"Could not run fq2bam" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial data - Parabricks

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My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB). Here is my printout from the nvidia-smi: Thu Nov 28 10:00:04 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.183.01 Driver Version: 535.183.01 CUDA Version: 12.2 | |-..." /> <meta name="twitter:description" content="Hello There I have encountered and issue that disallowes me to use parabricks, as it simply does not work, when used as presented in the fq2bam tutorial. My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB). 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href="/"> NVIDIA Developer Forums </a> </header> <div id="main-outlet" class="wrap" role="main"> <div id="topic-title"> <h1> <a href="/t/could-not-run-fq2bam-is-the-only-verbose-output-from-parabricks-4-4-0-1-and-4-3-2-1-on-tutorial-data/315052">"Could not run fq2bam" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial data</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" 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href='https://forums.developer.nvidia.com/t/could-not-run-fq2bam-is-the-only-verbose-output-from-parabricks-4-4-0-1-and-4-3-2-1-on-tutorial-data/315052'> <meta itemprop='datePublished' content='2024-11-28T10:03:12Z'> <meta itemprop='articleSection' content='Parabricks'> <meta itemprop='keywords' content='demos-and-tutorials, ai, fq2bam'> <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/michal66'><span itemprop='name'>michal66</span></a> </span> <link itemprop="mainEntityOfPage" href="https://forums.developer.nvidia.com/t/could-not-run-fq2bam-is-the-only-verbose-output-from-parabricks-4-4-0-1-and-4-3-2-1-on-tutorial-data/315052"> <span class="crawler-post-infos"> <time datetime='2024-11-28T10:03:12Z' class='post-time'> November 28, 2024, 10:03am </time> <meta itemprop='dateModified' content='2024-11-28T10:03:12Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <h1><a name="p-1528585-hello-there-1" class="anchor" href="#p-1528585-hello-there-1"></a>Hello There</h1> <p>I have encountered and issue that disallowes me to use parabricks, as it simply does not work, when used as presented in the fq2bam tutorial.</p> <p>My computational environment consists of 16vCPUs, 256GB of RAM and 1 Tesla A100 (80GB).</p> <p>Here is my printout from the nvidia-smi:</p> <pre><code class="lang-auto">Thu Nov 28 10:00:04 2024 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.183.01 Driver Version: 535.183.01 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 NVIDIA A100-SXM4-80GB Off | 00000000:00:10.0 Off | 0 | | N/A 23C P0 49W / 500W | 0MiB / 81920MiB | 0% Default | | | | Disabled | +-----------------------------------------+----------------------+----------------------+ +---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+ </code></pre> <p>My command, for running the fq2bam does not differ greatly from the original one from the tutorial (which also does not work properly) that i have tried, returns the least informative log i have had ever see. Literally no information can be inferred from that printout.</p> <pre><code class="lang-auto">Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation /usr/local/parabricks/run_pb.py fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options=-K 19 --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam --tmp-dir //1U548PMS [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and /workdir/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 /usr/local/parabricks/binaries/bin/pbbwa /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --mode pair-ended-gpu /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz -R @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 --nGPUs 1 --nstreams 4 --cpu-thread-pool 16 -K 19 -F 0 --min-read-size 1 --max-read-size 480 --markdups --write-bin --verbose For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Could not run fq2bam Exiting pbrun ... </code></pre> <p>And the command that I have used is here:</p> <pre><code class="lang-auto">docker run --gpus all --rm --volume $(pwd):/workdir --volume $(pwd):/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 pbrun fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options="-K 19" --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam </code></pre> <p>What would be the solution for that issue?</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/michal66'><span itemprop='name'>michal66</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-11-29T08:44:13Z' class='post-time'> November 29, 2024, 8:44am </time> <meta itemprop='dateModified' content='2024-11-29T08:44:13Z'> <span itemprop='position'>2</span> </span> </div> <div class='post' itemprop='text'> <p>Hi there nvidia.<br> Are you even working on support for developers?<br> There are a lot of problems just like mine, that have been ghosted for even longer than 24 hours.