From 8db37ac0231a581d712fdfc7e1808643a84b28ba Mon Sep 17 00:00:00 2001
From: JM Etancelin <jean-matthieu.etancelin@univ-pau.fr>
Date: Mon, 23 Mar 2020 09:38:37 +0100
Subject: [PATCH] move Examples interface (argument parser) to hysop internal
module. Should solve #40.
---
examples/analytic/analytic.py | 91 ++++++++++---------
examples/bubble/periodic_bubble.py | 2 +-
examples/bubble/periodic_bubble_levelset.py | 2 +-
.../periodic_bubble_levelset_penalization.py | 2 +-
examples/bubble/periodic_jet_levelset.py | 2 +-
examples/cylinder/oscillating_cylinder.py | 2 +-
examples/fixed_point/heat_equation.py | 2 +-
.../flow_around_sphere/flow_around_sphere.py | 2 +-
examples/multiresolution/scalar_advection.py | 2 +-
.../particles_above_salt_bc.py | 2 +-
.../particles_above_salt_bc_3d.py | 2 +-
.../particles_above_salt_periodic.py | 2 +-
.../particles_above_salt_symmetrized.py | 2 +-
examples/scalar_advection/levelset.py | 2 +-
examples/scalar_advection/scalar_advection.py | 2 +-
examples/scalar_diffusion/scalar_diffusion.py | 2 +-
examples/sediment_deposit/sediment_deposit.py | 2 +-
.../sediment_deposit_levelset.py | 2 +-
examples/shear_layer/shear_layer.py | 2 +-
examples/taylor_green/taylor_green.py | 2 +-
.../taylor_green/taylor_green_cpuFortran.py | 2 +-
{examples => hysop/examples}/__init__.py | 0
{examples => hysop/examples}/example_utils.py | 0
23 files changed, 66 insertions(+), 65 deletions(-)
rename {examples => hysop/examples}/__init__.py (100%)
rename {examples => hysop/examples}/example_utils.py (100%)
diff --git a/examples/analytic/analytic.py b/examples/analytic/analytic.py
index 631e14b44..39f15a551 100755
--- a/examples/analytic/analytic.py
+++ b/examples/analytic/analytic.py
@@ -1,63 +1,64 @@
#!/usr/bin/env python2
import numpy as np
import sympy as sm
-
+
+
def compute(args):
'''
HySoP Analytic Example: Initialize a field with a space and time dependent analytic formula.
'''
from hysop import Field, Box, IOParams, MPIParams, \
- Simulation, Problem, ScalarParameter
+ Simulation, Problem, ScalarParameter
from hysop.constants import Implementation
from hysop.operators import AnalyticField, HDF_Writer
-
+
# Define domain
npts = args.npts
- box = Box(origin=args.box_origin, length=args.box_length, dim=args.ndim)
-
+ box = Box(origin=args.box_origin, length=args.box_length, dim=args.ndim)
+
# Define parameters and field (time and analytic field)
- t = ScalarParameter('t', dtype=args.dtype)
+ t = ScalarParameter('t', dtype=args.dtype)
scalar = Field(domain=box, name='S0', dtype=args.dtype)
-
+
# We need to first get default MPI parameters (even for non MPI jobs)
# so we use default domain communicator and task.
mpi_params = MPIParams(comm=box.task_comm,
task_id=box.current_task())
-
+
# Setup implementation specific variables
impl = args.impl
op_kwds = {'mpi_params': mpi_params}
if (impl is Implementation.PYTHON):
# Setup python specific extra operator keyword arguments
# (mapping: variable name => variable value)
- op_kwds['extra_input_kwds'] = {'t': t}
+ op_kwds['extra_input_kwds'] = {'t': t}
elif (impl is Implementation.OPENCL):
