Merge branch 'fix-beam' into 'master'

[nb] subprocess.run needs shell=True when args are given as string.

See merge request ogs/ogs!5166

Author: bilke

Tests/Data/Parabolic/ComponentTransport/elder_jupyter/elder_jupyter.py

@@ -60,7 +60,7 @@
 # %%
 import matplotlib.pyplot as plt
 import ogstools as ogs
-from IPython.display import HTML, Image
+from IPython.display import HTML
 
 # %%
 ogs.plot.setup.dpi = 30  # resolution
@@ -142,15 +142,6 @@ def plot_func(ax: plt.Axes, timevalue: float) -> None:
 )
 HTML(anim.to_jshtml())
 
-# %% [markdown]
-# ### Compare simulation results OGS-5 vs. OGS-6
-#
-# Here, we compare numerical results of OGS-6 to those of OGS-5.
-# Settings of both simulators were chosen to be as identical as possible.
-# Simulation times were and for $3300 s$ OGS-6 and $7800 s$ OGS-5, respectively.
-
-# %%
-Image(url="../elder/elder.gif")
 
 # %% [markdown]
 # ## Literature

Tests/Data/PhaseField/beam_jupyter_notebook/beam.py

@@ -154,23 +154,32 @@ def ogs_beam(
     run(
         f"generateStructuredMesh -o {out_dir}/bar_.vtu -e hex --lx {beam_length} --nx {round(beam_length/h)} --ly {beam_height} --ny {round(beam_height/h)} --lz {beam_depth} --nz {round(beam_depth/h)} > {logfile}",
         check=True,
+        shell=True,
     )
     run(
         f"NodeReordering -i {out_dir}/bar_.vtu -o {out_dir}/bar.vtu >> {logfile}",
         check=True,
+        shell=True,
     )
     run(
         f"ExtractSurface -i {out_dir}/bar.vtu -o {out_dir}/bar_left.vtu -x 1 -y 0 -z 0 >> {logfile}",
         check=True,
+        shell=True,
     )
     run(
         f"extractSurface -i {out_dir}/bar.vtu -o {out_dir}/bar_right.vtu -x -1 -y 0 -z 0 >> {logfile}",
         check=True,
+        shell=True,
+    )
+    run(
+        f"partmesh -s -o {out_dir} -i {out_dir}/bar.vtu >> {logfile}",
+        check=True,
+        shell=True,
     )
-    run(f"partmesh -s -o {out_dir} -i {out_dir}/bar.vtu >> {logfile}", check=True)
     run(
         f"partmesh -m -n 3 -o {out_dir} -i {out_dir}/bar.vtu -- {out_dir}/bar_right.vtu {out_dir}/bar_left.vtu >> {logfile}",
         check=True,
+        shell=True,
     )
     # change properties in prj file
     model = ot.Project(
@@ -206,7 +215,9 @@ def ogs_beam(
     t0 = time.time()
     print("  > OGS started execution ...")
     run(
-        f"mpirun -n 3 ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}", check=True
+        f"mpirun -n 3 ogs {out_dir}/{prj_name} -o {output_dir} >> {logfile}",
+        check=True,
+        shell=True,
     )
     tf = time.time()
     print("  > OGS terminated execution. Elapsed time: ", round(tf - t0, 2), " s.")

web/content/docs/devguide/environments/redistributable-builds/index.md

@@ -40,11 +40,11 @@ If a binary runs on a different machine depends on a lot of factors. The followi
 
 #### For redistribution
 
-- `OGS_CPU_ARCHITECTURE`: set to `generic` for good balance between optimization and portability; set to `core2` for maximum portability, more info on [GCC docs](https://gcc.gnu.org/onlinedocs/gcc/gcc-command-options/machine-dependent-options/x86-options.html#cmdoption-x86-mtune)
+- `OGS_CPU_ARCHITECTURE`: set to `generic` for good balance between optimization and portability; set to `core2` for maximum portability, more info on [GCC docs](https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html)
 
 #### For optimization
 
-- `OGS_CPU_ARCHITECTURE`: tot to `native` for best optimization for your current CPU, possible values are [listed here](https://stackoverflow.com/a/25095818/80480), more info on [GCC docs](https://gcc.gnu.org/onlinedocs/gcc/gcc-command-options/machine-dependent-options/x86-options.html#cmdoption-x86-mtune)
+- `OGS_CPU_ARCHITECTURE`: tot to `native` for best optimization for your current CPU, possible values are [listed here](https://stackoverflow.com/a/25095818/80480), more info on [GCC docs](https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html)
 
 </div>