<br> It’s not even funny, since you are marketing your solutions as “for Healthcare & Life Sciences”. All of life sciences professionals would agree, that such form of support is unacceptable, especially since your software and tutorials seems to be quite erroneous and counter intuitive.</p> <p>It would be greatly appreciated if you would respond with something that could be usefull.</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="1" /> <span class='post-likes'>1 Like</span> </div> </div> <div id='post_3' 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/michal66'><span itemprop='name'>michal66</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-02T11:15:28Z' class='post-time'> December 2, 2024, 11:15am </time> <meta itemprop='dateModified' content='2024-12-02T11:15:28Z'> <span itemprop='position'>3</span> </span> </div> <div class='post' itemprop='text'> <p>Hi nvidia,<br> Any news on troubleshooting of your own tutorial?</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_4' 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/dpuleri'><span itemprop='name'>dpuleri</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-02T23:45:46Z' class='post-time'> December 2, 2024, 11:45pm </time> <meta itemprop='dateModified' content='2024-12-02T23:45:46Z'> <span itemprop='position'>4</span> </span> </div> <div class='post' itemprop='text'> <p>Hello, apologies for the late reply. We are based in the US and these posts came during the Thanksgiving holiday.</p> <p>We double-checked and the command from the tutorial works as displayed on <a href="https://docs.nvidia.com/clara/parabricks/latest/tutorials/fq2bam_tutorial.html" class="inline-onebox" rel="noopener nofollow ugc">FQ2BAM Tutorial - NVIDIA Docs</a>. The exact directories and directory structure may need to be changed to match your directory structure.</p> <p>Looking at the particular command you ran, you added <code>--bwa-options="-K 19"</code>. The option <code>-K #</code> for bwa-mem is a hidden parameter that controls the chunk size (in terms of number of bases) that is used for the window to determine the best alignment with output for paired-alignment. The number 19 is not bad, just very small and will severely hamper performance. Using a larger parameter like <code>--bwa-options="-K 10000000"</code> would yield better performance and still maintain reproducibility if you pass the same parameter to another run. However, that is not causing the crash you’re seeing.</p> <p>The strange thing with your run is that the actual binary is not being run. It seems to be getting a signal from docker or the host OS before getting to that stage (that is why fq2bam says “Exiting…” because it received a signal). Usually the signal that is received which could cause this printout is an out of memory signal but 256GB should be more than enough.</p> <p>Could you confirm that the sample data downloaded correctly? The md5sum I see for <code>parabricks_sample.tar.gz</code> is <code>05b51303a7b9939c9232f88e7ecd1444</code>.</p> <p>One other idea would be to explicitly set the temporary directory for work to be <code>--tmp-dir /workdir</code>. Although we have tested and we will print out an informative error if the disk is out of space.</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_5' 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/michal66'><span itemprop='name'>michal66</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-03T09:11:47Z' class='post-time'> December 3, 2024, 9:11am </time> <meta itemprop='dateModified' content='2024-12-03T09:11:47Z'> <span itemprop='position'>5</span> </span> </div> <div class='post' itemprop='text'> <p>Hi,<br> I do confirm that the md5sum is <code>05b51303a7b9939c9232f88e7ecd1444</code><br> The command<br> <code>docker run --gpus all --rm --volume $(pwd):/workdir --volume $(pwd):/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 pbrun fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options="-K 10000000" --tmp-dir /workdir --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam</code><br> have returned same output as before:</p> <pre><code class="lang-auto">Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation /usr/local/parabricks/run_pb.py fq2bam --num-gpus 1 --x3 --verbose --memory-limit 60 --bwa-options=-K 10000000 --tmp-dir /workdir/OHF980NE --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and /workdir/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 /usr/local/parabricks/binaries/bin/pbbwa /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --mode pair-ended-gpu /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz -R @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 --nGPUs 1 --nstreams 4 --cpu-thread-pool 16 -K 10000000 -F 0 --min-read-size 1 --max-read-size 480 --markdups --write-bin --verbose For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Could not run fq2bam Exiting pbrun ... </code></pre> <p>Moreover, when i check the config of nvidia container toolkit, everything seems to be fine, and the cuda sample tests are passed.