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Add numpy option (#39)
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* Add numpy option

* Spell profile correctly

* Temporarily use future mirgecom@production.

* Revert back to mirgecom@production

* Clean up messaging and arg parsing a bit.

* fix numpy usage, add numpy test, test accuracy

* libegl1

* add run_numpy.sh, set casenames in run*.sh

---------

Co-authored-by: Matthias Diener <[email protected]>
Co-authored-by: Matthias Diener <[email protected]>
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@MTCam @matthiasdiener
3 people authored Aug 14, 2023
1 parent d88b8ad commit 818f298
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Showing 8 changed files with 62 additions and 34 deletions.
24 changes: 23 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -39,7 +39,7 @@ jobs:
- uses: actions/checkout@v3
- name: Install emirge
run: |
[[ $(uname) == Linux ]] && sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev
[[ $(uname) == Linux ]] && sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev bsdmainutils libgl1-mesa-glx libegl1
[[ $(uname) == Darwin ]] && brew update && brew install mpich
./buildMirge.sh
cd emirge
Expand All @@ -66,12 +66,34 @@ jobs:
cd smoke_test
./run_restart.sh
- name: Numpy smoke test
run: |
source emirge/config/activate_env.sh
cd smoke_test
./run_numpy.sh
- name: Lazy smoke test
run: |
source emirge/config/activate_env.sh
cd smoke_test
./run_lazy.sh
- name: Compare smoke_test accuracy
run: |
source emirge/config/activate_env.sh
cd smoke_test/viz_data
TOL_LAZY=1e-2
TOL_NUMPY=1e-2
set -x
for vizfile in $(ls *-eager-*.vtu); do
lazy_vizfile=$(echo ${vizfile/eager/lazy})
python ../../emirge/mirgecom/bin/mirgecompare.py --tolerance $TOL_LAZY ${vizfile} ${lazy_vizfile}
numpy_vizfile=$(echo ${vizfile/eager/numpy})
python ../../emirge/mirgecom/bin/mirgecompare.py --tolerance $TOL_NUMPY ${vizfile} ${numpy_vizfile}
done
- name: Lazy smoke test without wall
run: |
source emirge/config/activate_env.sh
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18 changes: 6 additions & 12 deletions driver.py
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Expand Up @@ -28,6 +28,8 @@
help="enable lazy evaluation [OFF]")
parser.add_argument("--overintegration", action="store_true",
help="use overintegration in the RHS computations")
parser.add_argument("--numpy", action="store_true",
help="use numpy-based eager actx.")

args = parser.parse_args()

Expand All @@ -39,21 +41,13 @@
else:
print(f"Default casename {casename}")

from warnings import warn
if args.esdg:
if not args.lazy:
warn("ESDG requires lazy-evaluation, enabling --lazy.")
if not args.overintegration:
warn("ESDG requires overintegration, enabling --overintegration.")

lazy = args.lazy or args.esdg
if args.profile:
if lazy:
raise ValueError("Can't use lazy and profiling together.")
from mirgecom.simutil import ApplicationOptionsError
if args.esdg and not (args.lazy or args.numpy):
raise ApplicationOptionsError("ESDG requires lazy or numpy context.")

from mirgecom.array_context import get_reasonable_array_context_class
actx_class = get_reasonable_array_context_class(
lazy=lazy, distributed=True, profiling=args.profile)
lazy=args.lazy, distributed=True, profiling=args.profile, numpy=args.numpy)

restart_filename = None
if args.restart_file:
Expand Down
2 changes: 1 addition & 1 deletion smoke_test/run.sh
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@@ -1,3 +1,3 @@
#!/bin/bash
mpirun -n 2 python -u -O -m mpi4py driver.py -i run_params.yaml --log
mpirun -n 2 python -u -O -m mpi4py driver.py -i run_params.yaml --log --casename=prediction-eager
#mpirun -n 1 python -u -O -m mpi4py driver.py -i run_params.yaml --log
2 changes: 1 addition & 1 deletion smoke_test/run_lazy.sh
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@@ -1,2 +1,2 @@
#!/bin/bash
mpirun -n 2 python -u -O -m mpi4py driver.py -i run_params.yaml --log --lazy
mpirun -n 2 python -u -O -m mpi4py driver.py -i run_params.yaml --log --lazy --casename=prediction-lazy
2 changes: 2 additions & 0 deletions smoke_test/run_numpy.sh
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@@ -0,0 +1,2 @@
#!/bin/bash
mpirun -n 2 python -u -O -m mpi4py driver.py -i run_params.yaml --log --numpy --casename=prediction-numpy
2 changes: 1 addition & 1 deletion smoke_test/run_restart.sh
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@@ -1,2 +1,2 @@
#!/bin/bash
mpirun -n 2 python -u -O -m mpi4py driver.py -i restart_params.yaml -r restart_data/prediction-000000010 -t restart_data/prediction-000000000 --log
mpirun -n 2 python -u -O -m mpi4py driver.py -i restart_params.yaml -r restart_data/prediction-eager-000000010 -t restart_data/prediction-eager-000000000 --log
44 changes: 27 additions & 17 deletions y3prediction/prediction.py
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Expand Up @@ -1355,8 +1355,12 @@ def my_partitioner(mesh, tag_to_elements, num_ranks):
else:
logger.warning("No target file specied, using restart as target")

