From c2c5c533bcc48f35ae9e86fbb4cc5bbe0d6bf102 Mon Sep 17 00:00:00 2001
From: Milton Pividori <miltondp@gmail.com>
Date: Thu, 7 Sep 2023 23:11:25 -0600
Subject: [PATCH] ccc profiling: add notebook to test many samples with
 multiple CPUs

---
 .../17_00-2_CPUs-default-many_samples.ipynb   | 660 ++++++++++++++++
 ...01-2_CPUs-disable_numba-many_samples.ipynb | 739 ++++++++++++++++++
 ...ari_numba-many_samples-use_ari_numba.ipynb | 655 ++++++++++++++++
 .../py/17_00-2_CPUs-default-many_samples.py   | 103 +++
 ...17_01-2_CPUs-disable_numba-many_samples.py | 115 +++
 ...se_ari_numba-many_samples-use_ari_numba.py | 103 +++
 6 files changed, 2375 insertions(+)
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.ipynb
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.ipynb
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.ipynb
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/py/17_00-2_CPUs-default-many_samples.py
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/py/17_01-2_CPUs-disable_numba-many_samples.py
 create mode 100644 nbs/others/05_ccc_profiling/12_cm_optimized/py/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.py

diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.ipynb b/nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.ipynb
new file mode 100644
index 00000000..0b318692
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.ipynb
@@ -0,0 +1,660 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "88f4752f-914d-427a-9865-ff645ae4a61e",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001561,
+     "end_time": "2023-09-07T21:50:24.251694",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.250133",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Description"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "97b23c3d-292e-47ec-b76d-4b70f5653f4e",
+   "metadata": {
+    "papermill": {
+     "duration": 0.004786,
+     "end_time": "2023-09-07T21:50:24.266016",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.261230",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "Like `07_00` but using more CPU cores."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "274fca68-c617-481c-9615-dc6920ea24dc",
+   "metadata": {
+    "papermill": {
+     "duration": 0.002767,
+     "end_time": "2023-09-07T21:50:24.271162",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.268395",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Use multiple CPU core"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "48959a89-b227-4487-9b0e-d1499064d13b",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:24.277398Z",
+     "iopub.status.busy": "2023-09-07T21:50:24.277273Z",
+     "iopub.status.idle": "2023-09-07T21:50:24.282384Z",
+     "shell.execute_reply": "2023-09-07T21:50:24.282138Z"
+    },
+    "papermill": {
+     "duration": 0.009092,
+     "end_time": "2023-09-07T21:50:24.282970",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.273878",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: CM_N_JOBS=2\n",
+      "env: NUMBA_NUM_THREADS=2\n",
+      "env: MKL_NUM_THREADS=2\n",
+      "env: OPEN_BLAS_NUM_THREADS=2\n",
+      "env: NUMEXPR_NUM_THREADS=2\n",
+      "env: OMP_NUM_THREADS=2\n"
+     ]
+    }
+   ],
+   "source": [
+    "%env CM_N_JOBS=2\n",
+    "%env NUMBA_NUM_THREADS=2\n",
+    "%env MKL_NUM_THREADS=2\n",
+    "%env OPEN_BLAS_NUM_THREADS=2\n",
+    "%env NUMEXPR_NUM_THREADS=2\n",
+    "%env OMP_NUM_THREADS=2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "325cb06a-df7f-43e8-be3e-f704aaf015b0",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001104,
+     "end_time": "2023-09-07T21:50:24.285235",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.284131",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Remove pycache dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "73f954a6-1776-4b92-bd0e-fc3caf5df081",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:24.288343Z",
+     "iopub.status.busy": "2023-09-07T21:50:24.288276Z",
+     "iopub.status.idle": "2023-09-07T21:50:24.471706Z",
+     "shell.execute_reply": "2023-09-07T21:50:24.471438Z"
+    },
+    "papermill": {
+     "duration": 0.185755,
+     "end_time": "2023-09-07T21:50:24.472387",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.286632",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code\n"
+     ]
+    }
+   ],
+   "source": [
+    "!echo ${CODE_DIR}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d17492bb-34fe-4c34-a693-419180ba068e",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:24.483752Z",
+     "iopub.status.busy": "2023-09-07T21:50:24.483680Z",
+     "iopub.status.idle": "2023-09-07T21:50:24.673641Z",
+     "shell.execute_reply": "2023-09-07T21:50:24.673440Z"
+    },
+    "papermill": {
+     "duration": 0.200674,
+     "end_time": "2023-09-07T21:50:24.674313",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.473639",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code/libs/ccc/coef/__pycache__\n",
+      "/opt/code/libs/ccc/pytorch/__pycache__\n",
+      "/opt/code/libs/ccc/scipy/__pycache__\n",
+      "/opt/code/libs/ccc/utils/__pycache__\n",
+      "/opt/code/libs/ccc/__pycache__\n",
+      "/opt/code/libs/ccc/sklearn/__pycache__\n"
+     ]
+    }
+   ],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "5683e330-1782-43b3-bb78-255198f03620",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:24.685783Z",
+     "iopub.status.busy": "2023-09-07T21:50:24.685672Z",
+     "iopub.status.idle": "2023-09-07T21:50:24.876601Z",
+     "shell.execute_reply": "2023-09-07T21:50:24.876228Z"
+    },
+    "papermill": {
+     "duration": 0.201811,
+     "end_time": "2023-09-07T21:50:24.877421",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.675610",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -prune -exec rm -rf {} \\;"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "5cf4ce29-d611-4fc8-8880-293c09e5ab9a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:24.889188Z",
+     "iopub.status.busy": "2023-09-07T21:50:24.889097Z",
+     "iopub.status.idle": "2023-09-07T21:50:25.077437Z",
+     "shell.execute_reply": "2023-09-07T21:50:25.077119Z"
+    },
+    "papermill": {
+     "duration": 0.199437,
+     "end_time": "2023-09-07T21:50:25.078312",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:24.878875",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35a04385-a901-4726-82a6-a01f16281efe",
+   "metadata": {
+    "papermill": {
+     "duration": 0.009595,
