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Merge pull request #87 from NDF-Poli-USP/updating_github_runner
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Updating GitHub runner
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Olender authored Jun 30, 2023
2 parents 282f5e6 + 4e1c7e9 commit fef8f54
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16 changes: 8 additions & 8 deletions .github/workflows/python-tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,38 +17,38 @@ jobs:
- uses: actions/checkout@v3
- name: Running serial tests in parallel (only one test per core)
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
pytest -n 10 --cov-report=xml --cov=spyro test/
- name: Running serial tests for adjoint
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
pytest -n 10 --cov-report=xml --cov-append --cov=spyro test_ad/
- name: Running parallel tests
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
cp /home/olender/Testing_files/velocity_models/* velocity_models/
cp /home/olender/Testing_files/meshes/* meshes/
mpiexec -n 10 pytest test_parallel/test_forward.py
- name: Covering parallel tests
continue-on-error: true
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
cp /home/olender/Testing_files/velocity_models/* velocity_models/
cp /home/olender/Testing_files/meshes/* meshes/
mpiexec -n 10 pytest --cov-report=xml --cov-append --cov=spyro test_parallel/test_forward.py
- name: Running parallel 3D forward test
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
cp /home/olender/Testing_files/velocity_models/* velocity_models/
cp /home/olender/Testing_files/meshes/* meshes/
mpiexec -n 15 pytest test_3d/test_forward_3d.py
mpiexec -n 10 pytest test_3d/test_forward_3d.py
- name: Covering parallel 3D forward test
continue-on-error: true
run: |
source /opt/firedrake/bin/activate
source /home/olender/Firedrakes/main/firedrake/bin/activate
cp /home/olender/Testing_files/velocity_models/* velocity_models/
cp /home/olender/Testing_files/meshes/* meshes/
mpiexec -n 15 pytest --cov-report=xml --cov-append --cov=spyro test_3d/test_forward_3d.py
mpiexec -n 10 pytest --cov-report=xml --cov-append --cov=spyro test_3d/test_forward_3d.py
- name: Uploading coverage to Codecov
run: export CODECOV_TOKEN="6cd21147-54f7-4b77-94ad-4b138053401d" && bash <(curl -s https://codecov.io/bash)

6 changes: 3 additions & 3 deletions demos/run_fwi.py
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@
quad_rule = finat.quadrature.make_quadrature(
V.finat_element.cell, V.ufl_element().degree(), "KMV"
)
dxlump = dx(rule=quad_rule)
dxlump = dx(scheme=quad_rule)

water = np.where(vp.dat.data[:] < 1.51)

Expand All @@ -110,8 +110,8 @@ def regularize_gradient(vp, dJ, gamma):
"""Tikhonov regularization"""
m_u = TrialFunction(V)
m_v = TestFunction(V)
mgrad = m_u * m_v * dx(rule=qr_x)
ffG = dot(grad(vp), grad(m_v)) * dx(rule=qr_x)
mgrad = m_u * m_v * dx(scheme=qr_x)
ffG = dot(grad(vp), grad(m_v)) * dx(scheme=qr_x)
G = mgrad - ffG
lhsG, rhsG = lhs(G), rhs(G)
gradreg = Function(V)
Expand Down
6 changes: 3 additions & 3 deletions paper/run_fwi_2d.py
Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@ def get_memory_usage():
quad_rule = finat.quadrature.make_quadrature(
V.finat_element.cell, V.ufl_element().degree(), "KMV"
)
dxlump = dx(rule=quad_rule)
dxlump = dx(scheme=quad_rule)

water = np.where(vp.dat.data[:] < 1.51)

Expand All @@ -117,8 +117,8 @@ def regularize_gradient(vp, dJ):
"""Tikhonov regularization"""
m_u = TrialFunction(V)
m_v = TestFunction(V)
mgrad = m_u * m_v * dx(rule=quad_rule)
ffG = dot(grad(vp), grad(m_v)) * dx(rule=quad_rule)
mgrad = m_u * m_v * dx(scheme=quad_rule)
ffG = dot(grad(vp), grad(m_v)) * dx(scheme=quad_rule)
G = mgrad - ffG
lhsG, rhsG = lhs(G), rhs(G)
gradreg = Function(V)
Expand Down
6 changes: 3 additions & 3 deletions paper/run_fwi_3d.py
Original file line number Diff line number Diff line change
Expand Up @@ -115,7 +115,7 @@ def get_memory_usage():
quad_rule = finat.quadrature.make_quadrature(
V.finat_element.cell, V.ufl_element().degree(), "KMV"
)
dxlump = dx(rule=quad_rule)
dxlump = dx(scheme=quad_rule)

water = np.where(vp.dat.data[:] < 1.51)

