires
                        scheduler.yml either in $PWD or ~/.abinit/abipy.
    batch               Run scheduler in batch script.
    status              Show status table.
    set_status          Change the status of the task. WARNING: Option for
                        developers!
    cancel              Cancel the tasks in the queue. Not available if qtype
                        is shell.
    restart             Restart the tasks of the flow. By default, only the
                        task whose status==Unconverged are restarted. Use -S
                        `status` and/or -n node_ids to select particular
                        tasks.
    reset               Reset the tasks of the flow with the specified status.
    move                Move the flow to a new directory and change the
                        absolute paths.
    open                Open files in $EDITOR, type `abirun.py FLOWDIR open
                        --help` for help).
    abiopen             Open FILE with abiopen. Same interface as abiopen.py
    abibuild            Show ABINIT build information and exit.
    doc_scheduler       Document the options available in scheduler.yml.
    panel               Interact with the flow in the browser (requires panel
                        package).
    new_manager         Change the TaskManager.
    tail                Use unix tail to follow the main output files of the
                        flow.
    deps                Show dependencies.
    robot               Use a robot to analyze the results of multiple tasks
                        (requires ipython).
    cycles              Print self-consistent/relaxation cycles extracted from
                        the output of the tasks.Use `-t ScfTask` or
                        `FLOWDIR/w0/` or `FLOWDIR/w0/t1/` to select tasks by
                        class, by work or by workdir.
    dims                Print table with dimensions extracted from the output
                        of the tasks.
    inspect             Call matplotlib to inspect the tasks (execute
                        task.inspect method)
    inputs              Show the input files of the tasks.
    abivars             Show pandas dataframe with Abinit input variables.
    structures          Compare input/output structures of the tasks. Print
                        max force and pressure if available.
    ebands              Compare electronic bands produced by the tasks.
    hist                Compare HIST.nc files produced by the tasks.
    doc_manager         Document the TaskManager options.
    events              Show ABINIT events (error messages, warnings,
                        comments).
    corrections         Show AbiPy corrections performed at runtime.
    history             Show Node history.
    handlers            Show event handlers installed in the flow.
    notebook            Create and open an ipython notebook to interact with
                        the flow.
    ipython             Embed IPython. Useful for advanced operations or
                        debugging purposes.
    tar                 Create tarball file.
    tricky              Show tricky tasks i.e. tasks that have been restarted,
                        launched more than once or tasks that have been
                        corrected.
    debug               Analyze error files and log files for possible error
                        messages.
    debug_reset         Analyze error files and log files produced by reset
                        tasks for possible error messages.
    group               Group tasks according to property.
    diff                Compare files produced by two or three nodes.
    networkx            Draw flow and node dependencies with networkx package.
    graphviz            Draw flow and node dependencies with graphviz package.
                        Accept (FLOWDIR|WORKDIR|TASKDIR). See
                        https://graphviz.readthedocs.io/.
    listext             List all the output files with the given extension
                        that have been produced by the nodes.

Notes:

    If FLOWDIR is not given, abirun.py automatically selects the database located within
    the working directory. An Exception is raised if multiple databases are found.

    Note, moreover, that one can replace FLOWDIR with the directory of a work/task
    to make the command operate on this node of the flow without having to specify the node ids with --nids.
    For example, to have the list of events of the task in `FLOWDIR/w0/t1` use:

        abirun.py FLOWDIR/w0/t1 events

    instead of:

        abirun.py FLOWDIR events -n 123

    where 123 is the node identifier associated to w0/t1.

    To start the scheduler with a time interval of 30 seconds, use:

        nohup abirun.py FLOWDIR scheduler -s 30 > sched.log 2> sched.err

    Alternatively one can specify the scheduler options via the `scheduler.yml` file.
    Remember that AbiPy will first look for `scheduler.yml` and `manager.yml` files
    in the current working directory and then inside $HOME/.abinit/abipy/

    Use `abirun.py --help` for help and `abirun.py COMMAND --help` to get the documentation for `COMMAND`.
    Use `-v` to increase verbosity level (can be supplied multiple times e.g -vv).