# For the OpenCL implementation we need to setup the compute device
# and configure how the code is generated and compiled at runtime.
-
+
# Create an explicit OpenCL context from user parameters
from hysop.backend.device.opencl.opencl_tools import get_or_create_opencl_env, get_device_number
cl_env = get_or_create_opencl_env(
mpi_params=mpi_params,
- platform_id=args.cl_platform_id,
- device_id=box.machine_rank%get_device_number() if args.cl_device_id is None else None)
+ platform_id=args.cl_platform_id,
+ device_id=box.machine_rank % get_device_number() if args.cl_device_id is None else None)
# Configure OpenCL kernel generation and tuning (already done by HysopArgParser)
from hysop.methods import OpenClKernelConfig
method = {OpenClKernelConfig: args.opencl_kernel_config}
-
+
# Setup opencl specific extra operator keyword arguments
- op_kwds['cl_env'] = cl_env
- op_kwds['method'] = method
+ op_kwds['cl_env'] = cl_env
+ op_kwds['method'] = method
else:
- msg='Unknown implementation \'{}\'.'.format(impl)
+ msg = 'Unknown implementation \'{}\'.'.format(impl)
raise ValueError(msg)
-
+
# Analytic initialization method depends on chosen implementation
if (impl is Implementation.PYTHON):
# With the python implementation we can directly use a python method
# (using numpy arrays). Here each field component is stored in the
- # tuple 'data'. Coordinates will be passed as a tuple as a second
+ # tuple 'data'. Coordinates will be passed as a tuple as a second
# argument. Finally extra arguments (here t) are passed last.
# Note that t is a ScalarParameter, so we evaluate it to get its value.
def compute_scalar(data, coords, component, t):
@@ -77,21 +78,21 @@ def compute(args):
for xi in xs:
compute_scalar *= sm.cos(xi-ts)
else:
- msg='Unknown implementation {}.'.format(impl)
-
+ msg = 'Unknown implementation {}.'.format(impl)
+
# Finally build the operator
- analytic = AnalyticField(name='analytic',
- field=scalar, formula=compute_scalar,
- variables = {scalar: npts}, implementation=impl,
- **op_kwds)
+ analytic = AnalyticField(name='analytic',
+ field=scalar, formula=compute_scalar,
+ variables={scalar: npts}, implementation=impl,
+ **op_kwds)
# Write output field at given frequency
io_params = IOParams(filename='analytic', frequency=args.dump_freq)
df = HDF_Writer(name='S',
- io_params=io_params,
- variables={scalar: npts},
- **op_kwds)
-
+ io_params=io_params,
+ variables={scalar: npts},
+ **op_kwds)
+
# Create the problem we want to solve and insert our operator
problem = Problem()
problem.insert(analytic, df)
@@ -102,36 +103,36 @@ def compute(args):
if args.display_graph:
problem.display(args.visu_rank)
- # Create a simulation and solve the problem
+ # Create a simulation and solve the problem
# (do not forget to specify the time parameter here)
- simu = Simulation(start=args.tstart, end=args.tend,
- nb_iter=args.nb_iter, dt0=args.dt,
- max_iter=args.max_iter,
+ simu = Simulation(start=args.tstart, end=args.tend,
+ nb_iter=args.nb_iter, dt0=args.dt,
+ max_iter=args.max_iter,
times_of_interest=args.dump_times,
t=t)
-
- # Finally solve the problem
+
+ # Finally solve the problem
problem.solve(simu, dry_run=args.dry_run)
-
+
# Finalize
problem.finalize()
-if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
-
+if __name__ == '__main__':
+ from hysop.examples.example_utils import HysopArgParser, colors
+
prog_name = 'analytic'
default_dump_dir = '{}/hysop_examples/{}'.format(HysopArgParser.tmp_dir(), prog_name)
- description=colors.color('HySoP Analytic Example: ', fg='blue', style='bold')
- description+='Initialize a field with a space and time dependent analytic formula.'
