Clara-parabricks:4.3.1 fq2bam_meth is slow - Parabricks

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Are there any parameters that can be optimized? my command is : docker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth&hellip;"> <meta name="generator" content="Discourse 3.5.0.beta2-dev - https://github.com/discourse/discourse version 424da95128bd2e92c4d8e42baf65a947602e9c68"> <link rel="icon" type="image/png" href="https://global.discourse-cdn.com/nvidia/optimized/2X/0/0372ccc95874f71d7fbff64bbbff6f8c69dd850b_2_32x32.png"> <link rel="apple-touch-icon" type="image/png" href="https://global.discourse-cdn.com/nvidia/optimized/2X/8/819b2855e1f1f3249e77dc713405cf77d1eda57c_2_180x180.png"> <meta name="theme-color" media="all" content="#000000"> <meta name="color-scheme" content="light"> <meta name="viewport" content="width=device-width, initial-scale=1.0, minimum-scale=1.0, viewport-fit=cover"> <link rel="canonical" href="https://forums.developer.nvidia.com/t/clara-parabricks-4-3-1-fq2bam-meth-is-slow/299511" /> <link rel="search" 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Are there any parameters that can be optimized? my command is : docker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth_ATAC/integratioh/fq2bam:/mydata 74f2b983a773 /bin/bash time pbrun fq2bam_meth --ref hg38.fa --in-se-fq …/deep_board/Airway-S43-2_supplement/A10.1.fastq.gz --out-bam A10_2stream.bam --bwa-nstreams 2 --num-gpus 3 --gpuwrite --bwa-cpu-thread-pool 16 the output is : [Parabricks ..." /> <meta name="twitter:description" content="The speed of fq2bam_meth doesn’t seem as fast as I expected. Are there any parameters that can be optimized? my command is : docker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth_ATAC/integratioh/fq2bam:/mydata 74f2b983a773 /bin/bash time pbrun fq2bam_meth --ref hg38.fa --in-se-fq …/deep_board/Airway-S43-2_supplement/A10.1.fastq.gz --out-bam A10_2stream.bam --bwa-nstreams 2 --num-gpus 3 --gpuwrite --bwa-cpu-thread-pool 16 the output is : [Parabricks ..." /> <meta property="og:article:section" content="Healthcare & Life Sciences" /> <meta property="og:article:section:color" content="76B900" /> <meta property="og:article:section" content="Parabricks" /> <meta property="og:article:section:color" content="76B900" /> <meta property="og:article:tag" content="ai" /> <meta property="article:published_time" content="2024-07-11T16:32:29+00:00" /> <meta property="og:ignore_canonical" content="true" /> <script type="application/ld+json">{"@context":"http://schema.org","@type":"QAPage","name":"Clara-parabricks:4.3.1 fq2bam_meth is slow","mainEntity":{"@type":"Question","name":"Clara-parabricks:4.3.1 fq2bam_meth is slow","text":"The speed of fq2bam_meth doesn’t seem as fast as I expected. Are there any parameters that can be optimized?\n\nmy command is :\n\ndocker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth_ATAC/integratioh/fq2bam:/mydata 74f2b983a773 /bin/bash\n\ntime pbrun fq2bam_meth …","upvoteCount":0,"answerCount":0,"datePublished":"2024-07-11T16:32:29.267Z","author":{"@type":"Person","name":"wangyanni541","url":"https://forums.developer.nvidia.com/u/wangyanni541"}}}</script> </head> <body class="crawler browser-update"> <header> <a href="/"> NVIDIA Developer Forums </a> </header> <div id="main-outlet" class="wrap" role="main"> <div id="topic-title"> <h1> <a href="/t/clara-parabricks-4-3-1-fq2bam-meth-is-slow/299511">Clara-parabricks:4.3.1 fq2bam_meth is slow</a> </h1> <div class="topic-category" itemscope itemtype="http://schema.org/BreadcrumbList"> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/healthcare/parabricks/290" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #76B900'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Healthcare & Life Sciences</span> </span> </a> <meta itemprop="position" content="1" /> </span> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/healthcare/parabricks/290" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #76B900'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Parabricks</span> </span> </a> <meta