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
/usr/share/miniconda/envs/abipy/bin/abirun.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('abipy==0.9.8')
usage: abirun.py [-h] [-V]
[flowdir]
{single,rapid,scheduler,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,explain_works,explain_tasks,autoparal,panel,new_manager,tail,timeit,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,reset_jobids,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.
options:
-h, --help show this help message and exit
-V, --version show program's version number and exit
subcommands:
Valid subcommands
{single,rapid,scheduler,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,explain_works,explain_tasks,autoparal,panel,new_manager,tail,timeit,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,reset_jobids,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.
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.
explain_works Explain operations performed by Works
explain_tasks Explain operations performed by Tasks
autoparal Show autoparal configurations and optimal ones.
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.
timeit Extract timing data from Abinit output files.
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.
reset_jobids 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
/usr/share/miniconda/envs/abipy/bin/abirun.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('abipy==0.9.8')
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 running jobs
before exiting due to an error. (DEFAULT: "yes")
$ abirun.py . doc_manager
/usr/share/miniconda/envs/abipy/bin/abirun.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('abipy==0.9.8')
# 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
##########################################
# 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 other 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 enforce 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)
limits_for_task_class: # Dictionary mapping Task class names to a dictionary with limits to be used
# for this particular Task. Example (mind white spaces):
#
# limits_for_task_class: {
# NscfTask: {min_cores: 1, max_cores: 10},
# KerangeTask: {min_cores: 1, max_cores: 1, max_mem_per_proc: 1 GB},
# }
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 (Nov 21, 2024), 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,status,set_status,cancel,restart,reset,move,open,abiopen,abibuild,doc_scheduler,explain_works,explain_tasks,autoparal,panel,new_manager,tail,timeit,deps,robot,cycles,dims,inspect,inputs,abivars,structures,ebands,hist,doc_manager,events,corrections,history,handlers,notebook,ipython,tar,tricky,debug,debug_reset,reset_jobids,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, status, set_status, cancel, restart, reset, move, open, abiopen, abibuild, doc_scheduler, explain_works, explain_tasks, autoparal, panel, new_manager, tail, timeit, deps, robot, cycles, dims, inspect, inputs, abivars, structures, ebands, hist, doc_manager, events, corrections, history, handlers, notebook, ipython, tar, tricky, debug, debug_reset, reset_jobids, 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
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
explain_works¶
Explain operations performed by Works
abirun.py explain_works [-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.
explain_tasks¶
Explain operations performed by Tasks
abirun.py explain_tasks [-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.
autoparal¶
Show autoparal configurations and optimal ones.
abirun.py autoparal [-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.
panel¶
Interact with the flow in the browser (requires panel package).
abirun.py panel [-h] [-v] [--no-colors] [--no-logo] [--loglevel LOGLEVEL]
[--remove-lock]
[-n NIDS | -w WSLICE | -S TASK_STATUS | -t TASK_CLASS]
[-pnt PANEL_TEMPLATE] [--no-browser] [--port PORT]
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.
- -pnt, --panel-template
Specify template for panel dasboard.Possible values are: FastList, FastGrid, Golden, Bootstrap, Material, React, Vanilla.Default: FastList
Default:
'FastList'- --no-browser
Start the bokeh server to serve the panel app but don’t open the app in the browser. Use this option to connect remotely from localhost to the machine running the server
Default:
False- --port
Allows specifying a specific port when serving panel app.
Default:
0
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.
timeit¶
Extract timing data from Abinit output files.
abirun.py timeit [-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.
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’, ‘EDOS’, ‘GKQ’, ‘GPATH’, ‘GSR’, ‘GSTORE’, ‘GWR’, ‘HIST’, ‘MDF’, ‘OPTIC’, ‘PHBST’, ‘PSPS’, ‘RTA’, ‘SIGEPH’, ‘SIGRES’, ‘TRANSPORT’, ‘V1QAVG’, ‘VARPEQ’, ‘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’
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.
reset_jobids¶
Analyze error files and log files produced by reset tasks for possible error messages.
abirun.py reset_jobids [-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 ...]
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