+     "end_time": "2023-09-07T21:50:25.089323",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:25.079728",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Modules"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "a75c4496-d379-4668-905d-0e9136981f0c",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:25.097159Z",
+     "iopub.status.busy": "2023-09-07T21:50:25.096955Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.783808Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.783556Z"
+    },
+    "papermill": {
+     "duration": 3.690496,
+     "end_time": "2023-09-07T21:50:28.784522",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:25.094026",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from ccc.coef import ccc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "1a58ccf8-1bf5-4177-9b06-944a0d57655a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.796329Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.796236Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.800266Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.800135Z"
+    },
+    "papermill": {
+     "duration": 0.014803,
+     "end_time": "2023-09-07T21:50:28.800794",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.785991",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.20454545454545456"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# let numba compile all the code before profiling\n",
+    "ccc(np.random.rand(10), np.random.rand(10))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2c92a1ad-2fc9-4a16-a5f8-fce685246996",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001156,
+     "end_time": "2023-09-07T21:50:28.803229",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.802073",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "2316ffcd-a6e4-453f-bb52-779685c5c5bf",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.808468Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.808398Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.809674Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.809542Z"
+    },
+    "papermill": {
+     "duration": 0.004923,
+     "end_time": "2023-09-07T21:50:28.810233",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.805310",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "n_genes, n_samples = 10, 30000"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "b2f92fb1-113d-479b-8bbf-2be229e26e8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.813938Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.813857Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.815118Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.814988Z"
+    },
+    "papermill": {
+     "duration": 0.004026,
+     "end_time": "2023-09-07T21:50:28.815525",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.811499",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "np.random.seed(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "63638c0b-b436-48a9-93e0-db2adb939a61",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.821382Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.821248Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.823688Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.823563Z"
+    },
+    "papermill": {
+     "duration": 0.004618,
+     "end_time": "2023-09-07T21:50:28.824154",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.819536",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "data = np.random.rand(n_genes, n_samples)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "808017ed-9a8a-4bf7-a3dd-42317a39ce8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.827384Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.827128Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.829441Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.829254Z"
+    },
+    "papermill": {
+     "duration": 0.004407,
+     "end_time": "2023-09-07T21:50:28.829888",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.825481",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(10, 30000)"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data.shape"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "716e4219-cad5-453b-8331-47d310689e03",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001246,
+     "end_time": "2023-09-07T21:50:28.832473",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.831227",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With default `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "67807856-f337-4c6e-ae31-cd306577a314",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.835528Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.835388Z",
+     "iopub.status.idle": "2023-09-07T21:50:28.837187Z",
+     "shell.execute_reply": "2023-09-07T21:50:28.837009Z"
+    },
+    "papermill": {
+     "duration": 0.003781,
+     "end_time": "2023-09-07T21:50:28.837599",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.833818",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 10 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "2965a695-5c0c-4e9e-8435-dcbfa610eb81",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:50:28.840637Z",
+     "iopub.status.busy": "2023-09-07T21:50:28.840500Z",
+     "iopub.status.idle": "2023-09-07T21:51:18.270578Z",
+     "shell.execute_reply": "2023-09-07T21:51:18.270078Z"
+    },
+    "papermill": {
+     "duration": 49.433011,
+     "end_time": "2023-09-07T21:51:18.271967",
+     "exception": false,
+     "start_time": "2023-09-07T21:50:28.838956",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "3.07 s ± 1.62 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "025974ff-06d4-4d82-9b05-03f7a84d7211",
+   "metadata": {
+    "papermill": {
+     "duration": 0.00249,
+     "end_time": "2023-09-07T21:51:21.366393",
+     "exception": false,
+     "start_time": "2023-09-07T21:51:21.363903",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With reduced `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "c20c4ecf-8060-495e-92b0-eb8e0d0dfbf3",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:51:21.371305Z",
+     "iopub.status.busy": "2023-09-07T21:51:21.371197Z",
+     "iopub.status.idle": "2023-09-07T21:51:21.373116Z",
+     "shell.execute_reply": "2023-09-07T21:51:21.372833Z"
+    },
+    "papermill": {
+     "duration": 0.004744,
+     "end_time": "2023-09-07T21:51:21.373590",
+     "exception": false,
+     "start_time": "2023-09-07T21:51:21.368846",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 5 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "11259d8c-3bf3-4299-b47b-211556c3bc08",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-07T21:51:21.376796Z",
+     "iopub.status.busy": "2023-09-07T21:51:21.376723Z",