Usage example:

###########
# Execution
###########

  abirun.py FLOWDIR rapid                 => Keep repeating, stop when no task can be executed.
  abirun.py FLOWDIR scheduler             => Execute flow with the scheduler.
  abirun.py FLOWDIR status                => Show status table.
  abirun.py FLOWDIR events                => Print ABINIT events (Warnings/Errors/Comments) found in log files.
  abirun.py FLOWDIR history               => Print Task histories.
  abirun.py FLOWDIR cancel                => Cancel jobs in the queue.
  abirun.py FLOWDIR debug                 => Analyze error files and log files for possible error messages.
  abirun.py FLOWDIR corrections           => Show AbiPy corrections performed at runtime.
  abirun.py FLOWDIR handlers              => Show event handlers installed in the flow.

##########
# Analysis
##########

  abirun.py FLOWDIR inputs                => Print input files.
  abirun.py FLOWDIR abivars -vn ecut,nband  => Print table with these input variables.
  abirun.py FLOWDIR structures            => Compare input/output structures of the tasks.
  abirun.py FLOWDIR ebands -t NscfTask    => Print table with electronic properties computed in NscfTask
  abirun.py FLOWDIR hist -p               => Print table with last iteration in hist files and plot results.
  abirun.py FLOWDIR cycles -p             => Print (and plot) SCF/relaxation cycles extracted from the output of the tasks.
  abirun.py FLOWDIR robot hist            => Build robot for HIST files, start ipython shell to interact with the robot.
  abirun.py FLOWDIR dims                  => Print table with dimensions extracted from the output of the tasks.
  abirun.py FLOWDIR group -g task_class   => Print table with node ids and tasks grouped by class
  abirun.py FLOWDIR inspect               => Call matplotlib to inspect the tasks.
  abirun.py FLOWDIR tail                  => Use Unix tail to follow the main output files of the flow.
  abirun.py FLOWDIR deps                  => Show task dependencies.
  abirun.py FLOWDIR listext GSR SIGRES    => Show output files with the given extension(s).
  abirun.py FILE abiopen                  => Open FILE with abiopen. Same interface as abiopen.py

###############
# Miscelleanous
###############

  abirun.py FLOWDIR ipython               => Open flow in ipython terminal.
  abirun.py FLOWDIR notebook              => Generate jupyter notebook.
  abirun.py FLOWDIR networkx              => Plot flow graph with networkx.
  abirun.py FLOWDIR graphviz              => Plot flow graph with graphviz
                                            (can also select tasks/works and show files with -d).
  abirun.py abibuild                      => Show ABINIT build information and exit.

###############
# Documentation
###############

  abirun.py FLOWDIR doc_manager slurm     => Document the TaskManager options availabe for Slurm.
  abirun.py . doc_manager script          => Show the job script that will be produced with the current settings.
  abirun.py . doc_scheduler               => Document the options available in scheduler.yml.
$ abirun.py doc_scheduler
Options that can be specified in scheduler.yml:

            weeks: number of weeks to wait (DEFAULT: 0).
            days: number of days to wait (DEFAULT: 0).
            hours: number of hours to wait (DEFAULT: 0).
            minutes: number of minutes to wait (DEFAULT: 0).
            seconds: number of seconds to wait (DEFAULT: 0).
            mailto: The scheduler will send an email to `mailto` every `remindme_s` seconds.
                (DEFAULT: None i.e. not used).
            verbose: (int) verbosity level. (DEFAULT: 0)
            use_dynamic_manager: "yes" if the |TaskManager| must be re-initialized from
                file before launching the jobs. (DEFAULT: "no")
            max_njobs_inqueue: Limit on the number of jobs that can be present in the queue. (DEFAULT: 200)
            max_ncores_used: Maximum number of cores that can be used by the scheduler.
            remindme_s: The scheduler will send an email to the user specified
                by `mailto` every `remindme_s` seconds. (int, DEFAULT: 1 day).
            max_num_pyexcs: The scheduler will exit if the number of python exceptions is > max_num_pyexcs
                (int, DEFAULT: 0)
            max_num_abierrs: The scheduler will exit if the number of errored tasks is > max_num_abierrs
                (int, DEFAULT: 0)
            safety_ratio: The scheduler will exits if the number of jobs launched becomes greater than
               `safety_ratio` * total_number_of_tasks_in_flow. (int, DEFAULT: 5)
            max_nlaunches: Maximum number of tasks launched in a single iteration of the scheduler.
                (DEFAULT: -1 i.e. no limit)
            debug: Debug level. Use 0 for production (int, DEFAULT: 0)
            fix_qcritical: "yes" if the launcher should try to fix QCritical Errors (DEFAULT: "no")
            rmflow: If "yes", the scheduler will remove the flow directory if the calculation
                completed successfully. (DEFAULT: "no")
            killjobs_if_errors: "yes" if the scheduler should try to kill all the runnnig jobs
                before exiting due to an error. (DEFAULT: "yes")
$ abirun.py . doc_manager

