From ecb3ab33fde0db2faec395313eef483a2bd240c0 Mon Sep 17 00:00:00 2001
From: Feliks Kiszkurno <feliks-kuba.kiszkurno@ufz.de>
Date: Tue, 10 Dec 2024 09:11:27 +0100
Subject: [PATCH] Fix errors from CI
---
Tests/Data/Notebooks/SimplePETSc.py | 2 +-
.../Kregime_Propagating_jupyter.py | 6 ++++-
.../sen_shear.py | 17 ++++++++++--
.../Kregime_Static_jupyter.py | 1 +
.../surfing_pyvista.py | 3 +++
.../PhaseField/tpb_jupyter_notebook/TPB.py | 27 ++++++++++++++++---
6 files changed, 48 insertions(+), 8 deletions(-)
diff --git a/Tests/Data/Notebooks/SimplePETSc.py b/Tests/Data/Notebooks/SimplePETSc.py
index 22a47b305d1..43f3999f95f 100644
--- a/Tests/Data/Notebooks/SimplePETSc.py
+++ b/Tests/Data/Notebooks/SimplePETSc.py
@@ -44,7 +44,7 @@ if not out_dir.exists():
out_dir.mkdir(parents=True)
print(f"mpirun --bind-to none -np 2 ogs {prj_file} > out.txt")
-run(f"mpirun --bind-to none -np 2 ogs {prj_file} > out.txt", check=True)
+run(f"mpirun --bind-to none -np 2 ogs {prj_file} > out.txt", shell=True, check=True)
print(datetime.now())
diff --git a/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py b/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py
index c3bf01ee690..d436f331f88 100644
--- a/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py
+++ b/Tests/Data/PhaseField/Kregime_Propagating_jupyter_notebook/Kregime_Propagating_jupyter.py
@@ -310,7 +310,11 @@ def Hydraulic_Fracturing_Toughness_Dominated_numerical(h, phasefield_model):
# run simulation with ogs
t0 = time.time()
print(">>> OGS started execution ... <<<")
- run(f"ogs {out_dir}/{prj_name} -o {out_dir} > {out_dir}/log.txt", check=True)
+ run(
+ f"ogs {out_dir}/{prj_name} -o {out_dir} > {out_dir}/log.txt",
+ shell=True,
+ check=True,
+ )
tf = time.time()
print(">>> OGS terminated execution <<< Elapsed time: ", round(tf - t0, 2), " s.")
diff --git a/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.py b/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.py
index 94af9e238d7..0c521b63360 100644
--- a/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.py
+++ b/Tests/Data/PhaseField/PForthotropy_jupyter_notebook/sen_shear.py
@@ -133,10 +133,12 @@ def ogs_ortho(
# partition mesh
run(
f"NodeReordering -i shear.vtu -o {out_dir}/shear.vtu >> {logfile}",
+ shell=True,
check=True,
)
run(
f"constructMeshesFromGeometry -m {out_dir}/shear.vtu -g shear.gml >> {logfile}",
+ shell=True,
check=True,
)
shutil.move("shear_top.vtu", f"{out_dir}/shear_top.vtu")
@@ -149,14 +151,20 @@ def ogs_ortho(
shutil.move("shear_p_2.vtu", f"{out_dir}/shear_p_2.vtu")
shutil.move("shear_p_3.vtu", f"{out_dir}/shear_p_3.vtu")
- run(f"partmesh -s -o {out_dir} -i {out_dir}/shear.vtu >> {logfile}", check=True)
+ run(
+ f"partmesh -s -o {out_dir} -i {out_dir}/shear.vtu >> {logfile}",
+ shell=True,
+ check=True,
+ )
run(
f"partmesh -m -n {ncores} -o {out_dir} -i {out_dir}/shear.vtu -- {out_dir}/shear_top.vtu {out_dir}/shear_bottom.vtu {out_dir}/shear_left.vtu {out_dir}/shear_right.vtu >> {logfile}",
+ shell=True,
check=True,
)
else:
run(
f"NodeReordering -i shear.vtu -o {out_dir}/shear.vtu >> {logfile}",
+ shell=True,
check=True,
)
@@ -199,11 +207,16 @@ def ogs_ortho(
print(f" > OGS started execution with MPI - {ncores} cores...")
