bout-runners 2.0.0b0

Description:

boutrunners 2.0.0b0

Manage your BOUT++ runs through python

Overview
BOUT Runners is a package to manage and orchestrate your BOUT++ runs.
More specifically it’s a tool:

That automatically makes your project
Where you can override default parameters, and parameters found in BOUT.inp
Where you can submit a single run, or even a chain of runs either locally, or to a cluster
That automatically stores parameters and other metadata in a database (inspired by sacred)
Logs the entire process

Read the full documentation at ReadTheDocs


Getting Started
The simplest way to use BOUT Runners is by executing the following script in the root of your project directory (usually where your Makefile resides).
In this example we are using BOUT-dev/examples/conduction as the root
from bout_runners.runner.bout_runner import BoutRunner
BoutRunner().run()
The metadata from all the runs from this project can be found by executing
from bout_runners.metadata.status_checker import StatusChecker
status_checker = StatusChecker()
status_checker.check_and_update_status()
from bout_runners.metadata.metadata_reader import MetadataReader
metadata_reader = MetadataReader()
metadata = metadata_reader.get_all_metadata()
The metadata variable is a DataFrame, and contains the following table



run.id
run.latest_status
run.name
run.start_time
run.stop_time
run.submitted_time
all_boundaries.evolve_bndry
conduction.chi
file_modification.bout_git_sha
file_modification.bout_lib_modified
file_modification.project_executable_modified
file_modification.project_git_sha
file_modification.project_makefile_modified
global.append
global.async_send
global.datadir
global.dump_format
global.dump_on_restart
global.incintshear
global.mxg
global.myg
global.non_uniform
global.nout
global.optionfile
global.periodicx
global.restart
global.restart_format
global.settingsfile
global.stopcheck
global.timestep
global.twistshift
global.wall_limit
global.zmax
global.zmin
input.transform_from_field_aligned
mesh.calcparallelslices_on_communicate
mesh.dy
mesh.extrapolate_x
mesh.extrapolate_y
mesh.ixseps1
mesh.ixseps2
mesh.maxregionblocksize
mesh.nx
mesh.ny
mesh.nz
mesh.paralleltransform
mesh.staggergrids
mesh.symmetricglobalx
mesh.symmetricglobaly
mesh.type
mesh_ddz.fft_filter
output.enabled
output.floats
output.flush
output.flushfrequency
output.guards
output.init_missing
output.openclose
output.parallel
output.shiftinput
output.shiftoutput
restart.enabled
restart.floats
restart.flush
restart.flushfrequency
restart.guards
restart.init_missing
restart.openclose
restart.parallel
restart.shiftinput
restart.shiftoutput
solver.adams_moulton
solver.atol
solver.cvode_max_order
solver.cvode_stability_limit_detection
solver.diagnose
solver.func_iter
solver.is_nonsplit_model_diffusive
solver.max_timestep
solver.maxl
solver.min_timestep
solver.mms
solver.mms_initialise
solver.monitor_timestep
solver.mxorder
solver.mxstep
solver.nout
solver.output_step
solver.rtol
solver.start_timestep
solver.type
solver.use_jacobian
solver.use_precon
solver.use_vector_abstol
split.number_of_nodes
split.number_of_processors
split.processors_per_node
system_info.machine
system_info.node
system_info.processor
system_info.release
system_info.system
system_info.version
t.bndry_all
t.evolve_bndry
t.function
t.scale



0
1
complete
2020-06-09_07-14-39_981268
2020-06-09 07:14:53
2020-06-09 07:14:56
2020-06-09 07:14:52.943486
0
1.0
22c888152e49003c34723a2638504aabc25d87ba
2020-02-03 20:03:02.000000
2020-06-09 07:14:39.631118
22c888152e49003c34723a2638504aabc25d87ba
2020-02-03 19:48:41.000000
0
0
/root/bout-dev/examples/conduction/settings_run
nc
1
0
0
2
1
0
bout.inp
0
0
nc
bout.settings
0
0.1
0
-1
1
0
1
1
0.2
0
0
-1
-1
64
1
100
1
identity
0
1
1
bout
0
1
0
1
1
1
0
1
0
0
0
1
0
1
1
1
0
1
0
0
0
0
1e-12
-1
0
0
0
1
-1
5
-1
0
0
0
-1
500
0
0.1
1e-05
-1
cvode
0
0
0
1
1
1
x86_64
0f17950a0dcc

4.19.76-linuxkit
Linux
#1 SMP Tue May 26 11:42:35 UTC 2020
dirichlet_o4(0.0)
0
gauss(y-pi, 0.2)
1.0





Prerequisites

Python (versions above 3.6 are supported)
BOUT++, which can installed as stated in the manual, or by using bout_install



Installing
The package can be installed from pip
pip install bout-runners
Or from source
python setup.py install
After installation you can optionally call
bout_runners_config
in order to setup the path to your BOUT++ installation and to configure other parameters like logging.


Running the tests
The test suite can be executed through pytest or through codecov pytest-cov.
Installation through
pip install pytest
or
pip install codecov pytest-cov
and run with
pytest
or
pytest --cov=./
respectively


Contributing
Please read CONTRIBUTING.rst for details about how to contribute.


Authors

Michael Løiten - Initial work

See also the list of contributors who participated in this project.


License
This project is licensed under the GNU LESSER GENERAL PUBLIC LICENSE - see the LICENSE file for details



Acknowledgments

The BOUT++ team for fast and accurate response on the BOUT++ issue tracker and slack-channel