# TaskManager configuration file (YAML Format)

policy:
    # Dictionary with options used to control the execution of the tasks.

qadapters:
    # List of qadapters objects (mandatory)
    -  # qadapter_1
    -  # qadapter_2

db_connector:
    # Connection to MongoDB database (optional)

batch_adapter:
    # Adapter used to submit flows with batch script. (optional)

##########################################
# Individual entries are documented below:
##########################################

policy: 
    autoparal:                # (integer). 0 to disable the autoparal feature (DEFAULT: 1 i.e. autoparal is on)
    condition:                # condition used to filter the autoparal configurations (Mongodb-like syntax).
                              # DEFAULT: empty i.e. ignored.
    vars_condition:           # Condition used to filter the list of ABINIT variables reported by autoparal
                              # (Mongodb-like syntax). DEFAULT: empty i.e. ignored.
    frozen_timeout:           # A job is considered frozen and its status is set to ERROR if no change to
                              # the output file has been done for `frozen_timeout` seconds. Accepts int with seconds or
                              # string in slurm form i.e. days-hours:minutes:seconds. DEFAULT: 1 hour.
    precedence:               # Under development.
    autoparal_priorities:     # Under development.

qadapter: 
# Dictionary with info on the hardware available on this queue.
hardware:
    num_nodes:           # Number of nodes available on this queue (integer, MANDATORY).
    sockets_per_node:    # Number of sockets per node (integer, MANDATORY).
    cores_per_socket:    # Number of cores per socket (integer, MANDATORY).
                         # The total number of cores available on this queue is
                         # `num_nodes * sockets_per_node * cores_per_socket`.

# Dictionary with the options used to prepare the enviroment before submitting the job
job:
    setup:                # List of commands (strings) executed before running (DEFAULT: empty)
    omp_env:              # Dictionary with OpenMP environment variables (DEFAULT: empty i.e. no OpenMP)
    modules:              # List of modules to be imported before running the code (DEFAULT: empty).
                          # NB: Error messages produced by module load are redirected to mods.err
    shell_env:            # Dictionary with shell environment variables.
    mpi_runner:           # MPI runner. Possible values in ["mpirun", "mpiexec", "srun", None]
                          # DEFAULT: None i.e. no mpirunner is used.
    mpi_runner_options    # String with optional options passed to the `mpi_runner` e.g. "--bind-to None"
    shell_runner:         # Used for running small sequential jobs on the front-end. Set it to None
                          # if mpirun or mpiexec are not available on the fron-end. If not
                          # given, small sequential jobs are executed with `mpi_runner`.
    shell_runner_options  # Similar to mpi_runner_options but for the runner used on the front-end.
    pre_run:              # List of commands (strings) executed before the run (DEFAULT: empty)
    post_run:             # List of commands (strings) executed after the run (DEFAULT: empty)

# dictionary with the name of the queue and optional parameters
# used to build/customize the header of the submission script.
queue:
    qtype:                # String defining the qapapter type e.g. slurm, shell ...
    qname:                # Name of the submission queue (string, MANDATORY)
    qparams:              # Dictionary with values used to generate the header of the job script
                          # We use the *normalized* version of the options i.e dashes in the official name
                          # are replaced by underscores e.g. ``--mail-type`` becomes ``mail_type``
                          # See pymatgen.io.abinit.qadapters.py for the list of supported values.
                          # Use ``qverbatim`` to pass additional options that are not included in the template.

