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add installation of paraview to run on colab #1486

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merged 5 commits into from
Jan 7, 2025
Merged

add installation of paraview to run on colab #1486

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80a869b
add installation of paraview in environment to run on colab
AgnieszkaZaba Jan 3, 2025
0ffced2
Merge branch 'main' into paraview
AgnieszkaZaba Jan 3, 2025
cf9efc0
fix multiple imports on one line
AgnieszkaZaba Jan 3, 2025
3a91b9b
check ps2pdf only if not on Windows
AgnieszkaZaba Jan 4, 2025
57117fb
remove leftovers and add todo for binder
AgnieszkaZaba Jan 6, 2025
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195 changes: 117 additions & 78 deletions examples/PySDM_examples/_HOWTOs/paraview_hello_world.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -15,67 +15,105 @@
"id": "35dba30bf42bd326",
"metadata": {},
"source": [
"# TODO #1417\n",
"### TODO #1417 add description\n",
"### TODO #1490 fix installation on binder\n",
"For more informations about Paraview please refere to [Paraview documentation](https://docs.paraview.org/en/latest/Tutorials/SelfDirectedTutorial/)"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "93289adf665b5c7f",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:44:03.286946Z",
"start_time": "2024-12-24T09:44:03.263186Z"
"end_time": "2025-01-06T20:42:41.598955Z",
"start_time": "2025-01-06T20:42:41.591955Z"
}
},
"outputs": [],
"source": [
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" !pip --quiet install open-atmos-jupyter-utils\n",
" from open_atmos_jupyter_utils import pip_install_on_colab\n",
" pip_install_on_colab('PySDM-examples')"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "e3537b5faa81e11f",
"metadata": {
"ExecuteTime": {
"end_time": "2025-01-06T20:42:48.835403Z",
"start_time": "2025-01-06T20:42:42.286569Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"paraview version 5.13.1\n"
]
}
],
"outputs": [],
"execution_count": 4
"source": [
"import os\n",
"import subprocess\n",
"SUBPROCESS_ENV = os.environ.copy()\n",
"\n",
"if 'google.colab' in sys.modules:\n",
" !apt-get install -qq ghostscript\n",
" !wget -nv \"https://paraview.org/paraview-downloads/download.php?submit=Download&version=v5.13&type=binary&os=Linux&downloadFile=ParaView-5.13.1-egl-MPI-Linux-Python3.10-x86_64.tar.gz\" -O paraview.tar.gz\n",
" !tar xzf paraview.tar.gz\n",
" SUBPROCESS_ENV['PATH'] += ':' + subprocess.check_output(['bash', '-c', \"echo `pwd`/`dirname ParaView*/bin/pvpython`\"], text=True)[:-1]\n",
" \n",
" # check if Ghostscript's ps2pdf works\n",
" assert subprocess.check_call(['type', 'ps2pdf'], shell=True) == 0\n",
" \n",
"# check if Paraview's pvpython works\n",
"assert subprocess.check_call(['pvpython', '--version'], env=SUBPROCESS_ENV) == 0\n",
"assert subprocess.check_call(['pvpython', '-c', 'import paraview'], env=SUBPROCESS_ENV) == 0"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "ee889545",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:44:06.619086Z",
"start_time": "2024-12-24T09:44:03.326051Z"
"end_time": "2025-01-06T20:42:48.845075Z",
"start_time": "2025-01-06T20:42:48.842291Z"
}
},
"outputs": [],
"source": [
"from PySDM_examples.Arabas_et_al_2015 import Settings, SpinUp\n",
"from PySDM_examples.Szumowski_et_al_1998 import Simulation, Storage\n",
"from PySDM.exporters import VTKExporter\n",
"from PySDM_examples.utils import ProgBarController\n",
"from PySDM import products as PySDM_products\n",
"import subprocess\n",
"import glob\n",
"import platform"
],
"outputs": [],
"execution_count": 5
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "f0d2581f",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:44:06.635813Z",
"start_time": "2024-12-24T09:44:06.633731Z"
"end_time": "2025-01-06T20:42:49.673689Z",
"start_time": "2025-01-06T20:42:49.664256Z"
}
},
"outputs": [],
"source": [
"products = [\n",
" PySDM_products.EffectiveRadius(unit='um')\n",
"]"
],
"outputs": [],
"execution_count": 6
]
},
{
"cell_type": "markdown",
Expand All @@ -87,41 +125,41 @@
},
{
"cell_type": "code",
"execution_count": 5,
