From 4ff124bee09464e02b740f29fa7f4f05e6af7149 Mon Sep 17 00:00:00 2001
From: "Peter W. Draper" <p.w.draper@durham.ac.uk>
Date: Fri, 30 Nov 2018 15:24:52 +0000
Subject: [PATCH] Update documentation to show long options in preference to
short ones
---
README | 90 +++++++++----------
README.md | 12 +--
doc/RTD/source/CommandLineOptions/index.rst | 13 ++-
.../source/GettingStarted/running_example.rst | 2 +-
.../running_on_large_systems.rst | 2 +-
.../ParameterFiles/output_selection.rst | 6 +-
.../VELOCIraptorInterface/stfwithswift.rst | 5 +-
7 files changed, 64 insertions(+), 66 deletions(-)
diff --git a/README b/README
index e3bf5a6d6c..97d096ef18 100644
--- a/README
+++ b/README
@@ -1,9 +1,9 @@
Welcome to the cosmological hydrodynamical code
______ _________________
/ ___/ | / / _/ ___/_ __/
- \__ \| | /| / // // /_ / /
- ___/ /| |/ |/ // // __/ / /
- /____/ |__/|__/___/_/ /_/
+ \__ \| | /| / // // /_ / /
+ ___/ /| |/ |/ // // __/ / /
+ /____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Website: www.swiftsim.com
@@ -18,52 +18,52 @@ Usage: swift [options] [[--] param-file]
Parameters:
- -h, --help show this help message and exit
+ -h, --help show this help message and exit
Simulation options:
- -b, --feedback Run with stars feedback
- -c, --cosmology Run with cosmological time integration.
- -C, --cooling Run with cooling
+ -b, --feedback Run with stars feedback
+ -c, --cosmology Run with cosmological time integration.
+ -C, --cooling Run with cooling
+ -D, --drift-all Always drift all particles even the ones
+ far from active particles. This emulates
+ Gadget-[23] and GIZMO's default behaviours.
-F, --sourceterms
- -g, --external-gravity Run with an external gravitational potential.
- -G, --self-gravity Run with self-gravity.
- -M, --multipole-reconstruction Reconstruct the multipoles every time-step.
- -s, --hydrodynamics Run with hydrodynamics.
- -S, --stars Run with stars
- -x, --velociraptor Run with structure finding
+ -g, --external-gravity Run with an external gravitational potential.
+ -G, --self-gravity Run with self-gravity.
+ -M, --multipole-reconstruction Reconstruct the multipoles every time-step.
+ -s, --hydro Run with hydrodynamics.
+ -S, --stars Run with stars
+ -x, --velociraptor Run with structure finding
Control options:
- -a, --affinity Pin runners using processor affinity.
- -d, --dry-run Dry run. Read the parameter file, allocates
- memory but does not read the particles
- from ICs. Exits before the start of time
- integration. Checks the validity of
- parameters and IC files as well as memory
- limits.
- -D, --drift-all Always drift all particles even the ones
- far from active particles. This emulates
- Gadget-[23] and GIZMO's default behaviours.
- -e, --fpe Enable floating-point exceptions (debugging
- mode).
- -f, --cpu-frequency=<str> Overwrite the CPU frequency (Hz) to be
- used for time measurements.
- -n, --steps=<int> Execute a fixed number of time steps.
- When unset use the time_end parameter
- to stop.
- -o, --output-params=<str> Generate a default output parameter
- file.
- -P, --param=<str> Set parameter value, overwriting a value
- read from the parameter file. Can be used
- more than once {sec:par:value}.
- -r, --restart Continue using restart files.
- -t, --threads=<int> The number of threads to use on each MPI
- rank. Defaults to 1 if not specified.
- -T, --timers=<int> Print timers every time-step.
- -v, --verbose=<int> Run in verbose mode, in MPI mode 2 outputs
- from all ranks.
- -y, --task-dumps=<int> Time-step frequency at which task graphs
- are dumped.
- -Y, --threadpool-dumps=<int> Time-step frequency at which threadpool
- tasks are dumped.
+ -a, --pin Pin runners using processor affinity.