Expand All @@ -139,8 +139,8 @@ def regularize_gradient(vp, dJ):
"""Tikhonov regularization"""
m_u = TrialFunction(V)
m_v = TestFunction(V)
mgrad = m_u * m_v * dx(rule=quad_rule)
ffG = dot(grad(vp), grad(m_v)) * dx(rule=quad_rule)
mgrad = m_u * m_v * dx(scheme=quad_rule)
ffG = dot(grad(vp), grad(m_v)) * dx(scheme=quad_rule)
G = mgrad - ffG
lhsG, rhsG = lhs(G), rhs(G)
gradreg = Function(V)
Expand Down
38 changes: 19 additions & 19 deletions spyro/solvers/forward.py
Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ def forward(
(sigma_x + sigma_z)
* ((u - u_nm1) / Constant(2.0 * dt))
* v
* dx(rule=qr_x)
* dx(scheme=qr_x)
)
elif dim == 3:

Expand Down Expand Up @@ -178,12 +178,12 @@ def forward(
t = 0.0

# -------------------------------------------------------
m1 = ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(rule=qr_x)
a = c * c * dot(grad(u_n), grad(v)) * dx(rule=qr_x) # explicit
m1 = ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(scheme=qr_x)
a = c * c * dot(grad(u_n), grad(v)) * dx(scheme=qr_x) # explicit

nf = 0
if model["BCs"]["outer_bc"] == "non-reflective":
nf = c * ((u_n - u_nm1) / dt) * v * ds(rule=qr_s)
nf = c * ((u_n - u_nm1) / dt) * v * ds(scheme=qr_s)

FF = m1 + a + nf

Expand All @@ -192,41 +192,41 @@ def forward(
B = Function(W)

if dim == 2:
pml2 = sigma_x * sigma_z * u_n * v * dx(rule=qr_x)
pml3 = inner(pp_n, grad(v)) * dx(rule=qr_x)
pml2 = sigma_x * sigma_z * u_n * v * dx(scheme=qr_x)
pml3 = inner(pp_n, grad(v)) * dx(scheme=qr_x)
FF += pml1 + pml2 + pml3
# -------------------------------------------------------
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(rule=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(rule=qr_x)
dd = c * c * inner(grad(u_n), dot(Gamma_2, qq)) * dx(rule=qr_x)
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(scheme=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(scheme=qr_x)
dd = c * c * inner(grad(u_n), dot(Gamma_2, qq)) * dx(scheme=qr_x)
FF += mm1 + mm2 + dd
elif dim == 3:
pml1 = (
(sigma_x + sigma_y + sigma_z)
* ((u - u_n) / Constant(dt))
* v
* dx(rule=qr_x)
* dx(scheme=qr_x)
)
pml2 = (
(sigma_x * sigma_y + sigma_x * sigma_z + sigma_y * sigma_z)
* u_n
* v
* dx(rule=qr_x)
* dx(scheme=qr_x)
)
pml3 = (sigma_x * sigma_y * sigma_z) * psi_n * v * dx(rule=qr_x)
pml4 = inner(pp_n, grad(v)) * dx(rule=qr_x)
pml3 = (sigma_x * sigma_y * sigma_z) * psi_n * v * dx(scheme=qr_x)
pml4 = inner(pp_n, grad(v)) * dx(scheme=qr_x)

FF += pml1 + pml2 + pml3 + pml4
# -------------------------------------------------------
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(rule=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(rule=qr_x)
dd1 = c * c * inner(grad(u_n), dot(Gamma_2, qq)) * dx(rule=qr_x)
dd2 = -c * c * inner(grad(psi_n), dot(Gamma_3, qq)) * dx(rule=qr_x)
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(scheme=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(scheme=qr_x)
dd1 = c * c * inner(grad(u_n), dot(Gamma_2, qq)) * dx(scheme=qr_x)
dd2 = -c * c * inner(grad(psi_n), dot(Gamma_3, qq)) * dx(scheme=qr_x)

FF += mm1 + mm2 + dd1 + dd2
# -------------------------------------------------------
mmm1 = (dot((psi - psi_n), phi) / Constant(dt)) * dx(rule=qr_x)
uuu1 = (-u_n * phi) * dx(rule=qr_x)
mmm1 = (dot((psi - psi_n), phi) / Constant(dt)) * dx(scheme=qr_x)
uuu1 = (-u_n * phi) * dx(scheme=qr_x)