itemprop="position" content="2" /> </span> </div> <div class="topic-category"> <div class='discourse-tags list-tags'> <a href='https://forums.developer.nvidia.com/tag/ai' class='discourse-tag' rel="tag">ai</a> </div> </div> </div> <div itemscope itemtype='http://schema.org/DiscussionForumPosting'> <meta itemprop='headline' content='Clara-parabricks:4.3.1 fq2bam_meth is slow'> <link itemprop='url' href='https://forums.developer.nvidia.com/t/clara-parabricks-4-3-1-fq2bam-meth-is-slow/299511'> <meta itemprop='datePublished' content='2024-07-11T16:32:29Z'> <meta itemprop='articleSection' content='Parabricks'> <meta itemprop='keywords' content='ai'> <div itemprop='publisher' itemscope itemtype="http://schema.org/Organization"> <meta itemprop='name' content='NVIDIA'> <div itemprop='logo' itemscope itemtype="http://schema.org/ImageObject"> <meta itemprop='url' content='https://global.discourse-cdn.com/nvidia/original/3X/a/1/a1ef6e0c1fbd3fad5bf82538b78dfaa9c5fa1a61.png'> </div> </div> <div id='post_1' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" rel='nofollow' href='https://forums.developer.nvidia.com/u/wangyanni541'><span itemprop='name'>wangyanni541</span></a> </span> <link itemprop="mainEntityOfPage" href="https://forums.developer.nvidia.com/t/clara-parabricks-4-3-1-fq2bam-meth-is-slow/299511"> <link itemprop="image" href="https://global.discourse-cdn.com/nvidia/original/4X/8/2/8/8282524699b14c29a83820c4eed0a45fae7cc496.png"> <span class="crawler-post-infos"> <time datetime='2024-07-11T16:32:29Z' class='post-time'> July 11, 2024, 4:32pm </time> <meta itemprop='dateModified' content='2024-07-11T16:32:29Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <p>The speed of fq2bam_meth doesn’t seem as fast as I expected. Are there any parameters that can be optimized?<br> my command is :<br> <strong>docker run -it --gpus all -e NVIDIA_DRIVER_CAPABILITIES=all --volume /home/wang_yanni/sc_meth_ATAC/integratioh/fq2bam:/mydata 74f2b983a773 /bin/bash</strong><br> <strong>time pbrun fq2bam_meth --ref hg38.fa --in-se-fq …/deep_board/Airway-S43-2_supplement/A10.1.fastq.gz --out-bam A10_2stream.bam --bwa-nstreams 2 --num-gpus 3 --gpuwrite --bwa-cpu-thread-pool 16</strong><br> the output is :</p> <p>[Parabricks Options Mesg]: Checking argument compatibility<br> [Parabricks Options Mesg]: Automatically generating ID prefix<br> [Parabricks Options Mesg]: Read group created for /mydata/deep_board/Airway-S43-2_supplement/A10.R1.fastq.gz<br> [Parabricks Options Mesg]: <span class="mention">@RG</span>\tID:HWYGYDSX7.3\tLB:lib1\tPL:bar\tSM:sample\tPU:HWYGYDSX7.3<br> [PB Info 2024-Jul-11 16:00:15] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:00:15] || Parabricks accelerated Genomics Pipeline ||<br> [PB Info 2024-Jul-11 16:00:15] || Version 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:00:15] || GPU-PBBWA mem, Sorting Phase-I ||<br> [PB Info 2024-Jul-11 16:00:15] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:00:15] Mode = single-ended-gpu<br> [PB Info 2024-Jul-11 16:00:15] Running with 3 GPU(s), using 2 stream(s) per device with 16 worker threads per GPU<br> [PB Info 2024-Jul-11 16:00:25] # 10 0 0 0 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 0 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 262144 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 65536 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 327680 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 196608 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 393216 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 131072 reads before itself<br> [PB Info 2024-Jul-11 16:00:29] Single-ended recovery mode for batch with 458752 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Time spent reading: 0.655694 seconds<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 524288 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 