# dictionary with the constraints that must be fulfilled in order to run on this queue.
limits:
    min_cores:             # Minimum number of cores (integer, DEFAULT: 1)
    max_cores:             # Maximum number of cores (integer, MANDATORY). Hard limit to hint_cores:
                           # it's the limit beyond which the scheduler will not accept the job (MANDATORY).
    hint_cores:            # The limit used in the initial setup of jobs.
                           # Fix_Critical method may increase this number until max_cores is reached
    min_mem_per_proc:      # Minimum memory per MPI process in Mb, units can be specified e.g. 1.4 Gb
                           # (DEFAULT: hardware.mem_per_core)
    max_mem_per_proc:      # Maximum memory per MPI process in Mb, units can be specified e.g. `1.4Gb`
                           # (DEFAULT: hardware.mem_per_node)
    timelimit:             # Initial time-limit. Accepts time according to slurm-syntax i.e:
                           # "days-hours" or "days-hours:minutes" or "days-hours:minutes:seconds" or
                           # "minutes" or "minutes:seconds" or "hours:minutes:seconds",
    timelimit_hard:        # The hard time-limit for this queue. Same format as timelimit.
                           # Error handlers could try to submit jobs with increased timelimit
                           # up to timelimit_hard. If not specified, timelimit_hard == timelimit
    condition:             # MongoDB-like condition (DEFAULT: empty, i.e. not used)
    allocation:            # String defining the policy used to select the optimal number of CPUs.
                           # possible values are in ["nodes", "force_nodes", "shared"]
                           # "nodes" means that we should try to allocate entire nodes if possible.
                           # This is a soft limit, in the sense that the qadapter may use a configuration
                           # that does not fulfill this requirement. In case of failure, it will try to use the
                           # smallest number of nodes compatible with the optimal configuration.
                           # Use `force_nodes` to enfore entire nodes allocation.
                           # `shared` mode does not enforce any constraint (DEFAULT: shared).
    max_num_launches:      # Limit to the number of times a specific task can be restarted (integer, DEFAULT: 5)


qtype supported: ['bluegene', 'moab', 'pbspro', 'sge', 'shell', 'slurm', 'torque']
Use `abirun.py . manager slurm` to have the list of qparams for slurm.

At the time of writing (Feb 22, 2020), AbiPy supports the following resource managers:

To obtain the list of options supported by a particular resource manager e.g. slurm:

abirun.py . doc_manager slurm

Complete command line reference

usage: abirun.py [-h] [-V]
                 [flowdir]
                 {single,rapid,scheduler,batch,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,panel,new_manager,tail,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,group,diff,networkx,graphviz,listext}
                 ...

Positional Arguments

flowdir

File or directory containing the ABINIT flow/work/task. If not given, the flow in the current workdir is selected.

Named Arguments

-V, --version

show program’s version number and exit

subcommands

Valid subcommands

command

Possible choices: single, rapid, scheduler, batch, status, set_status, cancel, restart, reset, move, open, abiopen, abibuild, doc_scheduler, panel, new_manager, tail, deps, robot, cycles, dims, inspect, inputs, abivars, structures, ebands, hist, doc_manager, events, corrections, history, handlers, notebook, ipython, tar, tricky, debug, debug_reset, group, diff, networkx, graphviz, listext

sub-command help

Sub-commands:

single

Run single task and exit.

abirun.py single [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

rapid

Run all tasks in rapidfire mode.

abirun.py rapid [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock] [-m MAX_NLAUNCH]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-m, --max-nlaunch

Maximum number of launches. default: 10. Use -1 for no limit.