"id": "74c00944",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:45:09.597772Z",
"start_time": "2024-12-24T09:44:06.656496Z"
"end_time": "2025-01-06T20:43:31.937868Z",
"start_time": "2025-01-06T20:42:51.814553Z"
}
},
"source": [
"settings = Settings()\n",
"storage = Storage()\n",
"simulation = Simulation(settings, storage, SpinUp=SpinUp)\n",
"simulation.reinit(products)\n",
"\n",
"vtk_exporter = VTKExporter(path='.') \n",
"\n",
"simulation.run(ProgBarController(\"progress:\"), vtk_exporter=vtk_exporter)\n",
"vtk_exporter.write_pvd()"
],
"outputs": [
{
"data": {
"text/plain": [
"FloatProgress(value=0.0, description='progress:', max=1.0)"
],
"application/vnd.jupyter.widget-view+json": {
"model_id": "f9d581fdc60345ff804d5265fc156e1c",
"version_major": 2,
"version_minor": 0,
"model_id": "b4d654a45ee143bb86ba1784844568c0"
}
"version_minor": 0
},
"text/plain": [
"FloatProgress(value=0.0, description='progress:', max=1.0)"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"execution_count": 7
"source": [
"settings = Settings()\n",
"storage = Storage()\n",
"simulation = Simulation(settings, storage, SpinUp=SpinUp)\n",
"simulation.reinit(products)\n",
"\n",
"vtk_exporter = VTKExporter(path='.') \n",
"\n",
"simulation.run(ProgBarController(\"progress:\"), vtk_exporter=vtk_exporter)\n",
"vtk_exporter.write_pvd()"
]
},
{
"cell_type": "markdown",
Expand All @@ -133,34 +171,23 @@
},
{
"cell_type": "code",
"id": "94041d98fa896fba",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:45:09.607338Z",
"start_time": "2024-12-24T09:45:09.604990Z"
}
},
"source": [
"if 'google.colab' in sys.modules:\n",
" !apt-get -qq install python3-paraview\n",
" \n",
" # Workaround for a bug in Ubuntu package described here\n",
" # (https://discourse.paraview.org/t/paraview-error-while-loading-shared-libraries-libpdal-base-so-13-cannot-open-shared-object-file/14000);\n",
" # with solution taken from that comment: https://github.com/qgis/QGIS/issues/52433#issuecomment-1792285094.\n",
" ! if [ ! -f /usr/lib/libpdal_base.so.13 ]; then ln -s /usr/lib/libpdal_base.so.15 /usr/lib/libpdal_base.so.13; fi "
],
"outputs": [],
"execution_count": 8
},
{
"cell_type": "code",
"execution_count": 6,
"id": "2030d8e7",
"metadata": {
"ExecuteTime": {
"end_time": "2024-12-24T09:45:09.621096Z",
"start_time": "2024-12-24T09:45:09.615386Z"
"end_time": "2025-01-06T20:43:32.052989Z",
"start_time": "2025-01-06T20:43:32.046624Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting pvscript.py\n"
]
}
],
"source": [
"%%writefile pvscript.py\n",
"\n",
Expand Down Expand Up @@ -297,17 +324,7 @@
" Rasterize3Dgeometry= False,\n",
" GL2PSdepthsortmethod= 'BSP sorting (slow, best)',\n",
" )"
],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting pvscript.py\n"
]
}
],
"execution_count": 9
]
},
{
"cell_type": "markdown",
Expand All @@ -319,17 +336,29 @@
},
{
"cell_type": "code",
"execution_count": 7,
"id": "79477d3d",
"metadata": {
"ExecuteTime": {
"start_time": "2024-12-24T09:45:09.652231Z"
"end_time": "2025-01-06T20:44:22.171797Z",
"start_time": "2025-01-06T20:43:32.099529Z"
}
},
"source": [
"subprocess.run(['pvpython', '--force-offscreen-rendering', 'pvscript.py'], check=platform.system() != 'Windows')"
"outputs": [
{
"data": {
"text/plain": [
"CompletedProcess(args=['pvpython', '--force-offscreen-rendering', 'pvscript.py'], returncode=0)"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"execution_count": 10
"source": [
"subprocess.run(['pvpython', '--force-offscreen-rendering', 'pvscript.py'], check=platform.system() != 'Windows', env=SUBPROCESS_ENV)"
]
},
{
"cell_type": "markdown",
Expand All @@ -343,7 +372,12 @@
"cell_type": "code",
"execution_count": 8,
"id": "23e0cf61",
"metadata": {},
"metadata": {
"ExecuteTime": {
"end_time": "2025-01-06T20:44:32.623050Z",
"start_time": "2025-01-06T20:44:22.257021Z"
}
},
"outputs": [],
"source": [
"if platform.system() != 'Windows':\n",
Expand All @@ -354,9 +388,14 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"id": "9d3e4a35",
"metadata": {},
"metadata": {
"ExecuteTime": {
"end_time": "2025-01-06T20:42:10.669031Z",
"start_time": "2025-01-06T20:42:10.667667Z"
}
},
"outputs": [],
"source": []
}
Expand Down
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