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force atlas notebook changes to run in cugraph 23.08 container. #3656

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Merged
rapids-bot merged 16 commits into from
Jul 24, 2023
Merged

force atlas notebook changes to run in cugraph 23.08 container. #3656

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d072e38
changes to run with numpy 1.24 and beyond. Verified to run in 23.08 n…
acostadon Jun 12, 2023
62bb1bc
Merge remote-tracking branch 'upstream/branch-23.08' into fa_fix
acostadon Jun 22, 2023
6669bc8
Merge branch 'branch-23.08' into fa_fix
acostadon Jun 22, 2023
b904baa
Merge branch 'branch-23.08' into fa_fix
acostadon Jul 17, 2023
9d33a4f
add run instructions
acostadon Jul 17, 2023
b46922a
Merge remote-tracking branch 'upstream/branch-23.08' into fa_fix
acostadon Jul 17, 2023
342fff7
Merge branch 'fa_fix' of https://github.com/acostadon/cugraph into fa…
acostadon Jul 17, 2023
34e7368
works but still errors
acostadon Jul 18, 2023
594d595
now all the visualization is conditional.
acostadon Jul 18, 2023
3244da5
fixed some docs
acostadon Jul 18, 2023
9160ff7
Merge branch 'branch-23.08' into fa_fix
BradReesWork Jul 19, 2023
5ec4de3
fixed comments and added link and container info per review
acostadon Jul 19, 2023
85bbe0b
Merge branch 'fa_fix' of https://github.com/acostadon/cugraph into fa…
acostadon Jul 19, 2023
3ea10a4
revised visualization requirement text
acostadon Jul 19, 2023
96ee182
revised visualization again
acostadon Jul 19, 2023
3920bd3
revised visualization text
acostadon Jul 19, 2023
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169 changes: 94 additions & 75 deletions notebooks/algorithms/layout/Force-Atlas2.ipynb
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -9,6 +10,7 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -19,19 +21,14 @@
"| Author Credit | Date | Update | cuGraph Version | Test Hardware |\n",
"| -----------------|------------|------------------|-----------------|----------------|\n",
"| Hugo Linsenmaier | 11/16/2020 | created | 0.17 | GV100, CUDA 11.0\n",
"| Brad Rees | 01/11/2022 | tested / updated | 22.02 nightly | RTX A6000 CUDA 11.5\n",
"| Ralph Liu | 06/22/2022 | updated/tested | 22.08 | TV100, CUDA 11.5\n",
"| Don Acosta | 08/01/2022 | tested / updated | 22.08 nightly | DGX Tesla A100 CUDA 11.5 "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### This notebook will not currently run because there is a conflict between the version of CuPy required by cugraph (11.0) and the version supported in cuxfilter (7.8 to 10.0). Notebook will be updated when cuxfilter supports CuPy 11."
"| Brad Rees | 01/11/2022 | tested / updated | 22.02 nightly | RTX A6000 48GB CUDA 11.5\n",
"| Ralph Liu | 06/22/2022 | updated/tested | 22.08 nightly | V100, CUDA 11.5\n",
"| Don Acosta | 08/01/2022 | tested / updated | 22.08 nightly | DGX Tesla A100 CUDA 11.5 \n",
"| Don Acosta | 07/17/2023 | tested / updated | 23.08 nightly |RTX A6000 48GB CUDA 11.7 "
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -44,45 +41,20 @@
"See https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098679 for more details.\n",
"\n",
"\n",
"Please refer to the [documentation](https://docs.rapids.ai/api/cugraph/stable/api_docs/api/cugraph.force_atlas2.html) on how to use the different parameters.\n",
"\n",
"This library has some additional dependencies that need to be installed prior to running:\n",
"* Holoviews - provides "
"Please refer to the [documentation](https://docs.rapids.ai/api/cugraph/stable/api_docs/api/cugraph.force_atlas2.html) on how to use the different parameters.\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Import RAPIDS libraries\n",
"import cudf\n",
"import cugraph\n",
"import time"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Viz libraries\n",
"\n",
"from cuxfilter.charts.datashader.custom_extensions.graph_assets import calc_connected_edges\n",
"\n",
"import holoviews as hv\n",
"\n",
"from colorcet import fire\n",
"from datashader.bundling import directly_connect_edges, hammer_bundle\n",
"\n",
"from holoviews.operation.datashader import datashade, dynspread\n",
"from holoviews.operation import decimate\n",
"\n",
"from dask.distributed import Client"
]
},
{
"cell_type": "code",
"execution_count": null,