+     "iopub.status.idle": "2023-09-07T21:51:28.388036Z",
+     "shell.execute_reply": "2023-09-07T21:51:28.387633Z"
+    },
+    "papermill": {
+     "duration": 7.013668,
+     "end_time": "2023-09-07T21:51:28.388694",
+     "exception": false,
+     "start_time": "2023-09-07T21:51:21.375026",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "438 ms ± 219 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e2556204-1c10-4e01-8c6c-ea63ddb37530",
+   "metadata": {
+    "papermill": {
+     "duration": 0.005575,
+     "end_time": "2023-09-07T21:51:28.851104",
+     "exception": false,
+     "start_time": "2023-09-07T21:51:28.845529",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "all,-execution,-papermill,-trusted",
+   "notebook_metadata_filter": "-jupytext.text_representation.jupytext_version",
+   "text_representation": {
+    "extension": ".py",
+    "format_name": "percent",
+    "format_version": "1.3"
+   }
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "papermill": {
+   "default_parameters": {},
+   "duration": 65.47885,
+   "end_time": "2023-09-07T21:51:29.069018",
+   "environment_variables": {},
+   "exception": null,
+   "input_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.ipynb",
+   "output_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_00-2_CPUs-default-many_samples.run.ipynb",
+   "parameters": {},
+   "start_time": "2023-09-07T21:50:23.590168",
+   "version": "2.3.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.ipynb b/nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.ipynb
new file mode 100644
index 00000000..a832caae
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.ipynb
@@ -0,0 +1,739 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4ac1bef9-a7b7-468d-9b3f-24a591c70af5",
+   "metadata": {
+    "papermill": {
+     "duration": 0.005746,
+     "end_time": "2023-09-08T05:00:53.948601",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.942855",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Description"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d5dbb153-96e6-45d9-b6b9-e5d15ee1ec7f",
+   "metadata": {
+    "papermill": {
+     "duration": 0.003163,
+     "end_time": "2023-09-08T05:00:53.954950",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.951787",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "Like `07_01` but using more CPU cores."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a2ba0f9f-aa06-40d0-becc-b9f347f44336",
+   "metadata": {
+    "papermill": {
+     "duration": 0.002838,
+     "end_time": "2023-09-08T05:00:53.960306",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.957468",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Use multiple CPU core"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "70532b5b-b477-41f9-b29e-899ed234b1ce",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:53.966295Z",
+     "iopub.status.busy": "2023-09-08T05:00:53.966162Z",
+     "iopub.status.idle": "2023-09-08T05:00:53.971655Z",
+     "shell.execute_reply": "2023-09-08T05:00:53.971399Z"
+    },
+    "papermill": {
+     "duration": 0.009689,
+     "end_time": "2023-09-08T05:00:53.972568",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.962879",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: CM_N_JOBS=2\n",
+      "env: NUMBA_NUM_THREADS=2\n",
+      "env: MKL_NUM_THREADS=2\n",
+      "env: OPEN_BLAS_NUM_THREADS=2\n",
+      "env: NUMEXPR_NUM_THREADS=2\n",
+      "env: OMP_NUM_THREADS=2\n"
+     ]
+    }
+   ],
+   "source": [
+    "%env CM_N_JOBS=2\n",
+    "%env NUMBA_NUM_THREADS=2\n",
+    "%env MKL_NUM_THREADS=2\n",
+    "%env OPEN_BLAS_NUM_THREADS=2\n",
+    "%env NUMEXPR_NUM_THREADS=2\n",
+    "%env OMP_NUM_THREADS=2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "874ffd00-afe1-4b51-bb22-350cbd9479f1",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001613,
+     "end_time": "2023-09-08T05:00:53.976349",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.974736",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Disable numba"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "502fe9ff-d27d-43bd-aa37-73edf7ba4f24",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:53.980252Z",
+     "iopub.status.busy": "2023-09-08T05:00:53.980203Z",
+     "iopub.status.idle": "2023-09-08T05:00:53.981834Z",
+     "shell.execute_reply": "2023-09-08T05:00:53.981690Z"
+    },
+    "papermill": {
+     "duration": 0.004234,
+     "end_time": "2023-09-08T05:00:53.982334",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.978100",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: NUMBA_DISABLE_JIT=1\n"
+     ]
+    }
+   ],
+   "source": [
+    "%env NUMBA_DISABLE_JIT=1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "325cb06a-df7f-43e8-be3e-f704aaf015b0",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001163,
+     "end_time": "2023-09-08T05:00:53.984723",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.983560",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Remove pycache dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "73f954a6-1776-4b92-bd0e-fc3caf5df081",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:53.987333Z",
+     "iopub.status.busy": "2023-09-08T05:00:53.987241Z",
+     "iopub.status.idle": "2023-09-08T05:00:54.175946Z",
+     "shell.execute_reply": "2023-09-08T05:00:54.175076Z"
+    },
+    "papermill": {
+     "duration": 0.192744,
+     "end_time": "2023-09-08T05:00:54.178662",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:53.985918",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "!echo ${CODE_DIR}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "d17492bb-34fe-4c34-a693-419180ba068e",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:54.196166Z",
+     "iopub.status.busy": "2023-09-08T05:00:54.195873Z",
+     "iopub.status.idle": "2023-09-08T05:00:54.404869Z",
+     "shell.execute_reply": "2023-09-08T05:00:54.403939Z"
+    },
+    "papermill": {
+     "duration": 0.223311,
+     "end_time": "2023-09-08T05:00:54.407528",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.184217",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code/libs/ccc/coef/__pycache__\r\n",
+      "/opt/code/libs/ccc/pytorch/__pycache__\r\n",
+      "/opt/code/libs/ccc/scipy/__pycache__\r\n",
+      "/opt/code/libs/ccc/utils/__pycache__\r\n",
+      "/opt/code/libs/ccc/__pycache__\r\n",
+      "/opt/code/libs/ccc/sklearn/__pycache__\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "5683e330-1782-43b3-bb78-255198f03620",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:54.424215Z",