Default: 10

scheduler

Run all tasks with a Python scheduler. Requires scheduler.yml either in $PWD or ~/.abinit/abipy.

abirun.py scheduler [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                    [--remove-lock] [-w WEEKS] [-d DAYS] [-hs HOURS]
                    [-m MINUTES] [-s SECONDS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-w, --weeks

Number of weeks to wait.

Default: 0

-d, --days

Number of days to wait.

Default: 0

-hs, --hours

Number of hours to wait.

Default: 0

-m, --minutes

Number of minutes to wait.

Default: 0

-s, --seconds

Number of seconds to wait.

Default: 0

batch

Run scheduler in batch script.

abirun.py batch [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock] [-t TIMELIMIT]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-t, --timelimit

Time limit for batch script. Accept int with seconds or string with time given in the slurm convention: days-hours:minutes:seconds. If timelimit is None, the default value specified in the batch_adapter entry of manager.yml is used.

status

Show status table.

abirun.py status [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                 [-d [DELAY]] [-s]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-d, --delay

Enter an infinite loop and delay execution for the given number of seconds. (default: 5 secs).

Default: 0

-s, --summary

Print short version with status counters.

Default: False

set_status

Change the status of the task. WARNING: Option for developers!

abirun.py set_status [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                     [--remove-lock]
                     [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                     new_status

Positional Arguments

new_status

New value of status. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

cancel

Cancel the tasks in the queue. Not available if qtype is shell.

abirun.py cancel [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS] [-r]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-r, --rmtree

Remove flow directory.

Default: False

restart

Restart the tasks of the flow. By default, only the task whose status==Unconverged are restarted. Use -S status and/or -n node_ids to select particular tasks.

abirun.py restart [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock]
                  [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

reset

Reset the tasks of the flow with the specified status.

abirun.py reset [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock]
                [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

move

Move the flow to a new directory and change the absolute paths.

abirun.py move [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               dest

Positional Arguments

dest

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

open

Open files in $EDITOR, type abirun.py FLOWDIR open –help for help).

abirun.py open [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
               [{i,o,f,j,l,e,q,all}]

Positional Arguments

what

Possible choices: i, o, f, j, l, e, q, all

Specify the files to open. Possible choices:

i ==> input_file o ==> output_file f ==> files_file j ==> job_file l ==> log_file e ==> stderr_file q ==> qout_file all ==> all files.

Default: o

Default: “o”

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

abiopen

Open FILE with abiopen. Same interface as abiopen.py

abirun.py abiopen [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock] [-nb] [--foreground] [-p]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-nb, --notebook

Open file in jupyter notebook

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print python object and return.

Default: False

abibuild

Show ABINIT build information and exit.

abirun.py abibuild [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                   [--remove-lock]
                   [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

doc_scheduler

Document the options available in scheduler.yml.

abirun.py doc_scheduler [-h] [-v] [--no-colors] [--no-logo]
                        [--loglevel LOGLEVEL] [--remove-lock]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

panel

Interact with the flow in the browser (requires panel package).

abirun.py panel [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

new_manager

Change the TaskManager.

abirun.py new_manager [-h] [-v] [--no-colors] [--no-logo]
                      [--loglevel LOGLEVEL] [--remove-lock]
                      [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                      manager_file

Positional Arguments

manager_file

YAML file with the new manager.

Default: “”

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

tail

Use unix tail to follow the main output files of the flow.

abirun.py tail [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
               [{o,l,e}]

Positional Arguments

what_tail

Possible choices: o, l, e

What to follow: o for output (default), l for logfile, e for stderr.

Default: “o”

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

deps

Show dependencies.

abirun.py deps [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

robot

Use a robot to analyze the results of multiple tasks (requires ipython).

abirun.py robot [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock]
                [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS] [-nb]
                [--foreground] [-p]
                [robot_ext]

Positional Arguments

robot_ext

The file extension of the output file (case insensitive). Must be in: [‘A2F’, ‘ABIWAN’, ‘DDB’, ‘GKQ’, ‘GSR’, ‘HIST’, ‘MDF’, ‘OPTIC’, ‘PHBST’, ‘SIGEPH’, ‘SIGRES’, ‘V1QAVG’, ‘abo’, ‘anaddb’]

Default: “GSR”

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print-dataframe

Invoke robot.get_dataframe() and printa table to terminal.

