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b/notebooks/resource-allocation/102023.1.ipynb |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": 1, |
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"metadata": { |
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"scrolled": false |
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}, |
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"outputs": [], |
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"source": [ |
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"import pandas as pd\n", |
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"import seaborn as sns\n", |
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"from datetime import datetime, timedelta, date\n", |
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"from humanize import naturalsize\n", |
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"import matplotlib.pyplot as plt\n", |
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"import numpy as np\n", |
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"\n", |
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"%matplotlib inline" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"# Qiita's resource allocation - quick update from previous version\n", |
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"\n", |
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"After the 2023.10 release we noticed that:\n", |
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"1. `job-output-folder` `VALIDATE` command didn't have valid request because those jobs do not have sample/column values\n", |
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"2. The default during a resource allocation for time is minutes and the calculations were done in seconds" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"# Loading data\n", |
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"\n", |
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"First you will need to run `generate-allocation-summary.py` in Qiita as the qiita user (or whatever user runs qiita in your system). The resulting file would be: `job_[date].tsv.gz`.\n", |
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"\n", |
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"The generated file will have these columns: `['JobID', 'ElapsedRaw', 'MaxRSS', 'Submit', 'Start', 'MaxRSS.1', 'CPUTimeRAW', 'ReqMem', 'AllocCPUS', 'AveVMSize', 'QiitaID', 'external_id', 'sId', 'sName', 'sVersion', 'cId', 'cName', 'samples', 'columns', 'input_size', 'extra_info'],`." |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 2, |
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"metadata": { |
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"scrolled": true |
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}, |
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"outputs": [], |
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"source": [ |
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"m1g = 2**30\n", |
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"df = pd.read_csv('jobs_2023-10-04.tsv.gz', sep='\\t', dtype={'extra_info': str})\n", |
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"df['ElapsedRawTime'] = pd.to_timedelta(df.ElapsedRawTime)" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 3, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"data": { |
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"text/plain": [ |
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"'There are 101147 successful jobs since we moved to barnacle2 and the largest external_id is: 1581986'" |
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] |
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}, |
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"execution_count": 3, |
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"metadata": {}, |
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"output_type": "execute_result" |
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} |
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], |
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"source": [ |
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"# for reference for the next iteration of this notebook\n", |
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"f'There are {df.shape[0]} successful jobs since we moved to barnacle2 and the largest external_id is: {df.external_id.max()}'" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"# 1. Getting the default values for `job-output-folder` `VALIDATE`" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 4, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"data": { |
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"text/html": [ |
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"<div>\n", |
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"<style scoped>\n", |
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" .dataframe tbody tr th:only-of-type {\n", |
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" vertical-align: middle;\n", |
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" }\n", |
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"\n", |
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" .dataframe tbody tr th {\n", |
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" vertical-align: top;\n", |
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" }\n", |
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"\n", |
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" .dataframe thead tr th {\n", |
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" text-align: left;\n", |
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" }\n", |
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"\n", |
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" .dataframe thead tr:last-of-type th {\n", |
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" text-align: right;\n", |
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" }\n", |
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"</style>\n", |
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"<table border=\"1\" class=\"dataframe\">\n", |
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" <thead>\n", |
