500 lines (499 with data), 19.7 kB
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"scrolled": false
},
"outputs": [],
"source": [
"import pandas as pd\n",
"import seaborn as sns\n",
"from datetime import datetime, timedelta, date\n",
"from humanize import naturalsize\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"\n",
"%matplotlib inline"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Qiita's resource allocation - quick update from previous version\n",
"\n",
"After the 2023.10 release we noticed that:\n",
"1. `job-output-folder` `VALIDATE` command didn't have valid request because those jobs do not have sample/column values\n",
"2. The default during a resource allocation for time is minutes and the calculations were done in seconds"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Loading data\n",
"\n",
"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",
"\n",
"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'],`."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"m1g = 2**30\n",
"df = pd.read_csv('jobs_2023-10-04.tsv.gz', sep='\\t', dtype={'extra_info': str})\n",
"df['ElapsedRawTime'] = pd.to_timedelta(df.ElapsedRawTime)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'There are 101147 successful jobs since we moved to barnacle2 and the largest external_id is: 1581986'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# for reference for the next iteration of this notebook\n",
"f'There are {df.shape[0]} successful jobs since we moved to barnacle2 and the largest external_id is: {df.external_id.max()}'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 1. Getting the default values for `job-output-folder` `VALIDATE`"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
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"\n",
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"\n",
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" text-align: left;\n",
" }\n",
"\n",
" .dataframe thead tr:last-of-type th {\n",
" text-align: right;\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr>\n",
" <th></th>\n",
" <th></th>\n",
" <th colspan=\"3\" halign=\"left\">ElapsedRawTime</th>\n",
" <th colspan=\"3\" halign=\"left\">MaxRSSRaw</th>\n",
" </tr>\n",
" <tr>\n",
" <th></th>\n",
" <th></th>\n",
" <th>count</th>\n",
" <th>min</th>\n",
" <th>max</th>\n",
" <th>count</th>\n",
" <th>min</th>\n",
" <th>max</th>\n",
" </tr>\n",
" <tr>\n",
" <th>cName</th>\n",
" <th>sName</th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th rowspan=\"12\" valign=\"top\">Validate</th>\n",
" <th>BIOM type - BIOM</th>\n",
" <td>687</td>\n",
" <td>0 days 00:00:55</td>\n",
" <td>0 days 01:03:49</td>\n",
" <td>687</td>\n",
" <td>222.8 MB</td>\n",
" <td>82.0 GB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diversity types - FeatureData</th>\n",
" <td>6</td>\n",
" <td>0 days 00:01:20</td>\n",
" <td>0 days 00:02:49</td>\n",
" <td>6</td>\n",
" <td>331.4 MB</td>\n",
" <td>384.3 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diversity types - alpha_vector</th>\n",
" <td>123</td>\n",
" <td>0 days 00:01:12</td>\n",
" <td>3 days 04:36:54</td>\n",
" <td>123</td>\n",
" <td>289.3 MB</td>\n",
" <td>101.5 GB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diversity types - distance_matrix</th>\n",
" <td>117</td>\n",
" <td>0 days 00:00:37</td>\n",
" <td>0 days 00:03:55</td>\n",
" <td>117</td>\n",
" <td>122.7 MB</td>\n",
" <td>12.5 GB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diversity types - ordination_results</th>\n",
" <td>107</td>\n",
" <td>0 days 00:00:39</td>\n",
" <td>0 days 00:03:19</td>\n",
" <td>107</td>\n",
" <td>117.2 MB</td>\n",
" <td>2.9 GB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Sequencing Data Type - Demultiplexed</th>\n",
" <td>43</td>\n",
" <td>0 days 00:00:35</td>\n",
" <td>0 days 00:12:23</td>\n",
" <td>43</td>\n",
" <td>83.4 MB</td>\n",
" <td>517.4 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Sequencing Data Type - FASTA</th>\n",
