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"<img width=\"800px\" src=\"../fidle/img/00-Fidle-header-01.svg\"></img>\n",
"# <!-- TITLE --> [GTSRB6] - Full convolutions as a batch\n",
"<!-- DESC --> Episode 6 : To compute bigger, use your notebook in batch mode\n",
"<!-- AUTHOR : Jean-Luc Parouty (CNRS/SIMaP) -->\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",
"Our main steps:\n",
" - Run Full-convolution.ipynb as a batch :\n",
" - Notebook mode\n",
" - Script mode \n",
"### Step 1 - Import and init \n",
"Not really useful here ;-)"
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"Version : 1.2b1 DEV\n",
"Notebook id : GTSRB6\n",
"Run time : Thursday 7 January 2021, 15:41:17\n",
"TensorFlow version : 2.2.0\n",
"Keras version : 2.3.0-tf\n",
"Datasets dir : /home/pjluc/datasets/fidle\n",
"Run dir : ./run\n",
"Update keras cache : False\n",
"Save figs : True\n",
"Path figs : ./run/figs\n"
]
}
],
"source": [
"import sys\n",
"datasets_dir = pwk.init('GTSRB6')"
]
},
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"\n",
"Two simple solutions are possible :-)\n",
"\n",
" - **Option 1 - As a notebook ! (a good choice)**\n",
" The result is the executed notebook, so we can retrieve all the cell'soutputs of the notebook : \n",
" ```jupyter nbconvert (...) --to notebook --execute <notebook>``` \n",
"\n",
" Example : \n",
" ```jupyter nbconvert --ExecutePreprocessor.timeout=-1 --to notebook --execute my_notebook.ipynb'``` \n",
" The result will be a notebook: 'my_notebook.nbconvert.ipynb'.\n",
" \n",
" See: [nbconvert documentation](https://nbconvert.readthedocs.io/en/latest/usage.html#convert-notebook)\n",
" - **Option 2 - As a script**\n",
"\n",
" Very simple too, but with some constraints on the notebook. \n",
" We will convert the notebook to a Python script (IPython, to be precise) : \n",
" ```jupyter nbconvert --to script <notebook>``` \n",
" Then we can execute this script : \n",
" ```ipython <script>```\n",
" \n",
" See: [nbconvert documentation](https://nbconvert.readthedocs.io/en/latest/usage.html#executable-script)"
]
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"\n",
"Maybe not always the best solution, but this solution is very rustic ! \n",
"\n",
"[NbConvertApp] Converting notebook 05-Full-convolutions.ipynb to script\n",
"[NbConvertApp] Writing 12854 bytes to 05-full_convolutions.py\n",
"-rw-r--r-- 1 pjluc pjluc 12854 Jan 7 15:41 05-full_convolutions.py\n"
"! jupyter nbconvert --to script --output='05-full_convolutions' '05-Full-convolutions.ipynb'\n",
"! ls -l *.py"
]
},
{
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"### 2.2 - Batch submission\n",
"\n",
"See the two examples of bash launch script :\n",
" - `batch_slurm.sh` using Slurm (like at IDRIS)\n",
" - `batch_oar.sh` using OAR (like at GRICAD)"
"On the frontal :\n",
"```bash\n",
"# hostname\n",
"jean-zay2\n",
"# sbatch $WORK/fidle/GTSRB/batch_slurm.sh \n",
"Submitted batch job 249794\n",
"#squeue -u $USER\n",
" JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)\n",
" 249794 gpu_p1 GTSRB Fu uja62cb PD 0:00 1 (Resources)\n",
"# ls -l _batch/\n",
"total 32769\n",
"-rw-r--r-- 1 uja62cb gensim01 13349 Sep 10 11:32 GTSRB_249794.err\n",
"-rw-r--r-- 1 uja62cb gensim01 489 Sep 10 11:31 GTSRB_249794.out\n",
"```"
]
},
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"source": [
"#### Example at GRICAD\n",
"\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/batch_oar.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 batch_oar_5896266.err\n",
"-rw-r--r-- 1 paroutyj l-simap 5703 Feb 28 15:58 batch_oar_5896266.out\n",
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"End time is : Thursday 7 January 2021, 15:41:18\n",
"Duration is : 00:00:01 101ms\n",
"This notebook ends here\n"
]
}
],
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"pwk.end()"
]
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"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>"
"<img width=\"80px\" src=\"../fidle/img/00-Fidle-logo-01.svg\"></img>"
}
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