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" <tr>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th colspan=\"3\" halign=\"left\">ElapsedRawTime</th>\n", |
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" <th colspan=\"3\" halign=\"left\">MaxRSSRaw</th>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th>count</th>\n", |
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" <th>min</th>\n", |
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" <th>max</th>\n", |
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" <th>count</th>\n", |
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" <th>min</th>\n", |
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" <th>max</th>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>cName</th>\n", |
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" <th>sName</th>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" <th></th>\n", |
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" </tr>\n", |
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" </thead>\n", |
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" <tbody>\n", |
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" <tr>\n", |
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" <th rowspan=\"12\" valign=\"top\">Validate</th>\n", |
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" <th>BIOM type - BIOM</th>\n", |
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" <td>687</td>\n", |
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" <td>0 days 00:00:55</td>\n", |
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" <td>0 days 01:03:49</td>\n", |
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" <td>687</td>\n", |
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" <td>222.8 MB</td>\n", |
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" <td>82.0 GB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Diversity types - FeatureData</th>\n", |
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" <td>6</td>\n", |
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" <td>0 days 00:01:20</td>\n", |
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" <td>0 days 00:02:49</td>\n", |
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" <td>6</td>\n", |
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" <td>331.4 MB</td>\n", |
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" <td>384.3 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Diversity types - alpha_vector</th>\n", |
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" <td>123</td>\n", |
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" <td>0 days 00:01:12</td>\n", |
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" <td>3 days 04:36:54</td>\n", |
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" <td>123</td>\n", |
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" <td>289.3 MB</td>\n", |
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" <td>101.5 GB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Diversity types - distance_matrix</th>\n", |
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" <td>117</td>\n", |
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" <td>0 days 00:00:37</td>\n", |
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" <td>0 days 00:03:55</td>\n", |
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" <td>117</td>\n", |
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" <td>122.7 MB</td>\n", |
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" <td>12.5 GB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Diversity types - ordination_results</th>\n", |
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" <td>107</td>\n", |
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" <td>0 days 00:00:39</td>\n", |
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" <td>0 days 00:03:19</td>\n", |
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" <td>107</td>\n", |
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" <td>117.2 MB</td>\n", |
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" <td>2.9 GB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Sequencing Data Type - Demultiplexed</th>\n", |
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" <td>43</td>\n", |
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" <td>0 days 00:00:35</td>\n", |
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" <td>0 days 00:12:23</td>\n", |
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" <td>43</td>\n", |
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" <td>83.4 MB</td>\n", |
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" <td>517.4 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Sequencing Data Type - FASTA</th>\n", |
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" <td>2</td>\n", |
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" <td>0 days 00:00:56</td>\n", |
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" <td>0 days 00:02:23</td>\n", |
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" <td>2</td>\n", |
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" <td>79.8 MB</td>\n", |
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" <td>83.6 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Sequencing Data Type - FASTQ</th>\n", |
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" <td>32</td>\n", |
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" <td>0 days 00:00:41</td>\n", |
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" <td>0 days 01:50:44</td>\n", |
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" <td>32</td>\n", |
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" <td>78.7 MB</td>\n", |
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" <td>84.4 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Sequencing Data Type - SFF</th>\n", |
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" <td>1</td>\n", |
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" <td>0 days 00:01:09</td>\n", |
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" <td>0 days 00:01:09</td>\n", |
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" <td>1</td>\n", |
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" <td>79.6 MB</td>\n", |