" <td>2</td>\n",
" <td>0 days 00:00:56</td>\n",
" <td>0 days 00:02:23</td>\n",
" <td>2</td>\n",
" <td>79.8 MB</td>\n",
" <td>83.6 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Sequencing Data Type - FASTQ</th>\n",
" <td>32</td>\n",
" <td>0 days 00:00:41</td>\n",
" <td>0 days 01:50:44</td>\n",
" <td>32</td>\n",
" <td>78.7 MB</td>\n",
" <td>84.4 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Sequencing Data Type - SFF</th>\n",
" <td>1</td>\n",
" <td>0 days 00:01:09</td>\n",
" <td>0 days 00:01:09</td>\n",
" <td>1</td>\n",
" <td>79.6 MB</td>\n",
" <td>79.6 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Sequencing Data Type - per_sample_FASTQ</th>\n",
" <td>73</td>\n",
" <td>0 days 00:00:36</td>\n",
" <td>0 days 18:13:21</td>\n",
" <td>73</td>\n",
" <td>77.6 MB</td>\n",
" <td>83.6 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Visualization types - q2_visualization</th>\n",
" <td>133</td>\n",
" <td>0 days 00:00:36</td>\n",
" <td>0 days 00:24:56</td>\n",
" <td>133</td>\n",
" <td>51.5 MB</td>\n",
" <td>67.5 MB</td>\n",
" </tr>\n",
" <tr>\n",
" <th>qtp-job-output-folder - job-output-folder</th>\n",
" <td>228</td>\n",
" <td>0 days 00:00:31</td>\n",
" <td>0 days 00:04:06</td>\n",
" <td>228</td>\n",
" <td>18.3 MB</td>\n",
" <td>46.7 MB</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" ElapsedRawTime \\\n",
" count \n",
"cName sName \n",
"Validate BIOM type - BIOM 687 \n",
" Diversity types - FeatureData 6 \n",
" Diversity types - alpha_vector 123 \n",
" Diversity types - distance_matrix 117 \n",
" Diversity types - ordination_results 107 \n",
" Sequencing Data Type - Demultiplexed 43 \n",
" Sequencing Data Type - FASTA 2 \n",
" Sequencing Data Type - FASTQ 32 \n",
" Sequencing Data Type - SFF 1 \n",
" Sequencing Data Type - per_sample_FASTQ 73 \n",
" Visualization types - q2_visualization 133 \n",
" qtp-job-output-folder - job-output-folder 228 \n",
"\n",
" \\\n",
" min \n",
"cName sName \n",
"Validate BIOM type - BIOM 0 days 00:00:55 \n",
" Diversity types - FeatureData 0 days 00:01:20 \n",
" Diversity types - alpha_vector 0 days 00:01:12 \n",
" Diversity types - distance_matrix 0 days 00:00:37 \n",
" Diversity types - ordination_results 0 days 00:00:39 \n",
" Sequencing Data Type - Demultiplexed 0 days 00:00:35 \n",
" Sequencing Data Type - FASTA 0 days 00:00:56 \n",
" Sequencing Data Type - FASTQ 0 days 00:00:41 \n",
" Sequencing Data Type - SFF 0 days 00:01:09 \n",
" Sequencing Data Type - per_sample_FASTQ 0 days 00:00:36 \n",
" Visualization types - q2_visualization 0 days 00:00:36 \n",
" qtp-job-output-folder - job-output-folder 0 days 00:00:31 \n",
"\n",
" MaxRSSRaw \\\n",
" max count \n",
"cName sName \n",
"Validate BIOM type - BIOM 0 days 01:03:49 687 \n",
" Diversity types - FeatureData 0 days 00:02:49 6 \n",
" Diversity types - alpha_vector 3 days 04:36:54 123 \n",
" Diversity types - distance_matrix 0 days 00:03:55 117 \n",
" Diversity types - ordination_results 0 days 00:03:19 107 \n",
" Sequencing Data Type - Demultiplexed 0 days 00:12:23 43 \n",
" Sequencing Data Type - FASTA 0 days 00:02:23 2 \n",
" Sequencing Data Type - FASTQ 0 days 01:50:44 32 \n",
" Sequencing Data Type - SFF 0 days 00:01:09 1 \n",
" Sequencing Data Type - per_sample_FASTQ 0 days 18:13:21 73 \n",
" Visualization types - q2_visualization 0 days 00:24:56 133 \n",
" qtp-job-output-folder - job-output-folder 0 days 00:04:06 228 \n",
"\n",
" \n",
" min max \n",
"cName sName \n",
"Validate BIOM type - BIOM 222.8 MB 82.0 GB \n",
" Diversity types - FeatureData 331.4 MB 384.3 MB \n",
" Diversity types - alpha_vector 289.3 MB 101.5 GB \n",
" Diversity types - distance_matrix 122.7 MB 12.5 GB \n",
" Diversity types - ordination_results 117.2 MB 2.9 GB \n",
" Sequencing Data Type - Demultiplexed 83.4 MB 517.4 MB \n",
" Sequencing Data Type - FASTA 79.8 MB 83.6 MB \n",
" Sequencing Data Type - FASTQ 78.7 MB 84.4 MB \n",
" Sequencing Data Type - SFF 79.6 MB 79.6 MB \n",
" Sequencing Data Type - per_sample_FASTQ 77.6 MB 83.6 MB \n",