+     "iopub.status.busy": "2023-09-08T05:00:54.423812Z",
+     "iopub.status.idle": "2023-09-08T05:00:54.632666Z",
+     "shell.execute_reply": "2023-09-08T05:00:54.631336Z"
+    },
+    "papermill": {
+     "duration": 0.221592,
+     "end_time": "2023-09-08T05:00:54.635797",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.414205",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -prune -exec rm -rf {} \\;"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "5cf4ce29-d611-4fc8-8880-293c09e5ab9a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:54.654315Z",
+     "iopub.status.busy": "2023-09-08T05:00:54.653925Z",
+     "iopub.status.idle": "2023-09-08T05:00:54.859654Z",
+     "shell.execute_reply": "2023-09-08T05:00:54.859102Z"
+    },
+    "papermill": {
+     "duration": 0.218446,
+     "end_time": "2023-09-08T05:00:54.861009",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.642563",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35a04385-a901-4726-82a6-a01f16281efe",
+   "metadata": {
+    "papermill": {
+     "duration": 0.009754,
+     "end_time": "2023-09-08T05:00:54.874289",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.864535",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Modules"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "a75c4496-d379-4668-905d-0e9136981f0c",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:54.881414Z",
+     "iopub.status.busy": "2023-09-08T05:00:54.881172Z",
+     "iopub.status.idle": "2023-09-08T05:00:54.995178Z",
+     "shell.execute_reply": "2023-09-08T05:00:54.994989Z"
+    },
+    "papermill": {
+     "duration": 0.11861,
+     "end_time": "2023-09-08T05:00:54.995954",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.877344",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from ccc.coef import ccc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "1a58ccf8-1bf5-4177-9b06-944a0d57655a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:54.999234Z",
+     "iopub.status.busy": "2023-09-08T05:00:54.999177Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.003427Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.003294Z"
+    },
+    "papermill": {
+     "duration": 0.006394,
+     "end_time": "2023-09-08T05:00:55.003896",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:54.997502",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.20454545454545456"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# let numba compile all the code before profiling\n",
+    "ccc(np.random.rand(10), np.random.rand(10))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2c92a1ad-2fc9-4a16-a5f8-fce685246996",
+   "metadata": {
+    "papermill": {
+     "duration": 0.00129,
+     "end_time": "2023-09-08T05:00:55.006717",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.005427",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "2316ffcd-a6e4-453f-bb52-779685c5c5bf",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.009652Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.009583Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.010906Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.010771Z"
+    },
+    "papermill": {
+     "duration": 0.003378,
+     "end_time": "2023-09-08T05:00:55.011447",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.008069",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "n_genes, n_samples = 10, 30000"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "b2f92fb1-113d-479b-8bbf-2be229e26e8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.014434Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.014326Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.015556Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.015414Z"
+    },
+    "papermill": {
+     "duration": 0.003101,
+     "end_time": "2023-09-08T05:00:55.015931",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.012830",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "np.random.seed(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "63638c0b-b436-48a9-93e0-db2adb939a61",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.018963Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.018855Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.021241Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.021109Z"
+    },
+    "papermill": {
+     "duration": 0.004286,
+     "end_time": "2023-09-08T05:00:55.021621",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.017335",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "data = np.random.rand(n_genes, n_samples)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "808017ed-9a8a-4bf7-a3dd-42317a39ce8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.024584Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.024472Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.026043Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.025903Z"
+    },
+    "papermill": {
+     "duration": 0.003521,
+     "end_time": "2023-09-08T05:00:55.026504",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.022983",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(10, 30000)"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data.shape"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "716e4219-cad5-453b-8331-47d310689e03",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001292,
+     "end_time": "2023-09-08T05:00:55.029223",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.027931",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With default `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "67807856-f337-4c6e-ae31-cd306577a314",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.032221Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.032157Z",
+     "iopub.status.idle": "2023-09-08T05:00:55.033514Z",
+     "shell.execute_reply": "2023-09-08T05:00:55.033383Z"
+    },
+    "papermill": {
+     "duration": 0.003351,
+     "end_time": "2023-09-08T05:00:55.033936",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.030585",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 10 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "2965a695-5c0c-4e9e-8435-dcbfa610eb81",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:00:55.037170Z",
+     "iopub.status.busy": "2023-09-08T05:00:55.037067Z",
+     "iopub.status.idle": "2023-09-08T05:01:33.383384Z",
+     "shell.execute_reply": "2023-09-08T05:01:33.383211Z"
+    },
+    "papermill": {
+     "duration": 38.350271,
+     "end_time": "2023-09-08T05:01:33.385683",
+     "exception": false,