</p> <pre><code class="lang-auto">$ docker run --rm --gpus all nvcr.io/nvidia/k8s/cuda-sample:vectoradd-cuda10.2 [Vector addition of 50000 elements] Copy input data from the host memory to the CUDA device CUDA kernel launch with 196 blocks of 256 threads Copy output data from the CUDA device to the host memory Test PASSED Done $ docker run --rm --gpus all nvcr.io/nvidia/k8s/cuda-sample:devicequery /cuda-samples/sample Starting... CUDA Device Query (Runtime API) version (CUDART static linking) Detected 1 CUDA Capable device(s) Device 0: "NVIDIA A100-SXM4-80GB" CUDA Driver Version / Runtime Version 12.5 / 12.5 CUDA Capability Major/Minor version number: 8.0 Total amount of global memory: 81038 MBytes (84974239744 bytes) (108) Multiprocessors, (064) CUDA Cores/MP: 6912 CUDA Cores GPU Max Clock rate: 1410 MHz (1.41 GHz) Memory Clock rate: 1593 Mhz Memory Bus Width: 5120-bit L2 Cache Size: 41943040 bytes Maximum Texture Dimension Size (x,y,z) 1D=(131072), 2D=(131072, 65536), 3D=(16384, 16384, 16384) Maximum Layered 1D Texture Size, (num) layers 1D=(32768), 2048 layers Maximum Layered 2D Texture Size, (num) layers 2D=(32768, 32768), 2048 layers Total amount of constant memory: 65536 bytes Total amount of shared memory per block: 49152 bytes Total shared memory per multiprocessor: 167936 bytes Total number of registers available per block: 65536 Warp size: 32 Maximum number of threads per multiprocessor: 2048 Maximum number of threads per block: 1024 Max dimension size of a thread block (x,y,z): (1024, 1024, 64) Max dimension size of a grid size (x,y,z): (2147483647, 65535, 65535) Maximum memory pitch: 2147483647 bytes Texture alignment: 512 bytes Concurrent copy and kernel execution: Yes with 3 copy engine(s) Run time limit on kernels: No Integrated GPU sharing Host Memory: No Support host page-locked memory mapping: Yes Alignment requirement for Surfaces: Yes Device has ECC support: Enabled Device supports Unified Addressing (UVA): Yes Device supports Managed Memory: Yes Device supports Compute Preemption: Yes Supports Cooperative Kernel Launch: Yes Supports MultiDevice Co-op Kernel Launch: Yes Device PCI Domain ID / Bus ID / location ID: 0 / 0 / 16 Compute Mode: < Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 12.5, CUDA Runtime Version = 12.5, NumDevs = 1 Result = PASS </code></pre> </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_6' 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/dpuleri'><span itemprop='name'>dpuleri</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-03T14:48:54Z' class='post-time'> December 3, 2024, 2:48pm </time> <meta itemprop='dateModified' content='2024-12-03T14:48:54Z'> <span itemprop='position'>6</span> </span> </div> <div class='post' itemprop='text'> <p>Thanks for checking your CUDA install. That was going to be my next question.</p> <p>Can you do one more run that gets killed and then right after the run check your system log to see what happened:</p> <p><code>sudo journalctl -k --since "10 minutes ago" | grep "Killed process"</code></p> <p>For example, I forced one of my fq2bam processes to be killed by not giving it enough memory and I got the following:</p> <pre data-code-wrap="bash"><code class="lang-bash">sudo journalctl -k --since "10 minutes ago" | grep "Killed process" Dec 03 09:43:01 computer kernel: Memory cgroup out of memory: Killed process 697849 (pbbwa) total-vm:5651832kB, anon-rss:5212224kB, file-rss:7296kB, shmem-rss:0kB, UID:0 pgtables:10296kB oom_score_adj:0 </code></pre> </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_7' 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/michal66'><span itemprop='name'>michal66</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-04T08:26:47Z' class='post-time'> December 4, 2024, 8:26am </time> <meta itemprop='dateModified' content='2024-12-04T08:26:47Z'> <span itemprop='position'>7</span> </span> </div> <div class='post' itemprop='text'> <p>Hi,<br> Unfortunetely the journalctl does not return anything, as no process has been killed.<br> On the other hand, there is a new printout while trying to run the process within the container.</p> <p>After entering the container with<br> <code>$ docker run --gpus all -it --rm --volume $(pwd):/workdir --volume $(pwd):/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 /bin/bash</code></p> <p>and running this command inside of it<br> <code>/usr/local/parabricks/binaries/bin/pbbwa /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --mode pair-ended-gpu /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz -R @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 --nGPUs 1 --nstreams 4 --cpu-thread-pool 16 -K 10000000 -F 0 --min-read-size 1 --max-read-size 480 --markdups --write-bin --verbose</code></p> <p>The output I’m getting is pointing directly to the culprit<br> <code>/usr/local/parabricks/binaries/bin/pbbwa: error while loading shared libraries: libfilehandle.so: cannot open shared object file: No such file or directory</code></p> <p>This seems like the parabricks container in version 4.4.0-1 has not been created properly and there are errors within shared libraries.