" Visualization types - q2_visualization 51.5 MB 67.5 MB \n",
" qtp-job-output-folder - job-output-folder 18.3 MB 46.7 MB "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"cname = 'Validate'\n",
"_df = df[(df.cName == cname)].copy()\n",
"\n",
"summary = _df[_df['samples'].isnull() & _df['columns'].isnull()].groupby(\n",
" ['cName', 'sName'])[['ElapsedRawTime', 'MaxRSSRaw']].agg(['count', 'min', 'max']).copy()\n",
"\n",
"summary[('MaxRSSRaw', 'min')] = summary[('MaxRSSRaw', 'min')].apply(naturalsize)\n",
"summary[('MaxRSSRaw', 'max')] = summary[('MaxRSSRaw', 'max')].apply(naturalsize)\n",
"\n",
"display(summary)\n",
"\n",
"# New allocation: -p qiita -N 1 -n 1 --mem 100mb --time 00:40:00"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# 2. Updates for the seconds to minute confusion"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**30)+({samples}*150000) '\n",
" || '--time 240'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**30)+({samples}*150000) '\n",
" || '--time 4'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'delete_sample_or_column';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem {samples}*10000000'\n",
" || '--time 61200'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem {samples}*10000000'\n",
" || '--time 1020'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Sequence Processing Pipeline';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 --mem 4g --time 900'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 --mem 4g --time 15'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Filter samples from table [filter_samples]';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**31)+({input_size}*6) if\n",
"(2**31)+({input_size}*6) < 13958643712 else 13958643712 '\n",
" || '--time 2400'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**31)+({input_size}*6) if\n",
"(2**31)+({input_size}*6) < 13958643712 else 13958643712 '\n",
" || '--time 40'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Rarefy table [rarefy]';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem 14g'\n",
" || '--time 360'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem 14g '\n",
" || '--time 6'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Alpha diversity (phylogenetic) [alpha_phylogenetic]';\n",
"\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**33)+(2**30)+(({samples}*{columns}*{input_size})/4500000)'\n",
" || '--time 1800'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem\n",
"(2**33)+(2**30)+(({samples}*{columns}*{input_size})/4500000) '\n",
" || '--time 30'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Visualize and Interact with Principal Coordinates Analysis\n",
"Plots [plot]';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**32)+(({samples}*{columns}*{input_size}')/20000)'\n",
" || '--time 90000'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**32)+(({samples}*{columns}*{input_size})/20000) '\n",
" || '--time 1500'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Alpha rarefaction curves [alpha_rarefaction]';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem 2*(2**30)+{input_size} if 2*(2**30)+{input_size} < 16*(2**30) else 16*(2**30)'\n",
" || '--time 36000'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem 2*(2**30)+{input_size} if 2*(2**30)+{input_size}\n",
"< 16*(2**30) else 16*(2**30) '\n",
" || '--time 600'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'Trimming';\n",
"\n",
"=============\n",
"=============\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**30)+({samples}*{columns}*2000)'\n",
" || '--time 2300'\n",
"\n",
"UPDATE qiita.processing_job_resource_allocation set\n",
" allocation = '-p qiita -N 1 -n 1 '\n",
" || '--mem (2**30)+({samples}*{columns}*2000) '\n",
" || '--time 39'\n",
" WHERE job_type = 'RESOURCE_PARAMS_COMMAND' and\n",
" name = 'update_sample_template';"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
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