A CLI to automate mundane tasks with Idefix
Project description
idefix_cli
This is a CLI helper tool for the hexascale portable MHD code Idefix, written by Geoffroy Lesur et al.
It provides a family of commands to help with repetitive tasks such as configuration and cleanup in a single tool.
- Installation
- Internal documentation
- Commands
- IO operations for inifiles
- Contribution guidelines
- Testing
Installation
It is recommended to install this tool in isolation with pipx as
$ pipx install idefix_cli
Otherwise, the way to install the latest stable version is
$ python3 -m pip install -u idefix_cli
Note that most idfx commands explicitly require that the env variable $IDEFIX_DIR be
set at runtime.
Internal documentation
The following contains usage examples. Get a complete description of available options with
$ idfx --help
Likewise, get help for each command therein as, for instance
$ idfx run --help
Configuration
idfx_cli supports persistent configuration. It follows the last version of
$IDEFIX_DIR/configure.py and looks for options stored in
$HOME/.config/idefix.cfg.
Command specific options are stored in corresponding sections
, e.g., idfx conf looks into the [idfx conf] section.
In the following, more detail is given for each option available.
Commands
idfx clone
Clone an idefix problem directory by copying the main source files
(definitions.hpp, setup.cpp, idefix.ini).
$ idfx clone $IDEFIX_DIR/test/HD/KHI/ /tmp/myKHI
More
Instead of making hard copies, files can be symbolically linked to instead of
copied, with --shallow.
Additional files may be included in the clone using the --include argument. They
can be specified either by name or POSIX pattern, e.g.
$ idfx clone $IDEFIX_DIR/test/HD/KHI/ /tmp/myKHI --include "*.log"
Note that extra patterns need be escaped, else they'd be interpreted by the
shell before they make it to idefix_cli.
Configuration
Arbitrary patterns can also be stored in the configuration file. For example
# idefix.cfg
[idfx clone]
include = *py README.*
Note that the --include argument can be combined with idefix.cfg.
idfx conf
idfx conf is a unified wrapper for cmake and the historical Python script
$IDEFIX_DIR/configure.py. All arguments and flags are passed down to the
relevant configuration system.
Arguments that were originally implemented in
$IDEFIX_DIR/configure.py (-mhd, -mpi, -openmp, -cxx, -arch, -gpu)
are converted on the fly for cmake.
For instance
$ idfx conf -mhd -mpi -gpu -arch Ampere86 -cxx g++
is equivalent to
$ cmake $IDEFIX_DIR \
-DIdefix_MHD=ON \
-DIdefix_MPI=ON \
-DKokkos_ENABLE_CUDA=ON \
-DKokkos_ARCH_AMPERE86=ON \
-DCMAKE_CXX_COMPILER=g++
Configuration
Some configuration options like prefered compiler and target architecture rarely need to be changed on a single machine.
For instance, one can select a persistent build target (say Ampere86) and custom compiler as
# idefix.cfg
[compilation]
GPU = Ampere86
compiler = g++
A prefered configuration engine can also be stored as
# idefix.cfg
[idfx conf]
engine = python # use configure.py
# or
engine = cmake
though this is mostly useful for testing purposes. In general idfx conf
automatically determines which configuration system to use based on
resources available. Cmake is prefered over Python when both are available.
Any option passed on the command line will override its equivalent persistent configuration.
Lastly, it is possible invoke ccmake instead of cmake by passing the
-i/--interactive flag to idfx conf.
idfx run
This command is intended as a simple assistant to continuously check soundness of your setup as your developing it, and run tests problems locally for very short periods of time.
idfx run essentially invokes the idefix binary, but will also (re)compiles
it if necessary. If source files were edited since last compilation, an
interactive prompt will offer to recompile.
Note that this command will fail if neither idefix or Makefile are found in the
specified directory. Use idfx conf to generate the Makefile.
Additional, arbitrary arguments may be passed to the idefix executable via this
command.
minimal example: run a test sequentially
$ idfx run --dir $IDEFIX_DIR/test/HD/KHI
The default behaviour is to use idefix.ini contained in the specified directory. If you
want to run a different one, use -i/--inifile
$ idfx run -i myconf.ini
Note that idfx run looks for the inifile relative to the cwd, and then relative to
the specified directory.
running a shorter version of a problem
Use the --duration and --time-step arguments to run a modified version of a base
inifile.
$ idfx run --duration 1e-4
Note that --time-step maps to Idefix's inifile TimeIntegrator.first_dt.
Use --one-step/--one to run a single time step (total simulation time equates to the
first time step).
The length of the time step can be adjusted in combination with --time-step, however,
--one-step is incompatible with --duration.
$ idfx run --one
is a shortcut for
$ idfx run --duration x --time-step x
where x, is the existing value found in the inifile. idfx run --one also
optionally accepts arbitrary output format identifiers. For instance
$ idfx run --one dmp vtk
will run the curdir setup for one time step and output both a dmp file and a vtk file.
running in parallel
idfx run also wraps around mpirun -> idefix via the --nproc optional argument.
For instance
$ idfx run --dir mydir --nproc 2
is equivalent to
$ pushd mydir ; mpirun -n 2 ./idefix ; popd
idfx clean
Removes intermediate compilation files (*.o, *.host, *.cuda) as well as
CMake cache files and directories
$ idfx clean .
This command will print a list of purgable files, and will not remove anything without confirmation.
To also remove Makefile, idefix executables, use the --all flag
$ idfx clean . --all
Use the --dry-run/--dry flag to skip the prompt and only display the list of
purgeable items, without actually deleting anything.
idfx stamp
Prints key data for reproduction and development to stdout.
$ idfx stamp
v0.5
daff799bb64b0993f058f50779873d594376d5bf
lesurg
f-dahu
Sat Jan 16 16:15:28 2021
More
This command is roughly equivalent to
$ cd $IDEFIX_DIR \
&& git describe --tags \
&& cd - > /dev/null \
&& date \
&& hostname \
&& echo $USER
Additionnally, one can get the underlying data in json-serializable format
$ idfx stamp --json
{
"tag": "v0.5",
"sha": "daff799bb64b0993f058f50779873d594376d5bf",
"user": "glesur",
"host": "f-dahu",
"date": "Sat Jan 16 16:15:54 2021"
}
This is helpful to quickly store important metadata next to one's datafiles. The git tag may be of critical value for reproductability, especially when bugs in Idefix are found after simulations are run, like so
$ idfx stamp --json > metadata.json
IO operations for inifiles
idfx read
Read an Idefix inifile and print the resulting dictionnary to stdout in a json parsable format. This is useful to inspect inifiles programatically in combination with tools like jq
$ idfx read $IDEFIX_DIR/test/HD/KHI/idefix.ini | jq '.Output.vtk' --compact-output
[0.01,-1,"single_file"]
By default, the ouptut of idfx read is flat. Optionnaly, you can use --indent <N> to
improve human-readability.
idfx write
Conversely, idfx write converts from json formatted strings to Idefix inifile format
$ idfx write save.ini $(cat save.json)
arbitrary patching
idfx read and idfx write methods can be combined with jq to arbitrarily patch an inifile
$ idfx read test/HD/KHI/idefix.ini | jq .TimeIntegrator.CFL=1e6 | idfx write idefix_patched.ini
Contribution guidelines
We use the pre-commit framework to automatically lint for code style and common pitfals.
Before you commit to your local copy of the repo, please run this from the top level
$ python3 -m pip install -u -e .[dev]
$ pre-commit install
Testing
We use the pytest framework to test idfx's
internal components. The test suite can be run from the top level with a simple pytest
invocation.
$ pytest
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