Skip to content

Commit e3669f2

Browse files
jorgensdjorgensd
authored
Various updates to cope with changes in interpolation points behavior (jorgensd#89)
* Various updates to cope with changes in interpolation points behavior and hdf5 zlib issues * Rename nightly tests * update Keira K(nightly) * Delete various duplicate installations * Debugg * More debug * Simplify CI * Update docker images
1 parent f4438cf commit e3669f2

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

47 files changed

+388
-383
lines changed

Diff for: ‎.github/workflows/build-publish.yml

+11-1
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ jobs:
2020
build:
2121
# The type of runner that the job will run on
2222
runs-on: ubuntu-latest
23-
container: dokken92/dolfinx_custom:15072022
23+
container: dokken92/dolfinx_custom:10082022
2424

2525
env:
2626
HDF5_MPI: "ON"
@@ -34,6 +34,16 @@ jobs:
3434
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
3535
- uses: actions/checkout@v2
3636

37+
- name: Reinstall hdf5 with zlib enabled
38+
run: |
39+
export HDF5_SERIES=1.12
40+
export HDF5_PATCH=2
41+
wget -nc --quiet https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}.tar.gz
42+
tar xfz hdf5-${HDF5_SERIES}.${HDF5_PATCH}.tar.gz
43+
cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-${HDF5_SERIES}.${HDF5_PATCH}
44+
cmake --build build-dir
45+
cmake --install build-dir
46+
3747
- name: Test complex notebooks in parallel
3848
run: |
3949
export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH

Diff for: ‎.github/workflows/main-test.yml renamed to ‎.github/workflows/nightly.yml

+4-8
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# This is a basic workflow to help you get started with Actions
2-
name: Test against DOLFINx main
2+
name: Test against DOLFINx nightly build
33

44
# Controls when the action will run.
55
on:
@@ -23,7 +23,7 @@ jobs:
2323
test-against-master:
2424
# The type of runner that the job will run on
2525
runs-on: ubuntu-latest
26-
container: dolfinx/lab
26+
container: dolfinx/lab:nightly
2727

2828
env:
2929
HDF5_MPI: "ON"
@@ -37,14 +37,10 @@ jobs:
3737
- name: Install dependencies
3838
run: |
3939
pip3 install --upgrade pip setuptools
40-
CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/lib/x86_64-linux-gnu/hdf5/mpich/" pip3 install --no-cache-dir -r docker/requirements.txt
40+
CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/local/" pip3 install --no-cache-dir -r docker/requirements.txt
4141
apt-get -qq update
4242
apt-get install -y libgl1-mesa-dev xvfb nodejs
43-
apt-get clean
44-
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
45-
jupyter nbextension enable --py --sys-prefix ipygany
46-
rm -rf /usr/local/share/.cache/*
47-
jupyter-book -h
43+
4844
- name: Test complex notebooks in parallel
4945
run: |
5046
export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH

Diff for: ‎.vscode/c_cpp_properties.json

+1-1
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
"defines": [],
1515
"compilerPath": "/usr/bin/gcc",
1616
"cStandard": "c11",
17-
"cppStandard": "c++17",
17+
"cppStandard": "c++20",
1818
"intelliSenseMode": "clang-x64",
1919
"configurationProvider": "vector-of-bool.cmake-tools"
2020
}

Diff for: ‎Dockerfile

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
FROM dokken92/dolfinx_custom:15072022
1+
FROM dokken92/dolfinx_custom:10082022
22