</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_8' 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/dpuleri'><span itemprop='name'>dpuleri</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2024-12-04T14:28:36Z' class='post-time'> December 4, 2024, 2:28pm </time> <meta itemprop='dateModified' content='2024-12-04T14:28:36Z'> <span itemprop='position'>8</span> </span> </div> <div class='post' itemprop='text'> <p>We set the <code>LD_LIBRARY_PATH</code> when running through <code>pbrun</code>. That is the entry point for users. The shared libraries are correct in the container and all paths will be set if you run through <code>pbrun</code>.</p> <p>We have not had other reports of users having issues with the container.</p> <p>Can you give a full description of your environment? Are you running in the cloud? If so, what image, instance, etc. On-prem? What OS? CUDA driver version? Can you confirm that the container was downloaded correctly by confirming the sha256sum?</p> <p>If you have NVIDIA Enterprise Support, the best way to get the issue resolved is by contacting our dedicated Enterprise Support Team. You can contact our support team via web portal, phone, or web form. You can find this information listed on our <a href="https://www.nvidia.com/en-us/support/enterprise/" rel="noopener nofollow ugc">Enterprise Customer Support page</a>.</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_9' 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/snandi'><span itemprop='name'>snandi</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2025-01-15T10:26:18Z' class='post-time'> January 15, 2025, 10:26am </time> <meta itemprop='dateModified' content='2025-01-15T10:26:18Z'> <span itemprop='position'>9</span> </span> </div> <div class='post' itemprop='text'> <p>Hi,<br> I am trying to run fq2bam as follows:</p> <p><code>> docker run --gpus all --rm --volume $(pwd)/input:/workdir --volume $(pwd)/output:/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 pbrun fq2bam --tmp-dir /workdir --ref /workdir/hg38.ucsc.fa --in-fq /workdir/LP6008408-DNA_A02_1.paired.fq.gz /workdir/LP6008408-DNA_A02_2.paired.fq.gz --out-bam /outputdir/fq2bam_output.bam</code></p> <p>But it is terminating/crashing as follows:</p> <pre><code class="lang-auto">[PB Info 2025-Jan-14 13:32:49] # 100 7 100 7 0 0 pool: 98 132814476683 bases/GPU/minute: 2166340497.0 For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation Could not run fq2bam Exiting pbrun ... </code></pre> <p>As suggested by dbuleri to run<br> <code>sudo journalctl -k --since "10 minutes ago" | grep "Killed process"</code><br> which outputs:<br> <code>Jan 14 14:32:56 vs2000.vll.se kernel: Out of memory: Killed process 1026330 (pbbwa) total-vm:729249424kB, anon-rss:389526672kB, file-rss:164352kB, shmem-rss:274944kB, UID:0 pgtables:826756kB oom_score_adj:0</code></p> <p>However, the example files worked well with me.</p> <p>The fastq file I am using is of ~30GB after ziped. If I unzip it it is around 150GB. I can run bwa-mem without any memory issue normally with CPUs.</p> <p>I am running the program on dual H100; RAM: 384G; Ubuntu 22.</p> <p>Thanks</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_10' 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/dpuleri'><span itemprop='name'>dpuleri</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2025-01-15T15:08:02Z' class='post-time'> January 15, 2025, 3:08pm </time> <meta itemprop='dateModified' content='2025-01-15T15:08:02Z'> <span itemprop='position'>10</span> </span> </div> <div class='post' itemprop='text'> <p>Hi snandi,</p> <p>Thank you for checking the system logs. Your job did indeed run out of memory. Did your job print out something that said “recovery mode”? That typically incurs a penalty for RAM. We will be making updates in our next release to reduce memory use and give users more control over peak memory use.</p> <p>One thing you can try now is to pass <code>--bwa-options="--reduce-batch-size"</code> as that may help. Otherwise the other option would be to use a system with more RAM for this particular case.</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_11' 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/snandi'><span itemprop='name'>snandi</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2025-01-16T08:15:58Z' class='post-time'> January 16, 2025, 8:15am </time> <meta itemprop='dateModified' content='2025-01-16T08:15:58Z'> <span itemprop='position'>11</span> </span> </div> <div class='post' itemprop='text'> <p>Thanks dpuleri,</p> <p>The</p> <blockquote> <p>–bwa-options=“–reduce-batch-size”</p> </blockquote> <p>worked!