786432 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 720896 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 851968 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 589824 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 655360 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 917504 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1179648 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1048576 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 983040 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1245184 reads before itself<br> [PB Info 2024-Jul-11 16:00:30] Single-ended recovery mode for batch with 1310720 reads before itself<br> [PB Info 2024-Jul-11 16:00:31] Single-ended recovery mode for batch with 1114112 reads before itself<br> [PB Info 2024-Jul-11 16:00:35] # 0 1 0 0 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:00:45] # 0 1 0 0 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:00:55] # 0 0 0 30789160 bases/GPU/minute: 61578320.0<br> [PB Info 2024-Jul-11 16:01:05] # 0 0 0 30789160 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:01:15] # 0 0 0 59753069 bases/GPU/minute: 57927818.0<br> [PB Info 2024-Jul-11 16:01:25] # 0 0 0 59753069 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:01:35] # 0 0 0 88726172 bases/GPU/minute: 57946206.0<br> [PB Info 2024-Jul-11 16:01:45] # 0 0 0 88726172 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:01:55] # 0 0 0 117878289 bases/GPU/minute: 58304234.0<br> [PB Info 2024-Jul-11 16:02:05] # 0 0 0 147031106 bases/GPU/minute: 58305634.0<br> [PB Info 2024-Jul-11 16:02:15] # 0 0 0 147031106 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:02:25] # 0 0 0 176147936 bases/GPU/minute: 58233660.0<br> [PB Info 2024-Jul-11 16:02:35] # 0 0 0 176147936 bases/GPU/minute: 0.0<br> [PB Info 2024-Jul-11 16:02:45] # 0 0 0 205281290 bases/GPU/minute: 58266708.0<br> [PB Info 2024-Jul-11 16:02:55] Rate stats (based on sampling every 10 seconds):<br> min rate: 0.0 bases/GPU/minute<br> max rate: 61578320.0 bases/GPU/minute<br> avg rate: 27370838.7 bases/GPU/minute<br> [PB Info 2024-Jul-11 16:02:55] Time spent monitoring (multiple of 10): 160.010<br> [PB Info 2024-Jul-11 16:02:55] bwalib run finished in 151.575 seconds<br> [PB Info 2024-Jul-11 16:02:55] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:02:55] || Program: GPU-PBBWA mem, Sorting Phase-I ||<br> [PB Info 2024-Jul-11 16:02:55] || Version: 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:02:55] || Start Time: Thu Jul 11 16:00:15 2024 ||<br> [PB Info 2024-Jul-11 16:02:55] || End Time: Thu Jul 11 16:02:55 2024 ||<br> [PB Info 2024-Jul-11 16:02:55] || Total Time: 2 minutes 40 seconds ||<br> [PB Info 2024-Jul-11 16:02:55] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:02:58] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:02:58] || Parabricks accelerated Genomics Pipeline ||<br> [PB Info 2024-Jul-11 16:02:58] || Version 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:02:58] || Sorting Phase-II ||<br> [PB Info 2024-Jul-11 16:02:58] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:02:58] progressMeter - Percentage<br> [PB Info 2024-Jul-11 16:02:58] 0.0<br> [PB Info 2024-Jul-11 16:03:03] Sorting and Marking: 5.001 seconds<br> [PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:03:03] || Program: Sorting Phase-II ||<br> [PB Info 2024-Jul-11 16:03:03] || Version: 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:03:03] || Start Time: Thu Jul 11 16:02:58 2024 ||<br> [PB Info 2024-Jul-11 16:03:03] || End Time: Thu Jul 11 16:03:03 2024 ||<br> [PB Info 2024-Jul-11 16:03:03] || Total Time: 5 seconds ||<br> [PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:03:03] || Parabricks accelerated Genomics Pipeline ||<br> [PB Info 2024-Jul-11 16:03:03] || Version 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:03:03] || Marking Duplicates, BQSR ||<br> [PB Info 2024-Jul-11 16:03:03] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:03:03] CuBamWriter