disc_msg = f"Making {dim}D order {order} discretization"
if use_overintegration:
disc_msg = disc_msg + f" with quadrature order {quadrature_order}"
disc_msg = disc_msg + "."
if rank == 0:
logger.info("Making discretization")
logger.info(disc_msg)

dcoll = create_discretization_collection(
actx,
Expand Down Expand Up @@ -1413,7 +1417,7 @@ def my_partitioner(mesh, tag_to_elements, num_ranks):
char_length_wall = force_evaluation(actx,
characteristic_lengthscales(actx, dcoll, dd=dd_vol_wall))
xpos_wall = wall_nodes[0]
char_length_wall = char_length_wall + actx.zeros_like(xpos_wall)
char_length_wall = char_length_wall + actx.np.zeros_like(xpos_wall)
"""
smoothness_diffusivity_wall = \
smooth_char_length_alpha*char_length_wall**2/current_dt
Expand Down Expand Up @@ -1810,8 +1814,8 @@ def update_smoothness(state, time):

cv = cv + 0.*fluid_rhs

wall_mass_rhs = actx.zeros_like(wv.mass)
wall_ox_mass_rhs = actx.zeros_like(wv.mass)
wall_mass_rhs = actx.np.zeros_like(wv.mass)
wall_ox_mass_rhs = actx.np.zeros_like(wv.mass)
wall_rhs = wall_time_scale * WallVars(
mass=wall_mass_rhs,
energy=wall_energy_rhs,
Expand Down Expand Up @@ -1978,7 +1982,7 @@ def get_production_rates(cv, temperature):
restart_wv = WallVars(
mass=wall_mass,
energy=wall_mass * wall_cp * temp_wall,
ox_mass=actx.zeros_like(wall_mass))
ox_mass=actx.np.zeros_like(wall_mass))

if use_wall:
restart_wv = force_evaluation(actx, restart_wv)
Expand Down Expand Up @@ -2381,7 +2385,7 @@ def _sponge_sigma(sponge_field, x_vec):

get_sponge_sigma = actx.compile(_sponge_sigma)

sponge_sigma = actx.zeros_like(restart_cv.mass)
sponge_sigma = actx.np.zeros_like(restart_cv.mass)
sponge_sigma = get_sponge_sigma(sponge_sigma, fluid_nodes)

def _sponge_source(cv):
Expand Down Expand Up @@ -2437,12 +2441,18 @@ def _sponge_source(cv):

logmgr.add_watches([
("memory_usage_hwm.max",
"| \t memory hwm: {value:7g} Mb\n"),
("memory_usage_mempool_managed.max",
"| \t mempool total: {value:7g} Mb\n"),
("memory_usage_mempool_active.max",
"| \t mempool active: {value:7g} Mb")
])
"| \t memory hwm: {value:7g} Mb\n")])

from mirgecom.array_context import actx_class_is_numpy

if not actx_class_is_numpy(actx_class):
# numpy has no CL mempool
logmgr.add_watches([
("memory_usage_mempool_managed.max",
"| \t mempool total: {value:7g} Mb\n"),
("memory_usage_mempool_active.max",
"| \t mempool active: {value:7g} Mb")
])

if use_profiling:
logmgr.add_watches(["pyopencl_array_time.max"])
Expand Down Expand Up @@ -2610,8 +2620,8 @@ def compute_viz_fields_coupled(fluid_state, wv, wdv, time):

cv = cv + 0.*fluid_rhs

wall_mass_rhs = actx.zeros_like(wv.mass)
wall_ox_mass_rhs = actx.zeros_like(wv.mass)
wall_mass_rhs = actx.np.zeros_like(wv.mass)
wall_ox_mass_rhs = actx.np.zeros_like(wv.mass)
wall_rhs = wall_time_scale * WallVars(
mass=wall_mass_rhs,
energy=wall_energy_rhs,
Expand Down Expand Up @@ -3533,17 +3543,17 @@ def unfiltered_rhs(t, state):

if use_wall:
# wall mass loss
wall_mass_rhs = actx.zeros_like(wv.mass)
wall_mass_rhs = actx.np.zeros_like(wv.mass)
if use_wall_mass:
wall_mass_rhs = -wall_model.mass_loss_rate(
mass=wv.mass, ox_mass=wv.ox_mass,
temperature=wdv.temperature)

# wall oxygen diffusion
wall_ox_mass_rhs = actx.zeros_like(wv.mass)
wall_ox_mass_rhs = actx.np.zeros_like(wv.mass)
if use_wall_ox:
if nspecies == 0:
fluid_ox_mass = actx.zeros_like(cv.mass)
fluid_ox_mass = actx.np.zeros_like(cv.mass)
elif nspecies > 3:
fluid_ox_mass = cv.species_mass[i_ox]
else:
Expand Down
2 changes: 1 addition & 1 deletion y3prediction/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ def __call__(self, sponge_field, x_vec, *, time=0.0):
xpos = x_vec[0]
ypos = x_vec[1]
actx = xpos.array_context
zeros = actx.zeros_like(xpos)
zeros = actx.np.zeros_like(xpos)
x0 = zeros + self._x0

if abs(self._direction) == 1:
Expand Down

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