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" <td>79.6 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Sequencing Data Type - per_sample_FASTQ</th>\n", |
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" <td>73</td>\n", |
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" <td>0 days 00:00:36</td>\n", |
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" <td>0 days 18:13:21</td>\n", |
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" <td>73</td>\n", |
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" <td>77.6 MB</td>\n", |
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" <td>83.6 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>Visualization types - q2_visualization</th>\n", |
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" <td>133</td>\n", |
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" <td>0 days 00:00:36</td>\n", |
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" <td>0 days 00:24:56</td>\n", |
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" <td>133</td>\n", |
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" <td>51.5 MB</td>\n", |
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" <td>67.5 MB</td>\n", |
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" </tr>\n", |
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" <tr>\n", |
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" <th>qtp-job-output-folder - job-output-folder</th>\n", |
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" <td>228</td>\n", |
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" <td>0 days 00:00:31</td>\n", |
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" <td>0 days 00:04:06</td>\n", |
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" <td>228</td>\n", |
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" <td>18.3 MB</td>\n", |
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" <td>46.7 MB</td>\n", |
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" </tr>\n", |
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" </tbody>\n", |
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"</table>\n", |
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"</div>" |
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], |
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"text/plain": [ |
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" ElapsedRawTime \\\n", |
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" count \n", |
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"cName sName \n", |
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"Validate BIOM type - BIOM 687 \n", |
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" Diversity types - FeatureData 6 \n", |
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" Diversity types - alpha_vector 123 \n", |
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" Diversity types - distance_matrix 117 \n", |
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" Diversity types - ordination_results 107 \n", |
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" Sequencing Data Type - Demultiplexed 43 \n", |
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" Sequencing Data Type - FASTA 2 \n", |
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" Sequencing Data Type - FASTQ 32 \n", |
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" Sequencing Data Type - SFF 1 \n", |
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" Sequencing Data Type - per_sample_FASTQ 73 \n", |
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" Visualization types - q2_visualization 133 \n", |
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" qtp-job-output-folder - job-output-folder 228 \n", |
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"\n", |
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" \\\n", |
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" min \n", |
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"cName sName \n", |
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"Validate BIOM type - BIOM 0 days 00:00:55 \n", |
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" Diversity types - FeatureData 0 days 00:01:20 \n", |
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" Diversity types - alpha_vector 0 days 00:01:12 \n", |
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" Diversity types - distance_matrix 0 days 00:00:37 \n", |
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" Diversity types - ordination_results 0 days 00:00:39 \n", |
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" Sequencing Data Type - Demultiplexed 0 days 00:00:35 \n", |
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" Sequencing Data Type - FASTA 0 days 00:00:56 \n", |
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" Sequencing Data Type - FASTQ 0 days 00:00:41 \n", |
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" Sequencing Data Type - SFF 0 days 00:01:09 \n", |
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" Sequencing Data Type - per_sample_FASTQ 0 days 00:00:36 \n", |
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" Visualization types - q2_visualization 0 days 00:00:36 \n", |
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" qtp-job-output-folder - job-output-folder 0 days 00:00:31 \n", |
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"\n", |
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" MaxRSSRaw \\\n", |
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" max count \n", |
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"cName sName \n", |
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"Validate BIOM type - BIOM 0 days 01:03:49 687 \n", |
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" Diversity types - FeatureData 0 days 00:02:49 6 \n", |
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" Diversity types - alpha_vector 3 days 04:36:54 123 \n", |
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" Diversity types - distance_matrix 0 days 00:03:55 117 \n", |
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" Diversity types - ordination_results 0 days 00:03:19 107 \n", |
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" Sequencing Data Type - Demultiplexed 0 days 00:12:23 43 \n", |
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" Sequencing Data Type - FASTA 0 days 00:02:23 2 \n", |
