remove deprecated stuff

Former-commit-id: da6fdea

notebooks/06-Animating_PM_Fields.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# **Animating Particle Mesh density fields**\n",
+    "\n",
+    "In this tutorial, we will animate the density field of a particle mesh simulation. We will use the `manim` library to create the animation. \n",
+    "\n",
+    "The density fields are created exactly like in the notebook [**05-MultiHost_PM.ipynb**](05-MultiHost_PM.ipynb) using the same script [**05-MultiHost_PM.py**](05-MultiHost_PM.py)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To run a multi-host simulation, you first need to **allocate a job** with `salloc`. This command requests resources on an HPC cluster.\n",
+    "\n",
+    "just like in notebook [**05-MultiHost_PM.ipynb**]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!salloc --account=XXX@a100 -C a100 --gres=gpu:8 --ntasks-per-node=8 --time=00:40:00  --cpus-per-task=8 --hint=nomultithread --qos=qos_gpu-dev --nodes=4 & "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**A few hours later**\n",
+    "\n",
+    "Use `!squeue -u $USER -o \"%i %D %b\"` to **check the JOB ID** and verify your resource allocation.\n",
+    "\n",
+    "In this example, we’ve been allocated **32 GPUs split across 4 nodes**.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!squeue -u $USER -o \"%i %D %b\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Unset the following environment variables, as they can cause issues when using JAX in a distributed setting:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "del os.environ['VSCODE_PROXY_URI']\n",
+    "del os.environ['NO_PROXY']\n",
+    "del os.environ['no_proxy']"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Checking Available Compute Resources\n",
+    "\n",
+    "Run the following command to initialize JAX distributed computing and display the devices available for this job:\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!srun --jobid=467745 -n 32 python -c \"import jax; jax.distributed.initialize(); print(jax.devices()) if jax.process_index() == 0 else None\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Multi-Host Simulation Script with Arguments (reminder)\n",
+    "\n",
+    "This script is nearly identical to the single-host version, with the main addition being the call to `jax.distributed.initialize()` at the start, enabling multi-host parallelism. Here’s a breakdown of the key arguments:\n",
+    "\n",
+    "- **`--pdims`** (`-p`): Specifies processor grid dimensions as two integers, like `16 2` for 16 x 2 device mesh (default is `[1, jax.devices()]`).\n",
+    "- **`--mesh_shape`** (`-m`): Defines the simulation mesh shape as three integers (default is `[512, 512, 512]`).\n",
+    "- **`--box_size`** (`-b`): Sets the physical box size of the simulation as three floating-point values, e.g., `1000. 1000. 1000.` (default is `[500.0, 500.0, 500.0]`).\n",
+    "- **`--halo_size`** (`-H`): Specifies the halo size for boundary overlap across nodes (default is `64`).\n",
+    "- **`--solver`** (`-s`): Chooses the ODE solver (`leapfrog` or `dopri8`). The `leapfrog` solver uses a fixed step size, while `dopri8` is an adaptive Runge-Kutta solver with a PID controller (default is `leapfrog`).\n",
+    "- **`--snapthots`** (`-st`) : Number of snapshots to save (warning, increases memory usage)\n",
+    "\n",
+    "### Running the Multi-Host Simulation Script\n",
+    "\n",
+    "To create a smooth animation, we need a series of closely spaced snapshots to capture the evolution of the density field over time. In this example, we set the number of snapshots to **10** to ensure smooth transitions in the animation.\n",
+    "\n",
+    "Using a larger number of GPUs helps process these snapshots efficiently, especially with a large simulation mesh or high-resolution data. This allows us to achieve both the desired snapshot frequency and the necessary simulation detail without excessive runtime.\n",
+    "\n",
+    "The command to run the multi-host simulation with these settings will look something like this:\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import subprocess\n",
+    "\n",
+    "# Define parameters as variables\n",
+    "jobid = \"467745\"\n",
+    "num_processes = 32\n",
+    "script_name = \"05-MultiHost_PM.py\"\n",
+    "mesh_shape = (1024, 1024, 1024)\n",
+    "box_size = (1000., 1000., 1000.)\n",
+    "halo_size = 128\n",
+    "solver = \"leapfrog\"\n",
+    "pdims = (16, 2)\n",
+    "snapshots = 8\n",
+    "\n",
+    "# Build the command as a list, incorporating variables\n",
+    "command = [\n",
+    "    \"srun\",\n",
+    "    f\"--jobid={jobid}\",\n",
+    "    \"-n\", str(num_processes),\n",
+    "    \"python\", script_name,\n",
+    "    \"--mesh_shape\", str(mesh_shape[0]), str(mesh_shape[1]), str(mesh_shape[2]),\n",
+    "    \"--box_size\", str(box_size[0]), str(box_size[1]), str(box_size[2]),\n",
+    "    \"--halo_size\", str(halo_size),\n",
+    "    \"-s\", solver,\n",
+    "    \"--pdims\", str(pdims[0]), str(pdims[1]),\n",
+    "    \"--snapshots\", str(snapshots)\n",
+    "]\n",
+    "\n",
+    "# Execute the command as a subprocess\n",
+    "subprocess.run(command)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Projecting the 3D Density Fields to 2D\n",
+    "\n",
+    "To visualize the 3D density fields in 2D, we need to create a projection:\n",