+     "start_time": "2023-09-08T05:00:55.035412",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2.39 s ± 17.4 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cd74d8b8-517c-42cf-9dbf-27474b2c3822",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001501,
+     "end_time": "2023-09-08T05:01:33.397834",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:33.396333",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "These results are just slightly worse than the numba-compiled version (notebook `07`)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "025974ff-06d4-4d82-9b05-03f7a84d7211",
+   "metadata": {
+    "papermill": {
+     "duration": 0.0014,
+     "end_time": "2023-09-08T05:01:33.400682",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:33.399282",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With reduced `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "c20c4ecf-8060-495e-92b0-eb8e0d0dfbf3",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:01:33.404036Z",
+     "iopub.status.busy": "2023-09-08T05:01:33.403948Z",
+     "iopub.status.idle": "2023-09-08T05:01:33.405983Z",
+     "shell.execute_reply": "2023-09-08T05:01:33.405660Z"
+    },
+    "papermill": {
+     "duration": 0.004442,
+     "end_time": "2023-09-08T05:01:33.406560",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:33.402118",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 5 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "11259d8c-3bf3-4299-b47b-211556c3bc08",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:01:33.409870Z",
+     "iopub.status.busy": "2023-09-08T05:01:33.409812Z",
+     "iopub.status.idle": "2023-09-08T05:01:38.276121Z",
+     "shell.execute_reply": "2023-09-08T05:01:38.275871Z"
+    },
+    "papermill": {
+     "duration": 4.868725,
+     "end_time": "2023-09-08T05:01:38.276808",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:33.408083",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "303 ms ± 3.08 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ba154ea5-5301-4fd4-8fc7-71534435a2a5",
+   "metadata": {
+    "papermill": {
+     "duration": 0.009806,
+     "end_time": "2023-09-08T05:01:38.288275",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:38.278469",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "These results are slightly better than the numba-compiled version (notebook `07`), which is surprising. In the future, it would be interesting to disable threading here to get accurate profiling results to debug this issue."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e2556204-1c10-4e01-8c6c-ea63ddb37530",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001449,
+     "end_time": "2023-09-08T05:01:38.291365",
+     "exception": false,
+     "start_time": "2023-09-08T05:01:38.289916",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "all,-execution,-papermill,-trusted",
+   "notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "papermill": {
+   "default_parameters": {},
+   "duration": 45.129102,
+   "end_time": "2023-09-08T05:01:38.408234",
+   "environment_variables": {},
+   "exception": null,
+   "input_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.ipynb",
+   "output_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_01-2_CPUs-disable_numba-many_samples.run.ipynb",
+   "parameters": {},
+   "start_time": "2023-09-08T05:00:53.279132",
+   "version": "2.3.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.ipynb b/nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.ipynb
new file mode 100644
index 00000000..edb7f9c9
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.ipynb
@@ -0,0 +1,655 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "d08e8972-7897-4568-a2cc-a88e60f35329",
+   "metadata": {
+    "papermill": {
+     "duration": 0.005433,
+     "end_time": "2023-09-08T05:03:10.035747",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.030314",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Description"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1c0e6677-6256-4ba6-ba2c-ddca92a31e5c",
+   "metadata": {
+    "papermill": {
+     "duration": 0.005768,
+     "end_time": "2023-09-08T05:03:10.051408",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.045640",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "Like `07_02` but using more CPU cores."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fb686b34-1c32-4b3e-bf15-4d95303369d6",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001439,
+     "end_time": "2023-09-08T05:03:10.059273",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.057834",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Use multiple CPU core"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "bda7d08f-862b-4843-97e5-a5c648c05480",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.064850Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.064568Z",
+     "iopub.status.idle": "2023-09-08T05:03:10.071664Z",
+     "shell.execute_reply": "2023-09-08T05:03:10.071151Z"
+    },
+    "papermill": {
+     "duration": 0.011119,
+     "end_time": "2023-09-08T05:03:10.072288",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.061169",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: CM_N_JOBS=2\n",
+      "env: NUMBA_NUM_THREADS=2\n",
+      "env: MKL_NUM_THREADS=2\n",
+      "env: OPEN_BLAS_NUM_THREADS=2\n",
+      "env: NUMEXPR_NUM_THREADS=2\n",
+      "env: OMP_NUM_THREADS=2\n"
+     ]
+    }
+   ],
+   "source": [
+    "%env CM_N_JOBS=2\n",
+    "%env NUMBA_NUM_THREADS=2\n",
+    "%env MKL_NUM_THREADS=2\n",
+    "%env OPEN_BLAS_NUM_THREADS=2\n",
+    "%env NUMEXPR_NUM_THREADS=2\n",
+    "%env OMP_NUM_THREADS=2"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "325cb06a-df7f-43e8-be3e-f704aaf015b0",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001666,
+     "end_time": "2023-09-08T05:03:10.075218",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.073552",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Remove pycache dir"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "73f954a6-1776-4b92-bd0e-fc3caf5df081",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.080278Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.080067Z",
+     "iopub.status.idle": "2023-09-08T05:03:10.272483Z",
+     "shell.execute_reply": "2023-09-08T05:03:10.271593Z"
+    },
+    "papermill": {
+     "duration": 0.197838,
+     "end_time": "2023-09-08T05:03:10.275353",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.077515",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "!echo ${CODE_DIR}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d17492bb-34fe-4c34-a693-419180ba068e",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.293997Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.293500Z",