using CUDA device 2<br> [PB Info 2024-Jul-11 16:03:05] Using PBCuBamWriter for BAM writing (algo 0)<br> [PB Info 2024-Jul-11 16:03:05] progressMeter - Percentage<br> [PB Info 2024-Jul-11 16:03:15] 100.0<br> [PB Info 2024-Jul-11 16:03:16] BQSR and writing final BAM: 10.723 seconds<br> [PB Info 2024-Jul-11 16:03:16] ------------------------------------------------------------------------------<br> [PB Info 2024-Jul-11 16:03:16] || Program: Marking Duplicates, BQSR ||<br> [PB Info 2024-Jul-11 16:03:16] || Version: 4.3.1-1 ||<br> [PB Info 2024-Jul-11 16:03:16] || Start Time: Thu Jul 11 16:03:03 2024 ||<br> [PB Info 2024-Jul-11 16:03:16] || End Time: Thu Jul 11 16:03:16 2024 ||<br> [PB Info 2024-Jul-11 16:03:16] || Total Time: 13 seconds ||<br> [PB Info 2024-Jul-11 16:03:16] ------------------------------------------------------------------------------</p> <p>real 3m16.856s<br> user 105m42.950s<br> sys 0m54.351s</p> <p>nvidia-smi<br> <div class="lightbox-wrapper"><a class="lightbox" href="https://global.discourse-cdn.com/nvidia/original/4X/8/2/8/8282524699b14c29a83820c4eed0a45fae7cc496.png" data-download-href="/uploads/short-url/iCxhzzEI0z684BeRqh4a9iJoSb4.png?dl=1" title="image" rel="noopener nofollow ugc"><img src="https://global.discourse-cdn.com/nvidia/original/4X/8/2/8/8282524699b14c29a83820c4eed0a45fae7cc496.png" alt="image" data-base62-sha1="iCxhzzEI0z684BeRqh4a9iJoSb4" width="357" height="500" data-dominant-color="2B2B2B"><div class="meta"><svg class="fa d-icon d-icon-far-image svg-icon" aria-hidden="true"><use href="#far-image"></use></svg><span class="filename">image</span><span class="informations">1104×1542 56.1 KB</span><svg class="fa d-icon d-icon-discourse-expand svg-icon" aria-hidden="true"><use href="#discourse-expand"></use></svg></div></a></div></p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> </div> <div id='post_2' itemprop='comment' itemscope itemtype='http://schema.org/Comment' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" rel='nofollow' href='https://forums.developer.nvidia.com/u/wangyanni541'><span itemprop='name'>wangyanni541</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-07-11T16:39:18Z' class='post-time'> July 11, 2024, 4:39pm </time> <meta itemprop='dateModified' content='2024-07-11T16:39:18Z'> <span itemprop='position'>2</span> </span> </div> <div class='post' itemprop='text'> <p>the Volatile GPU-Util of my GPU is 0 %, Is this phenomenon normal</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="0" /> <span class='post-likes'></span> </div> </div> </div> <div id="related-topics" class="more-topics__list " role="complementary" aria-labelledby="related-topics-title"> <h3 id="related-topics-title" class="more-topics__list-title"> Related topics </h3> <div class="topic-list-container" itemscope itemtype='http://schema.org/ItemList'> <meta 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title='views'>548</span> </td> <td> July 23, 2024 </td> </tr> <tr class="topic-list-item" id="topic-list-item-250299"> <td class="main-link" itemprop='itemListElement' itemscope itemtype='http://schema.org/ListItem'> <meta itemprop='position' content='10'> <span class="link-top-line"> <a itemprop='url' href='https://forums.developer.nvidia.com/t/fq2bam-error-received-signal-11/250299' class='title raw-link raw-topic-link'>Fq2bam Error Received signal: 11</a> </span> <div class="link-bottom-line"> <a href='/c/healthcare/parabricks/290' class='badge-wrapper bullet'> <span class='badge-category-bg' style='background-color: #76B900'></span> <span class='badge-category clear-badge'> <span class='category-name'>Parabricks</span> </span> </a> <div class="discourse-tags"> <a href='https://forums.developer.nvidia.com/tag/cuda' class='discourse-tag'>cuda</a> ,  <a href='https://forums.developer.nvidia.com/tag/ai' class='discourse-tag'>ai</a> </div> </div> </td> <td class="replies"> <span 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