+ -d, --dry-run Dry run. Read the parameter file, allocates
+ memory but does not read the particles
+ from ICs. Exits before the start of time
+ integration. Checks the validity of
+ parameters and IC files as well as memory
+ limits.
+ -e, --fpe Enable floating-point exceptions (debugging
+ mode).
+ -f, --cpu-frequency=<str> Overwrite the CPU frequency (Hz) to be
+ used for time measurements.
+ -n, --steps=<int> Execute a fixed number of time steps.
+ When unset use the time_end parameter
+ to stop.
+ -o, --output-params=<str> Generate a default output parameter
+ file.
+ -P, --param=<str> Set parameter value, overiding the value
+ read from the parameter file. Can be used
+ more than once {sec:par:value}.
+ -r, --restart Continue using restart files.
+ -t, --threads=<int> The number of threads to use on each MPI
+ rank. Defaults to 1 if not specified.
+ -T, --timers=<int> Print timers every time-step.
+ -v, --verbose=<int> Run in verbose mode, in MPI mode 2 outputs
+ from all ranks.
+ -y, --task-dumps=<int> Time-step frequency at which task graphs
+ are dumped.
+ -Y, --threadpool-dumps=<int> Time-step frequency at which threadpool
+ tasks are dumped.
See the file examples/parameter_example.yml for an example of parameter file.
diff --git a/README.md b/README.md
index 96bda4d304..94e95776cd 100644
--- a/README.md
+++ b/README.md
@@ -72,25 +72,25 @@ Parameters:
-b, --feedback Run with stars feedback
-c, --cosmology Run with cosmological time integration.
-C, --cooling Run with cooling
+ -D, --drift-all Always drift all particles even the ones
+ far from active particles. This emulates
+ Gadget-[23] and GIZMO's default behaviours.
-F, --sourceterms
-g, --external-gravity Run with an external gravitational potential.
-G, --self-gravity Run with self-gravity.
-M, --multipole-reconstruction Reconstruct the multipoles every time-step.
- -s, --hydrodynamics Run with hydrodynamics.
+ -s, --hydro Run with hydrodynamics.
-S, --stars Run with stars
-x, --velociraptor Run with structure finding
Control options:
- -a, --affinity Pin runners using processor affinity.
+ -a, --pin Pin runners using processor affinity.
-d, --dry-run Dry run. Read the parameter file, allocates
memory but does not read the particles
from ICs. Exits before the start of time
integration. Checks the validity of
parameters and IC files as well as memory
limits.
- -D, --drift-all Always drift all particles even the ones
- far from active particles. This emulates
- Gadget-[23] and GIZMO's default behaviours.
-e, --fpe Enable floating-point exceptions (debugging
mode).
-f, --cpu-frequency=<str> Overwrite the CPU frequency (Hz) to be
@@ -100,7 +100,7 @@ Parameters:
to stop.
-o, --output-params=<str> Generate a default output parameter
file.
- -P, --param=<str> Set parameter value, overwriting a value
+ -P, --param=<str> Set parameter value, overiding the value
read from the parameter file. Can be used
more than once {sec:par:value}.
-r, --restart Continue using restart files.
diff --git a/doc/RTD/source/CommandLineOptions/index.rst b/doc/RTD/source/CommandLineOptions/index.rst
index e71c85be23..9fb9d784d6 100644
--- a/doc/RTD/source/CommandLineOptions/index.rst
+++ b/doc/RTD/source/CommandLineOptions/index.rst
@@ -19,25 +19,25 @@ can be found by typing ``./swift -h``::
-b, --feedback Run with stars feedback
-c, --cosmology Run with cosmological time integration.
-C, --cooling Run with cooling
+ -D, --drift-all Always drift all particles even the ones
+ far from active particles. This emulates
+ Gadget-[23] and GIZMO's default behaviours.
-F, --sourceterms
-g, --external-gravity Run with an external gravitational potential.
-G, --self-gravity Run with self-gravity.
-M, --multipole-reconstruction Reconstruct the multipoles every time-step.
- -s, --hydrodynamics Run with hydrodynamics.
+ -s, --hydro Run with hydrodynamics.
-S, --stars Run with stars
-x, --velociraptor Run with structure finding
Control options:
- -a, --affinity Pin runners using processor affinity.