+     "iopub.status.idle": "2023-09-08T05:03:10.497334Z",
+     "shell.execute_reply": "2023-09-08T05:03:10.496046Z"
+    },
+    "papermill": {
+     "duration": 0.218401,
+     "end_time": "2023-09-08T05:03:10.500077",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.281676",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/opt/code/libs/ccc/coef/__pycache__\r\n",
+      "/opt/code/libs/ccc/pytorch/__pycache__\r\n",
+      "/opt/code/libs/ccc/scipy/__pycache__\r\n",
+      "/opt/code/libs/ccc/utils/__pycache__\r\n",
+      "/opt/code/libs/ccc/__pycache__\r\n",
+      "/opt/code/libs/ccc/sklearn/__pycache__\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "5683e330-1782-43b3-bb78-255198f03620",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.519179Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.518731Z",
+     "iopub.status.idle": "2023-09-08T05:03:10.726062Z",
+     "shell.execute_reply": "2023-09-08T05:03:10.724984Z"
+    },
+    "papermill": {
+     "duration": 0.222731,
+     "end_time": "2023-09-08T05:03:10.729457",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.506726",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -prune -exec rm -rf {} \\;"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "5cf4ce29-d611-4fc8-8880-293c09e5ab9a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.746661Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.746461Z",
+     "iopub.status.idle": "2023-09-08T05:03:10.947894Z",
+     "shell.execute_reply": "2023-09-08T05:03:10.946701Z"
+    },
+    "papermill": {
+     "duration": 0.215285,
+     "end_time": "2023-09-08T05:03:10.950772",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.735487",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "!find ${CODE_DIR} -regex '^.*\\(__pycache__\\)$' -print"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35a04385-a901-4726-82a6-a01f16281efe",
+   "metadata": {
+    "papermill": {
+     "duration": 0.009972,
+     "end_time": "2023-09-08T05:03:10.967145",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.957173",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Modules"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "a75c4496-d379-4668-905d-0e9136981f0c",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:10.979172Z",
+     "iopub.status.busy": "2023-09-08T05:03:10.979005Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.684587Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.684201Z"
+    },
+    "papermill": {
+     "duration": 3.711968,
+     "end_time": "2023-09-08T05:03:14.685357",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:10.973389",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "from ccc.coef import ccc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "1a58ccf8-1bf5-4177-9b06-944a0d57655a",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.688456Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.688396Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.692601Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.692408Z"
+    },
+    "papermill": {
+     "duration": 0.006224,
+     "end_time": "2023-09-08T05:03:14.693029",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.686805",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "0.0"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# let numba compile all the code before profiling\n",
+    "ccc(np.random.rand(10), np.random.rand(10))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2c92a1ad-2fc9-4a16-a5f8-fce685246996",
+   "metadata": {
+    "papermill": {
+     "duration": 0.00134,
+     "end_time": "2023-09-08T05:03:14.695691",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.694351",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# Data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "2316ffcd-a6e4-453f-bb52-779685c5c5bf",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.698676Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.698544Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.699967Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.699784Z"
+    },
+    "papermill": {
+     "duration": 0.003378,
+     "end_time": "2023-09-08T05:03:14.700373",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.696995",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "n_genes, n_samples = 10, 30000"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "b2f92fb1-113d-479b-8bbf-2be229e26e8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.703201Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.703150Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.704507Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.704332Z"
+    },
+    "papermill": {
+     "duration": 0.003208,
+     "end_time": "2023-09-08T05:03:14.704908",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.701700",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "np.random.seed(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "63638c0b-b436-48a9-93e0-db2adb939a61",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.707778Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.707680Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.710246Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.710059Z"
+    },
+    "papermill": {
+     "duration": 0.004443,
+     "end_time": "2023-09-08T05:03:14.710664",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.706221",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "data = np.random.rand(n_genes, n_samples)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "808017ed-9a8a-4bf7-a3dd-42317a39ce8f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.713555Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.713440Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.715163Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.714996Z"
+    },
+    "papermill": {
+     "duration": 0.003608,
+     "end_time": "2023-09-08T05:03:14.715576",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.711968",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(10, 30000)"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "data.shape"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "716e4219-cad5-453b-8331-47d310689e03",
+   "metadata": {
+    "papermill": {
+     "duration": 0.001264,