Default: False

cycles

Print self-consistent/relaxation cycles extracted from the output of the tasks.Use -t ScfTask or FLOWDIR/w0/ or FLOWDIR/w0/t1/ to select tasks by class, by work or by workdir.

abirun.py cycles [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS] [-wok]
                 [-p [{combiplot,slideshow}]]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-wok, --exclude-ok-tasks

Exclude Tasks that have reached S_OK.

Default: False

-p, --plot-mode

Possible choices: combiplot, slideshow

Plot multiple cycles on the same figure if arg is specified. Use -p for gridplot. Use -p slideshow to iterate.

dims

Print table with dimensions extracted from the output of the tasks.

abirun.py dims [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

inspect

Call matplotlib to inspect the tasks (execute task.inspect method)

abirun.py inspect [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock]
                  [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

inputs

Show the input files of the tasks.

abirun.py inputs [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                 [-vn [VARNAMES]]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-vn, --varnames

Comma-separated variable names. Can be used to print only these variables.

abivars

Show pandas dataframe with Abinit input variables.

abirun.py abivars [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock]
                  [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS] -vn
                  VARNAMES

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-vn, --varnames

Comma-separated variable names e.g. -vn ecut,nband,ngkpt.

structures

Compare input/output structures of the tasks. Print max force and pressure if available.

abirun.py structures [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                     [--remove-lock]
                     [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                     [--what WHAT]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

--what

‘i’ for input structures, ‘o’ for output, ‘io’ for both.

Default: “io”

ebands

Compare electronic bands produced by the tasks.

abirun.py ebands [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                 [-p [{gridplot,combiplot,boxplot,combiboxplot,animate}]]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-p, --plot-mode

Possible choices: gridplot, combiplot, boxplot, combiboxplot, animate

Plot multiple bands if arg is specified. Use -p for gridplot. Supports multiple formats.

hist

Compare HIST.nc files produced by the tasks.

abirun.py hist [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
               [-p [{gridplot,combiplot}]]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-p, --plot-mode

Possible choices: gridplot, combiplot

Plot multiple HIST files if arg is present. Use -p for combiplot. Supports multiple formats.

doc_manager

Document the TaskManager options.

abirun.py doc_manager [-h] [-v] [--no-colors] [--no-logo]
                      [--loglevel LOGLEVEL] [--remove-lock]
                      [qtype]

Positional Arguments

qtype

Write job script to terminal if qtype=’script’ else document the qparams for the given QueueAdapter qtype e.g. slurm.

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

events

Show ABINIT events (error messages, warnings, comments).

abirun.py events [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]
                 [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

corrections

Show AbiPy corrections performed at runtime.

abirun.py corrections [-h] [-v] [--no-colors] [--no-logo]
                      [--loglevel LOGLEVEL] [--remove-lock]
                      [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

history

Show Node history.

abirun.py history [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock]
                  [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS] [-m]
                  [-f]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-m, --metadata

Print history metadata.

Default: False

-f, --full-history

Print full history set, including nodes with an empty history.

Default: False

handlers

Show event handlers installed in the flow.

abirun.py handlers [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                   [--remove-lock] [-d]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-d, --doc

Show documentation about all the handlers that can be installed.

Default: False

notebook

Create and open an ipython notebook to interact with the flow.

abirun.py notebook [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                   [--remove-lock] [--foreground]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

ipython

Embed IPython. Useful for advanced operations or debugging purposes.

abirun.py ipython [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock] [--argv [ARGV]]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

--argv

Command-line options passed to ipython. Must be enclosed by quotes. Example: –argv=’–matplotlib=wx’

Default: “”

tar

Create tarball file.

abirun.py tar [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
              [--remove-lock] [-s MAX_FILESIZE] [-e EXCLUDE_EXTS]
              [-d EXCLUDE_DIRS] [-l]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-s, --max-filesize

Exclude file whose size > max-filesize bytes. Accept integer or string e.g 1Mb.