33
# create user with a home directory
44
ARG NB_USER

Diff for: ‎chapter1/complex_mode.ipynb

+2-2
Original file line numberDiff line numberDiff line change
@@ -425,7 +425,7 @@
425425
{
426426
"data": {
427427
"application/vnd.jupyter.widget-view+json": {
428-
"model_id": "d78185ab2481475d8596d2e5cfa2f975",
428+
"model_id": "66c7da35aae94a36ba1d467abc3c2813",
429429
"version_major": 2,
430430
"version_minor": 0
431431
},
@@ -455,7 +455,7 @@
455455
{
456456
"data": {
457457
"application/vnd.jupyter.widget-view+json": {
458-
"model_id": "8594601f751740259e13087567cb8d79",
458+
"model_id": "5a0ab66cd1534a01b7c9accbb5195d17",
459459
"version_major": 2,
460460
"version_minor": 0
461461
},

Diff for: ‎chapter1/complex_mode.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (DOLFINx complex)
1212
# language: python

Diff for: ‎chapter1/fundamentals_code.ipynb

+7-7
Original file line numberDiff line numberDiff line change
@@ -501,14 +501,14 @@
501501
"name": "stderr",
502502
"output_type": "stream",
503503
"text": [
504-
"\u001b[0m\u001b[2m2022-07-15 17:29:58.326 ( 0.450s) [ A689B000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
505-
"\u001b[0m\u001b[2m2022-07-15 17:29:58.327 ( 0.451s) [ A689B000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
504+
"\u001b[0m\u001b[2m2022-08-02 20:46:58.678 ( 0.504s) [ E9A08000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
505+
"\u001b[0m\u001b[2m2022-08-02 20:46:58.680 ( 0.505s) [ E9A08000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
506506
]
507507
},
508508
{
509509
"data": {
510510
"application/vnd.jupyter.widget-view+json": {
511-
"model_id": "aa1c4a39e706471fbbbc7660e9e614cc",
511+
"model_id": "8833305ed85e4409a9fe2fdec6f65e1c",
512512
"version_major": 2,
513513
"version_minor": 0
514514
},
@@ -576,14 +576,14 @@
576576
"name": "stderr",
577577
"output_type": "stream",
578578
"text": [
579-
"\u001b[0m\u001b[2m2022-07-15 17:29:58.535 ( 0.659s) [ A689B000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
580-
"\u001b[0m\u001b[2m2022-07-15 17:29:58.536 ( 0.660s) [ A689B000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
579+
"\u001b[0m\u001b[2m2022-08-02 20:46:58.857 ( 0.682s) [ E9A08000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
580+
"\u001b[0m\u001b[2m2022-08-02 20:46:58.857 ( 0.683s) [ E9A08000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 144 edges\u001b[0m\n"
581581
]
582582
},
583583
{
584584
"data": {
585585
"application/vnd.jupyter.widget-view+json": {
586-
"model_id": "fe89f520dad64572a085fb57e0320767",
586+
"model_id": "279adf14586f46d3a74ff0b59508320e",
587587
"version_major": 2,
588588
"version_minor": 0
589589
},
@@ -628,7 +628,7 @@
628628
{
629629
"data": {
630630
"application/vnd.jupyter.widget-view+json": {
631-
"model_id": "239cddce9b5c4e09b0c82c36b5f3cac6",
631+
"model_id": "52757f88d1f94148abb73097db74fbfd",
632632
"version_major": 2,
633633
"version_minor": 0
634634
},

Diff for: ‎chapter1/fundamentals_code.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (ipykernel)
1212
# language: python