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" Sequencing Data Type - FASTQ 0 days 01:50:44 32 \n", |
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" Sequencing Data Type - SFF 0 days 00:01:09 1 \n", |
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" Sequencing Data Type - per_sample_FASTQ 0 days 18:13:21 73 \n", |
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" Visualization types - q2_visualization 0 days 00:24:56 133 \n", |
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" qtp-job-output-folder - job-output-folder 0 days 00:04:06 228 \n", |
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"\n", |
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" \n", |
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" min max \n", |
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"cName sName \n", |
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"Validate BIOM type - BIOM 222.8 MB 82.0 GB \n", |
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" Diversity types - FeatureData 331.4 MB 384.3 MB \n", |
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" Diversity types - alpha_vector 289.3 MB 101.5 GB \n", |
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" Diversity types - distance_matrix 122.7 MB 12.5 GB \n", |
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" Diversity types - ordination_results 117.2 MB 2.9 GB \n", |
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" Sequencing Data Type - Demultiplexed 83.4 MB 517.4 MB \n", |
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" Sequencing Data Type - FASTA 79.8 MB 83.6 MB \n", |
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" Sequencing Data Type - FASTQ 78.7 MB 84.4 MB \n", |
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" Sequencing Data Type - SFF 79.6 MB 79.6 MB \n", |
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" Sequencing Data Type - per_sample_FASTQ 77.6 MB 83.6 MB \n", |
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" Visualization types - q2_visualization 51.5 MB 67.5 MB \n", |
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" qtp-job-output-folder - job-output-folder 18.3 MB 46.7 MB " |
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] |
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}, |
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"metadata": {}, |
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"output_type": "display_data" |
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} |
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], |
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"source": [ |
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"cname = 'Validate'\n", |
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"_df = df[(df.cName == cname)].copy()\n", |
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"\n", |
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"summary = _df[_df['samples'].isnull() & _df['columns'].isnull()].groupby(\n", |
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" ['cName', 'sName'])[['ElapsedRawTime', 'MaxRSSRaw']].agg(['count', 'min', 'max']).copy()\n", |
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"\n", |
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"summary[('MaxRSSRaw', 'min')] = summary[('MaxRSSRaw', 'min')].apply(naturalsize)\n", |
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"summary[('MaxRSSRaw', 'max')] = summary[('MaxRSSRaw', 'max')].apply(naturalsize)\n", |
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"\n", |
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"display(summary)\n", |
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"\n", |
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"# New allocation: -p qiita -N 1 -n 1 --mem 100mb --time 00:40:00" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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342 |
"# 2. Updates for the seconds to minute confusion" |
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] |
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}, |
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{ |
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"cell_type": "markdown", |
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"metadata": {}, |
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"source": [ |
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"\n", |
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350 |
"=============\n", |
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"=============\n", |
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" allocation = '-p qiita -N 1 -n 1 '\n", |
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" || '--mem (2**30)+({samples}*150000) '\n", |
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" || '--time 240'\n", |
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"\n", |
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356 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
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" allocation = '-p qiita -N 1 -n 1 '\n", |
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358 |
" || '--mem (2**30)+({samples}*150000) '\n", |
|
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359 |
" || '--time 4'\n", |
|
|
360 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
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" name = 'delete_sample_or_column';\n", |
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"\n", |
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363 |
"=============\n", |
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364 |
"=============\n", |
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365 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
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366 |
" || '--mem {samples}*10000000'\n", |
|
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367 |
" || '--time 61200'\n", |
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"\n", |
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369 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
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370 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