run(
f"mpirun --bind-to none -np {ncores} ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}",
+ shell=True,
check=True,
)
else:
print(" > OGS started execution - ")
- run(f"ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}", check=True)
+ run(
+ f"ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}",
+ shell=True,
+ check=True,
+ )
tf = time.time()
print(" > OGS terminated execution. Elapsed time: ", round(tf - t0, 2), " s.")
diff --git a/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py b/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py
index e0df462d951..4b3d48982db 100644
--- a/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py
+++ b/Tests/Data/PhaseField/kregime_jupyter_notebook/Kregime_Static_jupyter.py
@@ -267,6 +267,7 @@ def sneddon_numerical(h):
print(">>> OGS started execution ... <<<")
run(
f"ogs {out_dir}/{prj_name} -o {out_dir} -m {out_dir} > {out_dir}/ogs-out.txt",
+ shell=True,
check=True,
)
tf = time.time()
diff --git a/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.py b/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.py
index ff66ae38243..d8ec72da54f 100644
--- a/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.py
+++ b/Tests/Data/PhaseField/surfing_jupyter_notebook/surfing_pyvista.py
@@ -186,10 +186,12 @@ if not out_dir.exists():
# https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
run(
f"generateStructuredMesh -o {out_dir}/surfing_quad_1x2.vtu -e quad --lx 2 --nx {round(2/h)+1} --ly 1 --ny {round(1/h)+1}",
+ shell=True,
check=True,
)
run(
f"NodeReordering -i {out_dir}/surfing_quad_1x2.vtu -o {out_dir}/surfing_quad_1x2_NR.vtu",
+ shell=True,
check=True,
)
@@ -269,6 +271,7 @@ t0 = time.time()
print(">>> OGS started execution ... <<<")
run(
f"ogs {out_dir}/{prj_name} -o {out_dir} -m {out_dir} > {out_dir}/ogs-out.txt",
+ shell=True,
check=True,
)
diff --git a/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.py b/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.py
index 8a3a5b409da..110560133da 100644
--- a/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.py
+++ b/Tests/Data/PhaseField/tpb_jupyter_notebook/TPB.py
@@ -139,22 +139,36 @@ def ogs_TPB(
if MPI:
# partition mesh
- run(f"NodeReordering -i TPB.vtu -o {out_dir}/TPB.vtu >> {logfile}", check=True)
+ run(
+ f"NodeReordering -i TPB.vtu -o {out_dir}/TPB.vtu >> {logfile}",
+ shell=True,
+ check=True,
+ )
run(
f"constructMeshesFromGeometry -m {out_dir}/TPB.vtu -g TPB.gml >> {logfile}",
+ shell=True,
check=True,
)
shutil.move("TPB_left.vtu", f"{out_dir}/TPB_left.vtu")
shutil.move("TPB_right.vtu", f"{out_dir}/TPB_right.vtu")
shutil.move("TPB_top.vtu", f"{out_dir}/TPB_top.vtu")
shutil.copy("TPB.gml", f"{out_dir}/TPB.gml")
- run(f"partmesh -s -o {out_dir} -i {out_dir}/TPB.vtu >> {logfile}", check=True)
+ run(
+ f"partmesh -s -o {out_dir} -i {out_dir}/TPB.vtu >> {logfile}",
+ shell=True,
+ check=True,
+ )
run(
f"partmesh -m -n {ncores} -o {out_dir} -i {out_dir}/TPB.vtu -- {out_dir}/TPB_right.vtu {out_dir}/TPB_left.vtu {out_dir}/TPB_top.vtu >> {logfile}",
+ shell=True,
check=True,
)
else:
- run(f"NodeReordering -i TPB.vtu -o {out_dir}/TPB.vtu >> {logfile}", check=True)
+ run(
+ f"NodeReordering -i TPB.vtu -o {out_dir}/TPB.vtu >> {logfile}",
+ shell=True,
+ check=True,
+ )
# change properties in prj file
model = ot.Project(
@@ -194,11 +208,16 @@ def ogs_TPB(
print(f" > OGS started execution with MPI - {ncores} cores...")
run(
f"mpirun --bind-to none -np {ncores} ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}",
+ shell=True,
check=True,
)
else:
print(" > OGS started execution ...")
- run(f"ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}", check=True)
+ run(
+ f"ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}",
+ shell=True,
+ check=True,
+ )
tf = time.time()
print(" > OGS terminated execution. Elapsed time: ", round(tf - t0, 2), " s.")
--
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