Expand All @@ -106,22 +78,7 @@
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Setup Viz\n",
"client = Client()\n",
"hv.notebook_extension('bokeh','matplotlib')\n",
"decimate.max_samples=20000\n",
"dynspread.threshold=0.01\n",
"datashade.cmap=fire[40:]\n",
"sz = dict(width=150,height=150)\n",
"%opts RGB [xaxis=None yaxis=None show_grid=False bgcolor=\"black\"]"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -134,11 +91,12 @@
"metadata": {},
"outputs": [],
"source": [
"G = netscience.get_graph()\n",
"G = netscience.get_graph(fetch=True)\n",
"G.number_of_nodes(), G.number_of_edges()"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -167,14 +125,31 @@
" verbose=False,\n",
" callback=None)\n",
"elapsed = time.time() - start\n",
"print(\"Cugraph time : \" + str(elapsed))"
"print(\"Cugraph time : \" + str(elapsed))\n",
"pos_gdf.head(5)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Visualize the graph\n",
"\n",
"The following section creates a visualization of the network using the locations generated by the Force Atlas algorithms. However, the following section is dependent on having the **cuxfilter** package installed. \n",
"\n",
"See the cuxfilter GitHub page for installation: https://github.com/rapidsai/cuxfilter. \n",
"\n",
"Alternatively, the package comes installed in the RAPIDS development Docker container. \n",
"See: https://hub.docker.com/r/rapidsai/rapidsai-dev/ \n",
"\n",
"<hr>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Convert a graph into paths suitable for datashading"
"Set up the visualization"
]
},
{
Expand All @@ -183,20 +158,54 @@
"metadata": {},
"outputs": [],
"source": [
"edges_gdf = netscience.get_edgelist()\n",
"import importlib.util\n",
"cux_spec = importlib.util.find_spec(\"cuxfilter\")\n",
"if cux_spec is None:\n",
" print(\"Visualization package is not available.\")\n",
"else:\n",
" from cuxfilter.charts.datashader.custom_extensions.graph_assets import calc_connected_edges\n",
" # Viz libraries\n",
" import holoviews as hv\n",
"\n",
" from colorcet import fire\n",
" from datashader.bundling import directly_connect_edges, hammer_bundle\n",
"\n",
" from holoviews.operation.datashader import datashade, dynspread\n",
" from holoviews.operation import decimate\n",
"\n",
"connected = calc_connected_edges(pos_gdf,\n",
" edges_gdf,\n",
" node_x=\"x\",\n",
" node_y=\"y\",\n",
" node_x_dtype=\"float32\",\n",
" node_y_dtype=\"float32\",\n",
" node_id=\"vertex\",\n",
" edge_source=\"src\",\n",
" edge_target=\"dst\",\n",
" edge_aggregate_col=None,\n",
" edge_render_type=\"direct\",\n",
" )"
" from dask.distributed import Client\n",
"\n",
" # Define the parameters \n",
" ITERATIONS=500\n",
" THETA=1.0\n",
" OPTIMIZE=True\n",
"\n",
" # Import a built-in dataset\n",
" from cugraph.experimental.datasets import netscience\n",
"\n",
" # Setup Viz\n",
" client = Client()\n",
" hv.notebook_extension('bokeh','matplotlib')\n",
" decimate.max_samples=20000\n",
" dynspread.threshold=0.01\n",
" datashade.cmap=fire[40:]\n",
" sz = dict(width=150,height=150)\n",
" %opts RGB [xaxis=None yaxis=None show_grid=False bgcolor=\"black\"]\n",
"\n",
" edges_gdf = netscience.get_edgelist()\n",
"\n",
" connected = calc_connected_edges(pos_gdf,\n",
" edges_gdf,\n",
" node_x=\"x\",\n",
" node_y=\"y\",\n",
" node_x_dtype=\"float32\",\n",
" node_y_dtype=\"float32\",\n",
" node_id=\"vertex\",\n",
" edge_source=\"src\",\n",
" edge_target=\"dst\",\n",
" edge_aggregate_col=None,\n",
" edge_render_type=\"direct\",\n",
" )\n"
]
},
{
Expand All @@ -206,23 +215,33 @@
"### Output"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%opts RGB [tools=[\"hover\"] width=800 height=800]\n",
"\n",
"r_direct = hv.Curve(connected, label=\"Direct\")\n",
"datashade(r_direct)"
"r_direct = None\n",
"if cux_spec is not None:\n",
" %opts RGB [tools=[\"hover\"] width=800 height=800]\n",
" r_direct = hv.Curve(connected, label=\"Direct\")\n",
" \n",
"r_direct"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"Copyright (c) 2020 - 2022, NVIDIA CORPORATION.\n",
"Copyright (c) 2020 - 2023, NVIDIA CORPORATION.\n",
"\n",
"Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0\n",
"\n",
Expand All @@ -246,7 +265,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.13"
"version": "3.10.12"
},
"vscode": {
"interpreter": {
Expand Down