+ description = colors.color('HySoP Analytic Example: ', fg='blue', style='bold')
+ description += 'Initialize a field with a space and time dependent analytic formula.'
parser = HysopArgParser(prog_name=prog_name,
- description=description,
- default_dump_dir=default_dump_dir)
+ description=description,
+ default_dump_dir=default_dump_dir)
- parser.set_defaults(box_start=(0.0,), box_length=(2*np.pi,),
- tstart=0.0, tend=10.0, nb_iter=100,
- dump_freq=5)
+ parser.set_defaults(box_start=(0.0,), box_length=(2*np.pi,),
+ tstart=0.0, tend=10.0, nb_iter=100,
+ dump_freq=5)
parser.run(compute)
diff --git a/examples/bubble/periodic_bubble.py b/examples/bubble/periodic_bubble.py
index af738c800..5de7e1e0e 100644
--- a/examples/bubble/periodic_bubble.py
+++ b/examples/bubble/periodic_bubble.py
@@ -302,7 +302,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class PeriodicBubbleArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/bubble/periodic_bubble_levelset.py b/examples/bubble/periodic_bubble_levelset.py
index 810a926e9..237bf8f67 100644
--- a/examples/bubble/periodic_bubble_levelset.py
+++ b/examples/bubble/periodic_bubble_levelset.py
@@ -300,7 +300,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class PeriodicBubbleArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/bubble/periodic_bubble_levelset_penalization.py b/examples/bubble/periodic_bubble_levelset_penalization.py
index 05a3ef5d5..7cf865cca 100644
--- a/examples/bubble/periodic_bubble_levelset_penalization.py
+++ b/examples/bubble/periodic_bubble_levelset_penalization.py
@@ -342,7 +342,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class PeriodicBubbleArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/bubble/periodic_jet_levelset.py b/examples/bubble/periodic_jet_levelset.py
index ac99a865c..9607f8fde 100644
--- a/examples/bubble/periodic_jet_levelset.py
+++ b/examples/bubble/periodic_jet_levelset.py
@@ -287,7 +287,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class PeriodicJetArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/cylinder/oscillating_cylinder.py b/examples/cylinder/oscillating_cylinder.py
index 73f3e41df..b51b85881 100644
--- a/examples/cylinder/oscillating_cylinder.py
+++ b/examples/cylinder/oscillating_cylinder.py
@@ -260,7 +260,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class OscillatingCylinderArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/fixed_point/heat_equation.py b/examples/fixed_point/heat_equation.py
index 518a77381..d54e802ac 100644
--- a/examples/fixed_point/heat_equation.py
+++ b/examples/fixed_point/heat_equation.py
@@ -197,7 +197,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class IMArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/flow_around_sphere/flow_around_sphere.py b/examples/flow_around_sphere/flow_around_sphere.py
index 807d0d26c..f01e5f9ef 100644
--- a/examples/flow_around_sphere/flow_around_sphere.py
+++ b/examples/flow_around_sphere/flow_around_sphere.py
@@ -327,7 +327,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
parser = HysopArgParser(prog_name="FlowAroundSphere",
description="""HySoP flow around a sphere.\n""",
default_dump_dir='{}/hysop_examples/FlowAroundSphere'.format(
diff --git a/examples/multiresolution/scalar_advection.py b/examples/multiresolution/scalar_advection.py
index 82e805e2b..98b763292 100644
--- a/examples/multiresolution/scalar_advection.py
+++ b/examples/multiresolution/scalar_advection.py
@@ -189,7 +189,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class MultiResolutionScalarAdvectionArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/particles_above_salt/particles_above_salt_bc.py b/examples/particles_above_salt/particles_above_salt_bc.py
index ce823f8c3..807120e6b 100644
--- a/examples/particles_above_salt/particles_above_salt_bc.py
+++ b/examples/particles_above_salt/particles_above_salt_bc.py
@@ -323,7 +323,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/particles_above_salt/particles_above_salt_bc_3d.py b/examples/particles_above_salt/particles_above_salt_bc_3d.py
index afcdbf826..3bd83aeb8 100644
--- a/examples/particles_above_salt/particles_above_salt_bc_3d.py