FF += mmm1 + uuu1
else:
Expand Down
8 changes: 4 additions & 4 deletions spyro/solvers/forward_AD.py
Original file line number Diff line number Diff line change
Expand Up @@ -89,16 +89,16 @@ def forward(

t = 0.0
m = 1 / (c * c)
m1 = m * ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(rule=qr_x)
a = dot(grad(u_n), grad(v)) * dx(rule=qr_x) # explicit
m1 = m * ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(scheme=qr_x)
a = dot(grad(u_n), grad(v)) * dx(scheme=qr_x) # explicit
f = Function(V)
nf = 0

if model["BCs"]["outer_bc"] == "non-reflective":
nf = c * ((u_n - u_nm1) / dt) * v * ds(rule=qr_s)
nf = c * ((u_n - u_nm1) / dt) * v * ds(scheme=qr_s)

h = CellSize(mesh)
FF = m1 + a + nf - (1 / (h / degree * h / degree)) * f * v * dx(rule=qr_x)
FF = m1 + a + nf - (1 / (h / degree * h / degree)) * f * v * dx(scheme=qr_x)
X = Function(V)

lhs_ = lhs(FF)
Expand Down
42 changes: 21 additions & 21 deletions spyro/solvers/gradient.py
Original file line number Diff line number Diff line change
Expand Up @@ -161,12 +161,12 @@ def gradient(
t = 0.0

# -------------------------------------------------------
m1 = ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(rule=qr_x)
a = c * c * dot(grad(u_n), grad(v)) * dx(rule=qr_x) # explicit
m1 = ((u - 2.0 * u_n + u_nm1) / Constant(dt**2)) * v * dx(scheme=qr_x)
a = c * c * dot(grad(u_n), grad(v)) * dx(scheme=qr_x) # explicit

nf = 0
if model["BCs"]["outer_bc"] == "non-reflective":
nf = c * ((u_n - u_nm1) / dt) * v * ds(rule=qr_s)
nf = c * ((u_n - u_nm1) / dt) * v * ds(scheme=qr_s)

FF = m1 + a + nf

Expand All @@ -175,39 +175,39 @@ def gradient(
B = Function(W)

if dim == 2:
pml1 = (sigma_x + sigma_z) * ((u - u_n) / dt) * v * dx(rule=qr_x)
pml2 = sigma_x * sigma_z * u_n * v * dx(rule=qr_x)
pml3 = c * c * inner(grad(v), dot(Gamma_2, pp_n)) * dx(rule=qr_x)
pml1 = (sigma_x + sigma_z) * ((u - u_n) / dt) * v * dx(scheme=qr_x)
pml2 = sigma_x * sigma_z * u_n * v * dx(scheme=qr_x)
pml3 = c * c * inner(grad(v), dot(Gamma_2, pp_n)) * dx(scheme=qr_x)

FF += pml1 + pml2 + pml3
# -------------------------------------------------------
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(rule=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(rule=qr_x)
dd = inner(qq, grad(u_n)) * dx(rule=qr_x)
mm1 = (dot((pp - pp_n), qq) / Constant(dt)) * dx(scheme=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(scheme=qr_x)
dd = inner(qq, grad(u_n)) * dx(scheme=qr_x)

FF += mm1 + mm2 + dd
elif dim == 3:
pml1 = (sigma_x + sigma_y + sigma_z) * ((u - u_n) / dt) * v * dx(rule=qr_x)
uuu1 = (-v * psi_n) * dx(rule=qr_x)
pml1 = (sigma_x + sigma_y + sigma_z) * ((u - u_n) / dt) * v * dx(scheme=qr_x)
uuu1 = (-v * psi_n) * dx(scheme=qr_x)
pml2 = (
(sigma_x * sigma_y + sigma_x * sigma_z + sigma_y * sigma_z)
* u_n
* v
* dx(rule=qr_x)
* dx(scheme=qr_x)
)
dd1 = c * c * inner(grad(v), dot(Gamma_2, pp_n)) * dx(rule=qr_x)
dd1 = c * c * inner(grad(v), dot(Gamma_2, pp_n)) * dx(scheme=qr_x)

FF += pml1 + pml2 + dd1 + uuu1
# -------------------------------------------------------
mm1 = (dot((pp - pp_n), qq) / dt) * dx(rule=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(rule=qr_x)
pml4 = inner(qq, grad(u_n)) * dx(rule=qr_x)
mm1 = (dot((pp - pp_n), qq) / dt) * dx(scheme=qr_x)
mm2 = inner(dot(Gamma_1, pp_n), qq) * dx(scheme=qr_x)
pml4 = inner(qq, grad(u_n)) * dx(scheme=qr_x)