-e, --exclude-exts

Exclude file extensions. Accept string or comma-separated strings. Ex: -eWFK or –exclude-exts=WFK,GSR

-d, --exclude-dirs

Exclude directories. Accept string or comma-separated strings. Ex: –exlude-dirs=indir,outdir

-l, --light

Create light-weight version of the tarball for debugging purposes. Other options are ignored.

Default: False

tricky

Show tricky tasks i.e. tasks that have been restarted, launched more than once or tasks that have been corrected.

abirun.py tricky [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                 [--remove-lock]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

debug

Analyze error files and log files for possible error messages.

abirun.py debug [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock]
                [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

debug_reset

Analyze error files and log files produced by reset tasks for possible error messages.

abirun.py debug_reset [-h] [-v] [--no-colors] [--no-logo]
                      [--loglevel LOGLEVEL] [--remove-lock]
                      [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

group

Group tasks according to property.

abirun.py group [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                [--remove-lock]
                [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
                [-g {status,task_class}]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

-g, --groupby

Possible choices: status, task_class

Select the attribute used to group tasks. Default: status.

Default: “status”

diff

Compare files produced by two or three nodes.

abirun.py diff [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
               [--remove-lock]
               [-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
               [what_diff]

Positional Arguments

what_diff

What to diff: i for input (default), o for output, l for logfile, e for stderr.

Default: “i”

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-n, --nids

Node identifier(s) used to select the task. Accept single integer, comma-separated list of integers or python slice. Use status command to get the node ids. Examples: –nids=12 –nids=12,13,16 –nids=10:12 to select 10 and 11 (slice syntax), –nids=2:5:2 to select 2,4.

-w, --wslice

Select the list of works to analyze (python syntax for slices): Examples: –wslice=1 to select the second workflow, –wslice=:3 for 0,1,2, –wslice=-1 for the last workflow, –wslice::2 for even indices.

-S, --task-status

Select only the tasks with the given status. Default: None i.e. ignored. Possible values: [‘Initialized’, ‘Locked’, ‘Ready’, ‘Submitted’, ‘Running’, ‘Done’, ‘AbiCritical’, ‘QCritical’, ‘Unconverged’, ‘Error’, ‘Completed’].

-t, --task-class

Select only tasks with the given class e.g. -t NscfTask.

networkx

Draw flow and node dependencies with networkx package.

abirun.py networkx [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                   [--remove-lock] [--nxmode NXMODE] [--edge-labels]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

--nxmode

Type of network plot. Possible values: status, network. Default: status.

Default: “status”

--edge-labels

Show edge labels.

Default: False

graphviz

Draw flow and node dependencies with graphviz package. Accept (FLOWDIR|WORKDIR|TASKDIR). See https://graphviz.readthedocs.io/.

abirun.py graphviz [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                   [--remove-lock] [-e ENGINE] [-d]

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False

-e, --engine

graphviz engine: [‘dot’, ‘neato’, ‘twopi’, ‘circo’, ‘fdp’, ‘sfdp’, ‘patchwork’, ‘osage’]. Default: automatic i.e. the engine is automatically selected. See http://www.graphviz.org/pdf/dot.1.pdf Use conda install python-graphviz or pip install graphviz to install the python package

Default: “automatic”

-d, --dirtree

Visualize files and directories in workdir instead of tasks/works.

Default: False

listext

List all the output files with the given extension that have been produced by the nodes.

abirun.py listext [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
                  [--remove-lock]
                  [listexts [listexts ...]]

Positional Arguments

listexts

List of Abinit file extensions. e.g DDB, GSR, WFK etc

Default: []

Named Arguments

-v, --verbose

verbose, can be supplied multiple times to increase verbosity.

Default: 0

--no-colors

Disable ASCII colors.

Default: False

--no-logo

Disable AbiPy logo.

Default: False

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG.

Default: “ERROR”

--remove-lock

Remove the lock on the pickle file used to save the status of the flow.

Default: False