Diff for: ‎chapter1/membrane_code.ipynb

+7-7
Original file line numberDiff line numberDiff line change
@@ -94,10 +94,10 @@
9494
"text": [
9595
"Info : Meshing 1D...\n",
9696
"Info : Meshing curve 1 (Ellipse)\n",
97-
"Info : Done meshing 1D (Wall 0.000842374s, CPU 0.000939s)\n",
97+
"Info : Done meshing 1D (Wall 0.000226477s, CPU 0.000384s)\n",
9898
"Info : Meshing 2D...\n",
9999
"Info : Meshing surface 1 (Plane, Frontal-Delaunay)\n",
100-
"Info : Done meshing 2D (Wall 0.0902373s, CPU 0.088198s)\n",
100+
"Info : Done meshing 2D (Wall 0.0965884s, CPU 0.086913s)\n",
101101
"Info : 1550 nodes 3099 elements\n"
102102
]
103103
}
@@ -244,7 +244,7 @@
244244
"outputs": [],
245245
"source": [
246246
"Q = fem.FunctionSpace(domain, (\"CG\", 5))\n",
247-
"expr = fem.Expression(p, Q.element.interpolation_points)\n",
247+
"expr = fem.Expression(p, Q.element.interpolation_points())\n",
248248
"pressure = fem.Function(Q)\n",
249249
"pressure.interpolate(expr)"
250250
]
@@ -268,14 +268,14 @@
268268
"name": "stderr",
269269
"output_type": "stream",
270270
"text": [
271-
"\u001b[0m\u001b[2m2022-07-15 17:30:39.952 ( 0.525s) [ 76AC1000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
272-
"\u001b[0m\u001b[2m2022-07-15 17:30:39.958 ( 0.531s) [ 76AC1000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 4521 edges\u001b[0m\n"
271+
"\u001b[0m\u001b[2m2022-08-02 20:47:36.095 ( 0.515s) [ AAFB6000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
272+
"\u001b[0m\u001b[2m2022-08-02 20:47:36.097 ( 0.517s) [ AAFB6000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 4521 edges\u001b[0m\n"
273273
]
274274
},
275275
{
276276
"data": {
277277
"application/vnd.jupyter.widget-view+json": {
278-
"model_id": "32d8b1feff23457cb167bf0dc36d7ab8",
278+
"model_id": "24700d1f20794182a8ddebf1c27e1932",
279279
"version_major": 2,
280280
"version_minor": 0
281281
},
@@ -324,7 +324,7 @@
324324
{
325325
"data": {
326326
"application/vnd.jupyter.widget-view+json": {
327-
"model_id": "1f73d1fd610047b7b68f4ebd6375eec0",
327+
"model_id": "f8634199f8414d71ae613c7e9874dcbd",
328328
"version_major": 2,
329329
"version_minor": 0
330330
},

Diff for: ‎chapter1/membrane_code.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (ipykernel)
1212
# language: python
@@ -103,7 +103,7 @@ def on_boundary(x):
103103
# We choose a high order function space to represent the function `p`, as it is rapidly varying in space.
104104

105105
Q = fem.FunctionSpace(domain, ("CG", 5))
106-
expr = fem.Expression(p, Q.element.interpolation_points)
106+
expr = fem.Expression(p, Q.element.interpolation_points())
107107
pressure = fem.Function(Q)
108108
pressure.interpolate(expr)
109109

Diff for: ‎chapter1/nitsche.ipynb

+4-4
Original file line numberDiff line numberDiff line change
@@ -51,7 +51,7 @@
5151
"uD = fem.Function(V)\n",
5252
"x = SpatialCoordinate(domain)\n",
5353
"u_ex = 1 + x[0]**2 + 2 * x[1]**2\n",
54-
"uD.interpolate(fem.Expression(u_ex, V.element.interpolation_points))\n",
54+
"uD.interpolate(fem.Expression(u_ex, V.element.interpolation_points()))\n",
5555
"f = -div(grad(u_ex))"
5656
]
5757
},
@@ -193,14 +193,14 @@
193193
"name": "stderr",
194194
"output_type": "stream",
195195
"text": [
196-
"\u001b[0m\u001b[2m2022-07-15 17:31:16.036 ( 0.500s) [ 16C12000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
197-
"\u001b[0m\u001b[2m2022-07-15 17:31:16.037 ( 0.501s) [ 16C12000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 208 edges\u001b[0m\n"
196+
"\u001b[0m\u001b[2m2022-08-02 20:48:31.960 ( 0.530s) [ 598FA000] vtkExtractEdges.cxx:435 INFO| \u001b[0mExecuting edge extractor: points are renumbered\u001b[0m\n",
197+
"\u001b[0m\u001b[2m2022-08-02 20:48:31.960 ( 0.530s) [ 598FA000] vtkExtractEdges.cxx:551 INFO| \u001b[0mCreated 208 edges\u001b[0m\n"
198198
]
199199
},
200200
{
201201
"data": {
202202
"application/vnd.jupyter.widget-view+json": {
203-
"model_id": "c1151bce0df445a5b20608eccb0dc6ee",
203+
"model_id": "1f2111a6e38446b2be61c5525121ee05",
204204
"version_major": 2,
205205
"version_minor": 0
206206
},