+    "\n",
+    "- **`project_to_2d` Function**: This function reduces the 3D array to 2D by summing over a portion of one axis.\n",
+    "  - We sum the top one-eighth of the data along the first axis to capture a slice of the density field.\n",
+    "\n",
+    "- **Creating 2D Projections**: Apply `project_to_2d` to each 3D field (`initial_conditions`, `lpt_displacements`, `ode_solution_0`, and `ode_solution_1`) to get 2D arrays that represent the density fields.\n",
+    "\n",
+    "### Applying the Magma Colormap\n",
+    "\n",
+    "To improve visualization, apply the \"magma\" colormap to each 2D projection:\n",
+    "\n",
+    "- **`apply_colormap` Function**: This function maps values in the 2D array to colors using the \"magma\" colormap.\n",
+    "  - First, normalize the array to the `[0, 1]` range.\n",
+    "  - Apply the colormap to create RGB images, which will be used for the animation.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from matplotlib import colormaps\n",
+    "\n",
+    "# Define a function to project the 3D field to 2D\n",
+    "def project_to_2d(field):\n",
+    "    sum_over = field.shape[0] // 8\n",
+    "    slicing = [slice(None)] * field.ndim\n",
+    "    slicing[0] = slice(None, sum_over)\n",
+    "    slicing = tuple(slicing)\n",
+    "\n",
+    "    return field[slicing].sum(axis=0)\n",
+    "\n",
+    "\n",
+    "def apply_colormap(array, cmap_name=\"magma\"):\n",
+    "    cmap = colormaps[cmap_name]\n",
+    "    normalized_array = (array - array.min()) / (array.max() - array.min())\n",
+    "    colored_image = cmap(normalized_array)[:, :, :3]  # Drop alpha channel for RGB\n",
+    "    return (colored_image * 255).astype(np.uint8)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Loading and Visualizing Results\n",
+    "\n",
+    "After running the multi-host simulation, we load the saved results from disk:\n",
+    "\n",
+    "- **`initial_conditions.npy`**: Initial conditions for the simulation.\n",
+    "- **`lpt_displacements.npy`**: Linear perturbation displacements.\n",
+    "- **`ode_solution_*.npy`** : Solutions from the ODE solver at each snapshot.\n",
+    "\n",
+    "We will now project the fields to 2D maps and apply the color map\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "initial_conditions = apply_colormap(project_to_2d(np.load('fields/initial_conditions.npy')))\n",
+    "lpt_displacements = apply_colormap(project_to_2d(np.load('fields/lpt_displacements.npy')))\n",
+    "ode_solutions = []\n",
+    "for i in range(8):\n",
+    "    ode_solutions.append(apply_colormap(project_to_2d(np.load(f'fields/ode_solution_{i}.npy'))))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Animating with Manim\n",
+    "\n",
+    "To create animations with `manim` in a Jupyter notebook, we start by configuring some settings to ensure the output displays correctly and without a background.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from manim import *\n",
+    "config.media_width = \"100%\"\n",
+    "config.verbosity = \"WARNING\"\n",
+    "config.background_color = \"#00000000\"  # Transparent background"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Defining the Animation in Manim\n",
+    "\n",
+    "This animation class, `FieldTransition`, smoothly transitions through the stages of the particle mesh density field evolution.\n",
+    "\n",
+    "- **Setup**: Each density field snapshot is loaded as an image and aligned for smooth transitions.\n",
+    "- **Animation Sequence**:\n",
+    "  - The animation begins with a fade-in of the initial conditions.\n",
+    "  - It then transitions through the stages in sequence, showing each snapshot of the density field evolution with brief pauses in between.\n",
+    "\n",
+    "To run the animation, execute `%manim -v WARNING -qm FieldTransition` to render it in the Jupyter Notebook.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Define the animation in Manim\n",
+    "class FieldTransition(Scene):\n",
+    "    def construct(self):\n",
+    "        init_conditions_img = ImageMobject(initial_conditions).scale(4)\n",
+    "        lpt_img = ImageMobject(lpt_displacements).scale(4)\n",
+    "        snapshots_imgs = [ImageMobject(sol).scale(4) for sol in ode_solutions]\n",
+    "\n",
+    "\n",
+    "        # Place the images on top of each other initially\n",
+    "        lpt_img.move_to(init_conditions_img)\n",
+    "        for img in snapshots_imgs:\n",
+    "            img.move_to(init_conditions_img)\n",
+    "\n",
+    "        # Show initial field and then transform between fields\n",
+    "        self.play(FadeIn(init_conditions_img))\n",
+    "        self.wait(0.2)\n",
+    "        self.play(Transform(init_conditions_img, lpt_img))\n",
+    "        self.wait(0.2)\n",
+    "        self.play(Transform(lpt_img, snapshots_imgs[0]))\n",
+    "        self.wait(0.2)\n",
+    "        for img1, img2 in zip(snapshots_imgs, snapshots_imgs[1:]):\n",
+    "            self.play(Transform(img1, img2))\n",
+    "            self.wait(0.2)\n",
+    "\n",
+    "%manim -v WARNING -qm -o anim.gif --format=gif FieldTransition "
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
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+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
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+ "nbformat_minor": 2
+}