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371 |
" || '--mem {samples}*10000000'\n", |
|
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372 |
" || '--time 1020'\n", |
|
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373 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
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374 |
" name = 'Sequence Processing Pipeline';\n", |
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"\n", |
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376 |
"=============\n", |
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377 |
"=============\n", |
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378 |
" allocation = '-p qiita -N 1 -n 1 --mem 4g --time 900'\n", |
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379 |
"\n", |
|
|
380 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
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381 |
" allocation = '-p qiita -N 1 -n 1 --mem 4g --time 15'\n", |
|
|
382 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
383 |
" name = 'Filter samples from table [filter_samples]';\n", |
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384 |
"\n", |
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385 |
"=============\n", |
|
|
386 |
"=============\n", |
|
|
387 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
388 |
" || '--mem (2**31)+({input_size}*6) if\n", |
|
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389 |
"(2**31)+({input_size}*6) < 13958643712 else 13958643712 '\n", |
|
|
390 |
" || '--time 2400'\n", |
|
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391 |
"\n", |
|
|
392 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
393 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
394 |
" || '--mem (2**31)+({input_size}*6) if\n", |
|
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395 |
"(2**31)+({input_size}*6) < 13958643712 else 13958643712 '\n", |
|
|
396 |
" || '--time 40'\n", |
|
|
397 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
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|
398 |
" name = 'Rarefy table [rarefy]';\n", |
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399 |
"\n", |
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|
400 |
"=============\n", |
|
|
401 |
"=============\n", |
|
|
402 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
403 |
" || '--mem 14g'\n", |
|
|
404 |
" || '--time 360'\n", |
|
|
405 |
"\n", |
|
|
406 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
407 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
408 |
" || '--mem 14g '\n", |
|
|
409 |
" || '--time 6'\n", |
|
|
410 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
411 |
" name = 'Alpha diversity (phylogenetic) [alpha_phylogenetic]';\n", |
|
|
412 |
"\n", |
|
|
413 |
"\n", |
|
|
414 |
"=============\n", |
|
|
415 |
"=============\n", |
|
|
416 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
417 |
" || '--mem (2**33)+(2**30)+(({samples}*{columns}*{input_size})/4500000)'\n", |
|
|
418 |
" || '--time 1800'\n", |
|
|
419 |
"\n", |
|
|
420 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
421 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
422 |
" || '--mem\n", |
|
|
423 |
"(2**33)+(2**30)+(({samples}*{columns}*{input_size})/4500000) '\n", |
|
|
424 |
" || '--time 30'\n", |
|
|
425 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
426 |
" name = 'Visualize and Interact with Principal Coordinates Analysis\n", |
|
|
427 |
"Plots [plot]';\n", |
|
|
428 |
"\n", |
|
|
429 |
"=============\n", |
|
|
430 |
"=============\n", |
|
|
431 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
432 |
" || '--mem (2**32)+(({samples}*{columns}*{input_size}')/20000)'\n", |
|
|
433 |
" || '--time 90000'\n", |
|
|
434 |
"\n", |
|
|
435 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
436 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
437 |
" || '--mem (2**32)+(({samples}*{columns}*{input_size})/20000) '\n", |
|
|
438 |
" || '--time 1500'\n", |
|
|
439 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
440 |
" name = 'Alpha rarefaction curves [alpha_rarefaction]';\n", |
|
|
441 |
"\n", |
|
|
442 |
"=============\n", |
|
|
443 |
"=============\n", |
|
|
444 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
445 |
" || '--mem 2*(2**30)+{input_size} if 2*(2**30)+{input_size} < 16*(2**30) else 16*(2**30)'\n", |
|
|
446 |
" || '--time 36000'\n", |
|
|
447 |
"\n", |
|
|
448 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
449 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
450 |
" || '--mem 2*(2**30)+{input_size} if 2*(2**30)+{input_size}\n", |
|
|
451 |
"< 16*(2**30) else 16*(2**30) '\n", |
|
|
452 |
" || '--time 600'\n", |
|
|
453 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
454 |
" name = 'Trimming';\n", |
|
|
455 |
"\n", |
|
|
456 |
"=============\n", |
|
|
457 |
"=============\n", |
|
|
458 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
459 |
" || '--mem (2**30)+({samples}*{columns}*2000)'\n", |
|
|
460 |
" || '--time 2300'\n", |
|
|
461 |
"\n", |
|
|
462 |
"UPDATE qiita.processing_job_resource_allocation set\n", |
|
|
463 |
" allocation = '-p qiita -N 1 -n 1 '\n", |
|
|
464 |
" || '--mem (2**30)+({samples}*{columns}*2000) '\n", |
|
|
465 |
" || '--time 39'\n", |
|
|
466 |
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n", |
|
|
467 |
" name = 'update_sample_template';" |
|
|
468 |
] |
|
|
469 |
}, |
|
|
470 |
{ |
|
|
471 |
"cell_type": "code", |
|
|
472 |
"execution_count": null, |
|
|
473 |
"metadata": {}, |
|
|
474 |
"outputs": [], |
|
|
475 |
"source": [] |
|
|
476 |
} |
|
|
477 |
], |
|
|
478 |
"metadata": { |
|
|
479 |
"kernelspec": { |
|
|
480 |
"display_name": "Python 3 (ipykernel)", |
|
|
481 |
"language": "python", |
|
|
482 |
"name": "python3" |
|
|
483 |
}, |
|
|
484 |
"language_info": { |
|
|
485 |
"codemirror_mode": { |
|
|
486 |
"name": "ipython", |
|
|
487 |
"version": 3 |
|
|
488 |
}, |
|
|
489 |
"file_extension": ".py", |
|
|
490 |
"mimetype": "text/x-python", |
|
|
491 |
"name": "python", |
|
|
492 |
"nbconvert_exporter": "python", |
|
|
493 |
"pygments_lexer": "ipython3", |
|
|
494 |
"version": "3.9.7" |
|
|
495 |
} |
|
|
496 |
}, |
|
|
497 |
"nbformat": 4, |
|
|
498 |
"nbformat_minor": 4 |
|
|
499 |
} |