Diff for: ‎chapter1/nitsche.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (ipykernel)
1212
# language: python
@@ -39,7 +39,7 @@
3939
uD = fem.Function(V)
4040
x = SpatialCoordinate(domain)
4141
u_ex = 1 + x[0]**2 + 2 * x[1]**2
42-
uD.interpolate(fem.Expression(u_ex, V.element.interpolation_points))
42+
uD.interpolate(fem.Expression(u_ex, V.element.interpolation_points()))
4343
f = -div(grad(u_ex))
4444

4545
# As opposed to the first tutorial, we now have to have another look at the variational form.

Diff for: ‎chapter2/diffusion_code.ipynb

+6-6
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,7 @@
192192
{
193193
"data": {
194194
"application/vnd.jupyter.widget-view+json": {
195-
"model_id": "8184884ce87c47cda0ca7923ae6474f1",
195+
"model_id": "048931ab619b41a8ac3f2375b33e332f",
196196
"version_major": 2,
197197
"version_minor": 0
198198
},
@@ -253,7 +253,7 @@
253253
{
254254
"data": {
255255
"application/vnd.jupyter.widget-view+json": {
256-
"model_id": "c69b7172698c4489aaa5ad8975c47054",
256+
"model_id": "c8102987cc1e47c5a7d15580bbf6b5e3",
257257
"version_major": 2,
258258
"version_minor": 0
259259
},
@@ -267,7 +267,7 @@
267267
{
268268
"data": {
269269
"application/vnd.jupyter.widget-view+json": {
270-
"model_id": "cba04856488a408a84dbee58c05162f1",
270+
"model_id": "64a729318221480fa6c767317c5ad623",
271271
"version_major": 2,
272272
"version_minor": 0
273273
},
@@ -281,7 +281,7 @@
281281
{
282282
"data": {
283283
"application/vnd.jupyter.widget-view+json": {
284-
"model_id": "6aa11e8fe8174a43be5a24a8ae0dc99f",
284+
"model_id": "66329a55399e4652b1aa04b27b3e544b",
285285
"version_major": 2,
286286
"version_minor": 0
287287
},
@@ -295,7 +295,7 @@
295295
{
296296
"data": {
297297
"application/vnd.jupyter.widget-view+json": {
298-
"model_id": "b3cb8e9dd647481c98fa550cc779698d",
298+
"model_id": "7ced58816f57424790b6e618f09dccad",
299299
"version_major": 2,
300300
"version_minor": 0
301301
},
@@ -309,7 +309,7 @@
309309
{
310310
"data": {
311311
"application/vnd.jupyter.widget-view+json": {
312-
"model_id": "8e3212f0f35b4953a4d4d91b8a4a7cf5",
312+
"model_id": "15e98a9021ed49e28f7eef30fc5f945d",
313313
"version_major": 2,
314314
"version_minor": 0
315315
},

Diff for: ‎chapter2/diffusion_code.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (ipykernel)
1212
# language: python

Diff for: ‎chapter2/heat_code.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
# extension: .py
77
# format_name: light
88
# format_version: '1.5'
9-
# jupytext_version: 1.13.8
9+
# jupytext_version: 1.14.1
1010
# kernelspec:
1111
# display_name: Python 3 (ipykernel)
1212
# language: python

0 commit comments

Comments
 (0)