+     "end_time": "2023-09-08T05:03:14.718203",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.716939",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With default `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "67807856-f337-4c6e-ae31-cd306577a314",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.721070Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.720978Z",
+     "iopub.status.idle": "2023-09-08T05:03:14.722492Z",
+     "shell.execute_reply": "2023-09-08T05:03:14.722312Z"
+    },
+    "papermill": {
+     "duration": 0.003352,
+     "end_time": "2023-09-08T05:03:14.722854",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.719502",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 10 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, use_ari_numba=True, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "2965a695-5c0c-4e9e-8435-dcbfa610eb81",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:03:14.725798Z",
+     "iopub.status.busy": "2023-09-08T05:03:14.725724Z",
+     "iopub.status.idle": "2023-09-08T05:04:04.880078Z",
+     "shell.execute_reply": "2023-09-08T05:04:04.879625Z"
+    },
+    "papermill": {
+     "duration": 50.157331,
+     "end_time": "2023-09-08T05:04:04.881548",
+     "exception": false,
+     "start_time": "2023-09-08T05:03:14.724217",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "3.07 s ± 1.43 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "025974ff-06d4-4d82-9b05-03f7a84d7211",
+   "metadata": {
+    "papermill": {
+     "duration": 0.002933,
+     "end_time": "2023-09-08T05:04:04.893577",
+     "exception": false,
+     "start_time": "2023-09-08T05:04:04.890644",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "source": [
+    "# With reduced `internal_n_clusters`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "c20c4ecf-8060-495e-92b0-eb8e0d0dfbf3",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:04:04.897237Z",
+     "iopub.status.busy": "2023-09-08T05:04:04.897120Z",
+     "iopub.status.idle": "2023-09-08T05:04:04.899551Z",
+     "shell.execute_reply": "2023-09-08T05:04:04.899153Z"
+    },
+    "papermill": {
+     "duration": 0.005369,
+     "end_time": "2023-09-08T05:04:04.900359",
+     "exception": false,
+     "start_time": "2023-09-08T05:04:04.894990",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def func():\n",
+    "    n_clust = list(range(2, 5 + 1))\n",
+    "    return ccc(data, internal_n_clusters=n_clust, use_ari_numba=True, n_jobs=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "11259d8c-3bf3-4299-b47b-211556c3bc08",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2023-09-08T05:04:04.905493Z",
+     "iopub.status.busy": "2023-09-08T05:04:04.905347Z",
+     "iopub.status.idle": "2023-09-08T05:04:11.910573Z",
+     "shell.execute_reply": "2023-09-08T05:04:11.910156Z"
+    },
+    "papermill": {
+     "duration": 7.008557,
+     "end_time": "2023-09-08T05:04:11.911267",
+     "exception": false,
+     "start_time": "2023-09-08T05:04:04.902710",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "437 ms ± 631 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%timeit func()\n",
+    "func()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e2556204-1c10-4e01-8c6c-ea63ddb37530",
+   "metadata": {
+    "papermill": {
+     "duration": 0.009712,
+     "end_time": "2023-09-08T05:04:11.922464",
+     "exception": false,
+     "start_time": "2023-09-08T05:04:11.912752",
+     "status": "completed"
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "all,-execution,-papermill,-trusted",
+   "notebook_metadata_filter": "-jupytext.text_representation.jupytext_version"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  },
+  "papermill": {
+   "default_parameters": {},
+   "duration": 62.77804,
+   "end_time": "2023-09-08T05:04:12.142929",
+   "environment_variables": {},
+   "exception": null,
+   "input_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.ipynb",
+   "output_path": "nbs/others/05_ccc_profiling/12_cm_optimized/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.run.ipynb",
+   "parameters": {},
+   "start_time": "2023-09-08T05:03:09.364889",
+   "version": "2.3.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_00-2_CPUs-default-many_samples.py b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_00-2_CPUs-default-many_samples.py
new file mode 100644
index 00000000..d3af0d04
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_00-2_CPUs-default-many_samples.py
@@ -0,0 +1,103 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: all,-execution,-papermill,-trusted
+#     notebook_metadata_filter: -jupytext.text_representation.jupytext_version
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# %% [markdown] tags=[]
+# # Description
+
+# %% [markdown] tags=[]
+# Like `07_00` but using more CPU cores.
+
+# %% [markdown] tags=[]
+# # Use multiple CPU core
+
+# %% tags=[]
+# %env CM_N_JOBS=2
+# %env NUMBA_NUM_THREADS=2
+# %env MKL_NUM_THREADS=2
+# %env OPEN_BLAS_NUM_THREADS=2
+# %env NUMEXPR_NUM_THREADS=2
+# %env OMP_NUM_THREADS=2
+
+# %% [markdown] tags=[]
+# # Remove pycache dir
+
+# %% tags=[]
+# !echo ${CODE_DIR}
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -prune -exec rm -rf {} \;
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% [markdown] tags=[]
+# # Modules
+
+# %% tags=[]
+import numpy as np
+
+from ccc.coef import ccc
+
+# %% tags=[]
+# let numba compile all the code before profiling
+ccc(np.random.rand(10), np.random.rand(10))
+
+# %% [markdown] tags=[]
+# # Data
+
+# %% tags=[]
+n_genes, n_samples = 10, 30000
+
+# %% tags=[]
+np.random.seed(0)
+
+# %% tags=[]
+data = np.random.rand(n_genes, n_samples)
+
+# %% tags=[]
+data.shape
+
+
+# %% [markdown] tags=[]
+# # With default `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 10 + 1))
+    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+
+# %% [markdown] tags=[]
+# # With reduced `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 5 + 1))
+    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+# %% tags=[]
diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_01-2_CPUs-disable_numba-many_samples.py b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_01-2_CPUs-disable_numba-many_samples.py
new file mode 100644
index 00000000..7bc0a85e
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_01-2_CPUs-disable_numba-many_samples.py
@@ -0,0 +1,115 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: all,-execution,-papermill,-trusted
+#     notebook_metadata_filter: -jupytext.text_representation.jupytext_version
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# %% [markdown] tags=[]
+# # Description
+
+# %% [markdown] tags=[]
+# Like `07_01` but using more CPU cores.