FF += mm1 + mm2 + pml4
# -------------------------------------------------------
pml3 = (sigma_x * sigma_y * sigma_z) * phi * u_n * dx(rule=qr_x)
mmm1 = (dot((psi - psi_n), phi) / dt) * dx(rule=qr_x)
mmm2 = -c * c * inner(grad(phi), dot(Gamma_3, pp_n)) * dx(rule=qr_x)
pml3 = (sigma_x * sigma_y * sigma_z) * phi * u_n * dx(scheme=qr_x)
mmm1 = (dot((psi - psi_n), phi) / dt) * dx(scheme=qr_x)
mmm2 = -c * c * inner(grad(phi), dot(Gamma_3, pp_n)) * dx(scheme=qr_x)

FF += mmm1 + mmm2 + pml3
else:
Expand All @@ -223,12 +223,12 @@ def gradient(
# Define gradient problem
m_u = TrialFunction(V)
m_v = TestFunction(V)
mgrad = m_u * m_v * dx(rule=qr_x)
mgrad = m_u * m_v * dx(scheme=qr_x)

uuadj = Function(V) # auxiliarly function for the gradient compt.
uufor = Function(V) # auxiliarly function for the gradient compt.

ffG = 2.0 * c * dot(grad(uuadj), grad(uufor)) * m_v * dx(rule=qr_x)
ffG = 2.0 * c * dot(grad(uuadj), grad(uufor)) * m_v * dx(scheme=qr_x)

G = mgrad - ffG
lhsG, rhsG = lhs(G), rhs(G)
Expand Down
4 changes: 2 additions & 2 deletions spyro/utils/estimate_timestep.py
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ def estimate_timestep(mesh, V, c, estimate_max_eigenvalue=True):
quad_rule = finat.quadrature.make_quadrature(
V.finat_element.cell, V.ufl_element().degree(), "KMV"
)
dxlump = fd.dx(rule=quad_rule)
dxlump = fd.dx(scheme=quad_rule)
A = fd.assemble(u * v * dxlump)
ai, aj, av = A.petscmat.getValuesCSR()
av_inv = []
Expand Down Expand Up @@ -51,7 +51,7 @@ def estimate_timestep(mesh, V, c, estimate_max_eigenvalue=True):

# print(max_eigval)
if np.sqrt(max_eigval) > 0.0:
max_dt = np.float(2 / np.sqrt(max_eigval))
max_dt = float(2 / np.sqrt(max_eigval))
else:
max_dt = 100000000
# print(
Expand Down
2 changes: 1 addition & 1 deletion test/not_a_test.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ def test_gradient_talyor_remainder_v2():
class L2Inner(object):
def __init__(self):
self.A = assemble(
TrialFunction(V) * TestFunction(V) * dx(rule=qr_x), mat_type="matfree"
TrialFunction(V) * TestFunction(V) * dx(scheme=qr_x), mat_type="matfree"
)
self.Ap = as_backend_type(self.A).mat()

Expand Down
4 changes: 2 additions & 2 deletions test/test_gradient.py
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ def _test_gradient(options, pml=False):

# compute the gradient of the control (to be verified)
dJ = gradient(options, mesh, comm, vp_guess, receivers, p_guess, misfit)
dJ *= mask
dJ.dat.data[:] = dJ.dat.data[:]*mask.dat.data[:]
File("gradient.pvd").write(dJ)

steps = [1e-3, 1e-4, 1e-5] # , 1e-6] # step length
Expand Down Expand Up @@ -145,7 +145,7 @@ def _test_gradient(options, pml=False):
)

Jp = functional(options, p_exact_recv - p_guess_recv)
projnorm = assemble(mask * dJ * delta_m * dx(rule=qr_x))
projnorm = assemble(mask * dJ * delta_m * dx(scheme=qr_x))
fd_grad = (Jp - Jm) / step
print(
"\n Cost functional for step "
Expand Down
2 changes: 1 addition & 1 deletion test/test_gradient_3d.py
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ def _test_gradient(options, pml=False):
)

Jp = functional(options, p_exact_recv - p_guess_recv)
projnorm = assemble(box1 * dJ * delta_m * dx(rule=qr_x))
projnorm = assemble(box1 * dJ * delta_m * dx(scheme=qr_x))
fd_grad = (Jp - Jm) / step
print(
"\n Cost functional for step "
Expand Down

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