+++ b/examples/particles_above_salt/particles_above_salt_bc_3d.py
@@ -338,7 +338,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/particles_above_salt/particles_above_salt_periodic.py b/examples/particles_above_salt/particles_above_salt_periodic.py
index 8a6fcb237..8eaac49a2 100644
--- a/examples/particles_above_salt/particles_above_salt_periodic.py
+++ b/examples/particles_above_salt/particles_above_salt_periodic.py
@@ -333,7 +333,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/particles_above_salt/particles_above_salt_symmetrized.py b/examples/particles_above_salt/particles_above_salt_symmetrized.py
index 904de36a6..f7a393327 100644
--- a/examples/particles_above_salt/particles_above_salt_symmetrized.py
+++ b/examples/particles_above_salt/particles_above_salt_symmetrized.py
@@ -320,7 +320,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/scalar_advection/levelset.py b/examples/scalar_advection/levelset.py
index 045bb3330..8e8dbe82c 100644
--- a/examples/scalar_advection/levelset.py
+++ b/examples/scalar_advection/levelset.py
@@ -215,7 +215,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class LevelsetArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/scalar_advection/scalar_advection.py b/examples/scalar_advection/scalar_advection.py
index 7b133555e..0e061844a 100644
--- a/examples/scalar_advection/scalar_advection.py
+++ b/examples/scalar_advection/scalar_advection.py
@@ -142,7 +142,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ScalarAdvectionArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/scalar_diffusion/scalar_diffusion.py b/examples/scalar_diffusion/scalar_diffusion.py
index 170359e41..085664f09 100755
--- a/examples/scalar_diffusion/scalar_diffusion.py
+++ b/examples/scalar_diffusion/scalar_diffusion.py
@@ -118,7 +118,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ScalarDiffusionArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/sediment_deposit/sediment_deposit.py b/examples/sediment_deposit/sediment_deposit.py
index 3041c495b..ea0b53c94 100644
--- a/examples/sediment_deposit/sediment_deposit.py
+++ b/examples/sediment_deposit/sediment_deposit.py
@@ -334,7 +334,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/sediment_deposit/sediment_deposit_levelset.py b/examples/sediment_deposit/sediment_deposit_levelset.py
index 5f5beda14..bb566be49 100644
--- a/examples/sediment_deposit/sediment_deposit_levelset.py
+++ b/examples/sediment_deposit/sediment_deposit_levelset.py
@@ -395,7 +395,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ParticleAboveSaltArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/shear_layer/shear_layer.py b/examples/shear_layer/shear_layer.py
index 520d42899..29a14fad5 100644
--- a/examples/shear_layer/shear_layer.py
+++ b/examples/shear_layer/shear_layer.py
@@ -205,7 +205,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class ShearLayerArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/taylor_green/taylor_green.py b/examples/taylor_green/taylor_green.py
index a8d07d76f..1d544f4d7 100644
--- a/examples/taylor_green/taylor_green.py
+++ b/examples/taylor_green/taylor_green.py
@@ -315,7 +315,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class TaylorGreenArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/taylor_green/taylor_green_cpuFortran.py b/examples/taylor_green/taylor_green_cpuFortran.py
index cc575e98a..d89e280f7 100644
--- a/examples/taylor_green/taylor_green_cpuFortran.py
+++ b/examples/taylor_green/taylor_green_cpuFortran.py
@@ -232,7 +232,7 @@ def compute(args):
if __name__=='__main__':
- from examples.example_utils import HysopArgParser, colors
+ from hysop.examples.example_utils import HysopArgParser, colors
class TaylorGreenArgParser(HysopArgParser):
def __init__(self):
diff --git a/examples/__init__.py b/hysop/examples/__init__.py
similarity index 100%
rename from examples/__init__.py
rename to hysop/examples/__init__.py
diff --git a/examples/example_utils.py b/hysop/examples/example_utils.py
similarity index 100%
rename from examples/example_utils.py
rename to hysop/examples/example_utils.py
--
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