+
+# %% [markdown] tags=[]
+# # Use multiple CPU core
+
+# %% tags=[]
+# %env CM_N_JOBS=2
+# %env NUMBA_NUM_THREADS=2
+# %env MKL_NUM_THREADS=2
+# %env OPEN_BLAS_NUM_THREADS=2
+# %env NUMEXPR_NUM_THREADS=2
+# %env OMP_NUM_THREADS=2
+
+# %% [markdown] tags=[]
+# # Disable numba
+
+# %% tags=[]
+# %env NUMBA_DISABLE_JIT=1
+
+# %% [markdown] tags=[]
+# # Remove pycache dir
+
+# %% tags=[]
+# !echo ${CODE_DIR}
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -prune -exec rm -rf {} \;
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% [markdown] tags=[]
+# # Modules
+
+# %% tags=[]
+import numpy as np
+
+from ccc.coef import ccc
+
+# %% tags=[]
+# let numba compile all the code before profiling
+ccc(np.random.rand(10), np.random.rand(10))
+
+# %% [markdown] tags=[]
+# # Data
+
+# %% tags=[]
+n_genes, n_samples = 10, 30000
+
+# %% tags=[]
+np.random.seed(0)
+
+# %% tags=[]
+data = np.random.rand(n_genes, n_samples)
+
+# %% tags=[]
+data.shape
+
+
+# %% [markdown] tags=[]
+# # With default `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 10 + 1))
+    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+
+# %% [markdown] tags=[]
+# These results are just slightly worse than the numba-compiled version (notebook `07`).
+
+# %% [markdown] tags=[]
+# # With reduced `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 5 + 1))
+    return ccc(data, internal_n_clusters=n_clust, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+# %% [markdown] tags=[]
+# These results are slightly better than the numba-compiled version (notebook `07`), which is surprising. In the future, it would be interesting to disable threading here to get accurate profiling results to debug this issue.
+
+# %% tags=[]
diff --git a/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.py b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.py
new file mode 100644
index 00000000..160c33d5
--- /dev/null
+++ b/nbs/others/05_ccc_profiling/12_cm_optimized/py/17_02-2_CPUs-use_ari_numba-many_samples-use_ari_numba.py
@@ -0,0 +1,103 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: all,-execution,-papermill,-trusted
+#     notebook_metadata_filter: -jupytext.text_representation.jupytext_version
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# %% [markdown] tags=[]
+# # Description
+
+# %% [markdown] tags=[]
+# Like `07_02` but using more CPU cores.
+
+# %% [markdown] tags=[]
+# # Use multiple CPU core
+
+# %% tags=[]
+# %env CM_N_JOBS=2
+# %env NUMBA_NUM_THREADS=2
+# %env MKL_NUM_THREADS=2
+# %env OPEN_BLAS_NUM_THREADS=2
+# %env NUMEXPR_NUM_THREADS=2
+# %env OMP_NUM_THREADS=2
+
+# %% [markdown] tags=[]
+# # Remove pycache dir
+
+# %% tags=[]
+# !echo ${CODE_DIR}
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -prune -exec rm -rf {} \;
+
+# %% tags=[]
+# !find ${CODE_DIR} -regex '^.*\(__pycache__\)$' -print
+
+# %% [markdown] tags=[]
+# # Modules
+
+# %% tags=[]
+import numpy as np
+
+from ccc.coef import ccc
+
+# %% tags=[]
+# let numba compile all the code before profiling
+ccc(np.random.rand(10), np.random.rand(10))
+
+# %% [markdown] tags=[]
+# # Data
+
+# %% tags=[]
+n_genes, n_samples = 10, 30000
+
+# %% tags=[]
+np.random.seed(0)
+
+# %% tags=[]
+data = np.random.rand(n_genes, n_samples)
+
+# %% tags=[]
+data.shape
+
+
+# %% [markdown] tags=[]
+# # With default `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 10 + 1))
+    return ccc(data, internal_n_clusters=n_clust, use_ari_numba=True, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+
+# %% [markdown] tags=[]
+# # With reduced `internal_n_clusters`
+
+# %% tags=[]
+def func():
+    n_clust = list(range(2, 5 + 1))
+    return ccc(data, internal_n_clusters=n_clust, use_ari_numba=True, n_jobs=2)
+
+
+# %% tags=[]
+# %%timeit func()
+func()
+
+# %% tags=[]