+ -a, --pin Pin runners using processor affinity.
-d, --dry-run Dry run. Read the parameter file, allocates
memory but does not read the particles
from ICs. Exits before the start of time
integration. Checks the validity of
parameters and IC files as well as memory
limits.
- -D, --drift-all Always drift all particles even the ones
- far from active particles. This emulates
- Gadget-[23] and GIZMO's default behaviours.
-e, --fpe Enable floating-point exceptions (debugging
mode).
-f, --cpu-frequency=<str> Overwrite the CPU frequency (Hz) to be
@@ -47,7 +47,7 @@ can be found by typing ``./swift -h``::
to stop.
-o, --output-params=<str> Generate a default output parameter
file.
- -P, --param=<str> Set parameter value, overwriting a value
+ -P, --param=<str> Set parameter value, overiding the value
read from the parameter file. Can be used
more than once {sec:par:value}.
-r, --restart Continue using restart files.
@@ -60,4 +60,3 @@ can be found by typing ``./swift -h``::
are dumped.
-Y, --threadpool-dumps=<int> Time-step frequency at which threadpool
tasks are dumped.
-
diff --git a/doc/RTD/source/GettingStarted/running_example.rst b/doc/RTD/source/GettingStarted/running_example.rst
index 7c9e333ca9..9dfbdd8c8e 100644
--- a/doc/RTD/source/GettingStarted/running_example.rst
+++ b/doc/RTD/source/GettingStarted/running_example.rst
@@ -14,7 +14,7 @@ as ``wget`` for grabbing the glass).
cd examples/SodShock_3D
./getGlass.sh
python makeIC.py
- ../swift -s -t 4 sodShock.yml
+ ../swift --hydro --threads=4 sodShock.yml
python plotSolution.py 1
diff --git a/doc/RTD/source/GettingStarted/running_on_large_systems.rst b/doc/RTD/source/GettingStarted/running_on_large_systems.rst
index 55eb812cef..8bd3a76985 100644
--- a/doc/RTD/source/GettingStarted/running_on_large_systems.rst
+++ b/doc/RTD/source/GettingStarted/running_on_large_systems.rst
@@ -38,5 +38,5 @@ each with 2x16 core processors for a total of 512 cores):
#SBATCH -N 16 # Number of nodes to run on
#SBATCH --tasks-per-node=2 # This system has 2 chips per node
- mpirun -np 32 swift_mpi -t 16 -a parameter.yml
+ mpirun -np 32 swift_mpi --threads=16 --pin parameter.yml
diff --git a/doc/RTD/source/ParameterFiles/output_selection.rst b/doc/RTD/source/ParameterFiles/output_selection.rst
index e22075392b..90ab0f9a7c 100644
--- a/doc/RTD/source/ParameterFiles/output_selection.rst
+++ b/doc/RTD/source/ParameterFiles/output_selection.rst
@@ -37,7 +37,7 @@ Example of file with redshift::
5
.. _Output_selection_label:
-
+
Output Selection
~~~~~~~~~~~~~~~~
@@ -59,7 +59,7 @@ waste of disk space. The corresponding section of the ``yaml``
parameter file would look like this::
SelectOutput:
- Masses_DM: 0
+ Masses_DM: 0
You can generate a ``yaml`` file containing all the possible fields
-available for a given configuration of SWIFT by running ``./swift -o output.yml``.
+available for a given configuration of SWIFT by running ``./swift --output-params output.yml``.
diff --git a/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst b/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst
index ac8dcc5b0b..245b455d58 100644
--- a/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst
+++ b/doc/RTD/source/VELOCIraptorInterface/stfwithswift.rst
@@ -85,10 +85,9 @@ the Small Cosmological Volume DMO example we can run a simulation with halo
finder as::
cd examples/SmallCosmoVolume_DM
- ../swift -c -s -G -x -t 8 small_cosmo_volume_dm.yml
+ ../swift --cosmology --hydro --self-gravity --velociraptor --threads=8 small_cosmo_volume_dm.yml
-In which there is an additional ``-x`` option which activates the VELOCIraptor
-interface.
+Which activates the VELOCIraptor interface.
.. _GitHub: https://github.com/pelahi/VELOCIraptor-STF
--
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