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"cells": [
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"source": [
"<img width=\"800px\" src=\"../fidle/img/00-Fidle-header-01.svg\"></img>\n",
"\n",
"# <!-- TITLE --> [GTS6] - CNN with GTSRB dataset - Full convolutions as a batch\n",
"<!-- DESC --> Episode 6 : Run Full convolution notebook as a batch\n",
"<!-- AUTHOR : Jean-Luc Parouty (CNRS/SIMaP) -->\n",
"\n",
"## Objectives :\n",
" - Run a notebook code as a **job**\n",
" - Follow up with Tensorboard\n",
" \n",
"The German Traffic Sign Recognition Benchmark (GTSRB) is a dataset with more than 50,000 photos of road signs from about 40 classes. \n",
"The final aim is to recognise them ! \n",
"Description is available there : http://benchmark.ini.rub.de/?section=gtsrb&subsection=dataset\n",
"\n",
"\n",
"## What we're going to do :\n",
"Our main steps:\n",
" - Run Full-convolution.ipynb as a batch :\n",
" - Notebook mode\n",
" - Script mode \n",
" - Tensorboard follow up"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Step 0 - Just for convenience"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
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"text": [
"\n",
"FIDLE 2020 - Practical Work Module\n",
"Version : 0.4.3\n",
"Run time : Friday 28 February 2020, 17:55:56\n",
"TensorFlow version : 2.0.0\n",
"Keras version : 2.2.4-tf\n"
]
}
],
"source": [
"import sys\n",
"sys.path.append('..')\n",
"import fidle.pwk as ooo\n",
"ooo.init()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Step 1 - Run a notebook as a batch\n",
"To run a notebook in a command line : \n",
"```jupyter nbconvert (...) --to notebook --execute <notebook>``` \n",
"\n",
"For example : \n",
"```jupyter nbconvert --ExecutePreprocessor.timeout=-1 --to notebook --output='./run/full_convolutions' --execute '05-Full-convolutions.ipynb'```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Step 2 - Export as a script (What we're going to do this time)\n",
"To export a notebook as a script : \n",
"```jupyter nbconvert --to script <notebook>``` \n",
"To run the script : \n",
"```ipython <script>```"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[NbConvertApp] Converting notebook 05-Full-convolutions.ipynb to script\n",
"[NbConvertApp] Writing 13061 bytes to ./run/full_convolutions_01.py\n"
]
}
],
"source": [
"%%bash\n",
"\n",
"# ---- This will convert a notebook to a notebook.py script\n",
"#\n",
"jupyter nbconvert --to script --output='./run/full_convolutions_01' '05-Full-convolutions.ipynb'"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-rwxr-xr-x 1 paroutyj l-simap 13061 Feb 28 17:56 ./run/full_convolutions_01.py\n"
]
}
],
"source": [
"!ls -l ./run/*.py"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Step 2 - Batch submission\n",
"### 2.1 - Create batch script :"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Overwriting ./run/full_convolutions_01.sh\n"
]
}
],
"source": [
"%%writefile \"./run/full_convolutions_01.sh\"\n",
"#!/bin/bash\n",
"#OAR -n Full convolutions\n",
"#OAR -t gpu\n",
"#OAR -l /nodes=1/gpudevice=1,walltime=01:00:00\n",
"#OAR --stdout full_convolutions_%jobid%.out\n",
"#OAR --stderr full_convolutions_%jobid%.err\n",
"#OAR --project fidle\n",
"\n",
"#---- With cpu\n",
"# use :\n",
"# OAR -l /nodes=1/core=32,walltime=02:00:00\n",
"# and add a 2>/dev/null to ipython xxx\n",
"\n",
"# ----------------------------------\n",
"# _ _ _\n",
"# | |__ __ _| |_ ___| |__\n",
"# | '_ \\ / _` | __/ __| '_ \\\n",
"# | |_) | (_| | || (__| | | |\n",
"# |_.__/ \\__,_|\\__\\___|_| |_|\n",
"# Full convolutions\n",
"# ----------------------------------\n",
"#\n",
"\n",
"CONDA_ENV=fidle\n",
"RUN_DIR=~/fidle/GTSRB\n",
"RUN_SCRIPT=./run/full_convolutions_01.py\n",
"\n",
"# ---- Cuda Conda initialization\n",
"#\n",
"echo '------------------------------------------------------------'\n",
"echo \"Start : $0\"\n",
"echo '------------------------------------------------------------'\n",
"#\n",
"source /applis/environments/cuda_env.sh dahu 10.0\n",
"source /applis/environments/conda.sh\n",
"#\n",
"conda activate \"$CONDA_ENV\"\n",
"\n",
"# ---- Run it...\n",
"#\n",
"cd $RUN_DIR\n",
"ipython $RUN_SCRIPT"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.2 - Have a look"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"-rwxr-xr-x 1 paroutyj l-simap 13061 Feb 28 16:31 ./run/full_convolutions_01.py\n",
"-rwxr-xr-x 1 paroutyj l-simap 1015 Feb 28 16:31 ./run/full_convolutions_01.sh\n"
]
}
],
"source": [
"%%bash\n",
"chmod 755 ./run/*.sh\n",
"chmod 755 ./run/*.py\n",
"ls -l ./run/*full_convolutions*"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.3 - Job submission\n",
"Have to be done on the frontal :\n",
"```bash\n",
"# hostname\n",
"f-dahu\n",
"\n",
"# pwd\n",
"/home/paroutyj\n",
"\n",
"# oarsub -S ~/fidle/GTSRB/run/full_convolutions_01.sh\n",
"[GPUNODE] Adding gpu node restriction\n",
"[ADMISSION RULE] Modify resource description with type constraints\n",
"\n",
"#oarstat -u\n",
"Job id S User Duration System message\n",
"--------- - -------- ---------- ------------------------------------------------\n",
"5878410 R paroutyj 0:19:56 R=8,W=1:0:0,J=I,P=fidle,T=gpu (Karma=0.005,quota_ok)\n",
"5896266 W paroutyj 0:00:00 R=8,W=1:0:0,J=B,N=Full convolutions,P=fidle,T=gpu\n",
"\n",
"# ls -l\n",
"total 8\n",
"-rw-r--r-- 1 paroutyj l-simap 0 Feb 28 15:58 full_convolutions_5896266.err\n",
"-rw-r--r-- 1 paroutyj l-simap 5703 Feb 28 15:58 full_convolutions_5896266.out\n",
"```\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<div class='todo'>\n",
" Your mission if you accept it: Run our full_convolution code in batch mode.<br>\n",
" For that :\n",
" <ul>\n",
" <li>Validate the full_convolution notebook on short tests</li>\n",
" <li>Submit it in batch mode for validation</li>\n",
" <li>Modify the notebook for a full run and submit it :-)</li>\n",
" </ul>\n",
" \n",
"</div>"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"---\n",
"<img width=\"80px\" src=\"../fidle/img/00-Fidle-logo-01.svg\"></img>"
]
}
],
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"display_name": "Python 3",
"language": "python",
"name": "python3"
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"name": "ipython",
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"file_extension": ".py",
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"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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