<br> My final command is:<br> docker run --gpus all --rm --volume $(pwd)/input:/workdir --volume $(pwd)/output:/outputdir <a href="http://nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1" rel="noopener nofollow ugc">nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1</a> pbrun fq2bam --tmp-dir /workdir --ref /workdir/hg38.ucsc.fa --in-fq /workdir/LP6008408-DNA_A02_1.paired.fq /workdir/LP6008408-DNA_A02_2.paired.fq --out-bam /outputdir/fq2bam_output.bam --bwa-options=“–reduce-batch-size”</p> <p>And yes, indeed my jobs printed “recovery mode” while running.</p> <pre><code class="lang-auto">... [PB Info 2025-Jan-16 07:19:24] Single-ended recovery mode for batch with 222265344 (both ends) reads before itself [PB Info 2025-Jan-16 07:19:28] Pair-ended recovery mode for batch with 220545024 (both ends) reads before itself [PB Info 2025-Jan-16 07:19:29] # 100 100 0 106 71 0 pool: 0 32819718088 bases/GPU/minute: 1062788712.0 [PB Info 2025-Jan-16 07:19:32] Pair-ended recovery mode for batch with 220528640 (both ends) reads before itself ... </code></pre> <p>Thanks!</p> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="1" /> <span class='post-likes'>1 Like</span> </div> </div> <div id='post_12' 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/dpuleri'><span itemprop='name'>dpuleri</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2025-01-16T14:56:36Z' class='post-time'> January 16, 2025, 2:56pm </time> <meta itemprop='dateModified' content='2025-01-16T14:56:36Z'> <span itemprop='position'>12</span> </span> </div> <div class='post' itemprop='text'> <p>Good to know. Thank you for following up!</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_13' 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/zasnuty'><span itemprop='name'>zasnuty</span></a> </span> <span class="crawler-post-infos"> <time itemprop='datePublished' datetime='2025-02-18T21:24:47Z' class='post-time'> February 18, 2025, 9:24pm </time> <meta itemprop='dateModified' content='2025-02-18T21:39:44Z'> <span itemprop='position'>13</span> </span> </div> <div class='post' itemprop='text'> <p>Hi,</p> <p>it looks I have similar problem as <a class="mention" href="/u/michal66">@michal66</a> .<br> I have a bare metal server with Debian bookworm installed, with nVidia L4 card.<br> I’m trying to run the tutorial, but it does not work, with no hint at all:</p> <pre><code class="lang-auto">$ time docker run --gpus all --rm --volume $(pwd):/workdir --volume $(pwd):/outputdir nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1 pbrun fq2bam --ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz /workdir/parabricks_sample/Data/sample_2.fq.gz --out-bam /outputdir/fq2bam_output.bam --low-memory [Parabricks Options Mesg]: Checking argument compatibility [Parabricks Options Mesg]: Set --bwa-options="-K #" to produce compatible pair-ended results with previous versions of fq2bam or BWA MEM. [Parabricks Options Mesg]: Automatically generating ID prefix [Parabricks Options Mesg]: Read group created for /workdir/parabricks_sample/Data/sample_1.fq.gz and /workdir/parabricks_sample/Data/sample_2.fq.gz [Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 [Parabricks Options Mesg]: Using --low-memory sets the number of streams in bwa mem to 1. For technical support visit https://docs.nvidia.com/clara/index.html#parabricks Exiting... Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation Could not run fq2bam Exiting pbrun ... real 0m0.899s user 0m0.018s sys 0m0.021s </code></pre> <p>Here is my nvidia-smi:</p> <pre><code class="lang-auto">$ nvidia-smi Tue Feb 18 22:22:58 2025 +---------------------------------------------------------------------------------------+ | NVIDIA-SMI 535.216.01 Driver Version: 535.216.01 CUDA Version: 12.2 | |-----------------------------------------+----------------------+----------------------+ | GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |=========================================+======================+======================| | 0 NVIDIA L4 On | 00000000:41:00.0 Off | 0 | | N/A 34C P8 11W / 72W | 0MiB / 23034MiB | 0% Default | | | | N/A | +-----------------------------------------+----------------------+----------------------+ +---------------------------------------------------------------------------------------+ | Processes: | | GPU GI CI PID Type Process name GPU Memory | | ID ID Usage | |=======================================================================================| | No running processes found | +---------------------------------------------------------------------------------------+ </code></pre> <p>Server has 256 GB of RAM, free. Pretty old CPU with 32 threads.<br> There is no “Killed process” on journalctl list.</p> <p>I’ve checked md5 sum, run</p> <pre><code class="lang-auto">docker run --rm --gpus all nvcr.io/nvidia/k8s/cuda-sample:vectoradd-cuda10.2 </code></pre> <p>as suggested above. 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"Could not run fq2bam" Is the only verbose output from Parabricks 4.4.0-1 and 4.3.2-1 on tutorial data - Parabricks - NVIDIA Developer Forums