# \[Nvidia/Parabricks\] Does pbrun support GPU options?

**URL:** <https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024>\
**Category:** Parabricks\
**Created:** [October 27, 2020, 3:39am UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024 "2020-10-27T03:39:50Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![tsungjung411](https://sea2.discourse-cdn.com/nvidia/user_avatar/forums.developer.nvidia.com/tsungjung411/32/46741_2.png) [@tsungjung411](https://forums.developer.nvidia.com/u/tsungjung411)\
**Post date:** [October 27, 2020, 3:39am UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024/1 "2020-10-27T03:39:50Z")

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hi, there

When I ran `pbrun fq2bam ...` to test a small dataset, I met a memory error as shown below.

```auto
$ pbrun fq2bam --ref /home/anonymous/parabricks/dataset/D99999_S99_L001/human_g1000_v37_decoy.fasta --in-fq /home/anonymous/parabricks/dataset/D99999_S99_L001/D99999_S99_L001_R1.fastq.gz /home/anonymous/parabricks/dataset/D99999_S99_L001/D99999_S99_L001_R2.fastq.gz --out-bam /home/anonymous/parabricks/dataset/D99999_S99_L001/out.bam
Please visit https://www.nvidia.com/en-us/docs/parabricks/ for detailed documentation

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for
/home/anonymous/parabricks/dataset/D99999_S99_L001/D99999_S99_L001_R1.fastq.gz and
/home/anonymous/parabricks/dataset/D99999_S99_L001/D99999_S99_L001_R2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:000000000-C54LP.1\tLB:lib1\tPL:bar\tSM:sample\tPU:000000000-C54LP.1
------------------------------------------------------------------------------
|| Parabricks accelerated Genomics Pipeline ||
|| Version v3.1.1 ||
|| GPU-BWA mem, Sorting Phase-I ||
|| Contact: Parabricks-Support@nvidia.com ||
------------------------------------------------------------------------------
Not enough available memory for these GPUs...
Please contact Parabricks-Support@nvidia.com if you are rightfully using the software but cannot run it.
Please contact Parabricks-Support@nvidia.com for any questions. Exiting...

Could not run fq2bam
Exiting pbrun ...

```

  

Here is the GPU summary of the Driver and CUDA versions

```auto
$ nvidia-smi

```

 ![image](https://global.discourse-cdn.com/nvidia/original/3X/e/c/ecc47172a42a2232dca3fd0ae6227d505baf6217.png)

Is there any methods to restrict the GPU usages ( memory\<= 11GB) to fulfill my requirements?

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<div class="post-metadata">

**Author:** ![tsungjung411](https://sea2.discourse-cdn.com/nvidia/user_avatar/forums.developer.nvidia.com/tsungjung411/32/46741_2.png) [@tsungjung411](https://forums.developer.nvidia.com/u/tsungjung411)\
**Post date:** [November 3, 2020, 9:42am UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024/2 "2020-11-03T09:42:52Z")

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> Not enough available memory for these GPUs…

Attached the log:

```auto
cudaSafeCall() failed at ParaBricks/src/memoryManager.cu:78 : out of memory
cudaSafeCall() failed at ParaBricks/src/samGenerator.cu:781 : out of memory
cudaSafeCall() failed at ParaBricks/src/samGenerator.cu:781 : out of memory
cudaSafeCall() failed at ParaBricks/src/samGenerator.cu:781 : out of memory
Please contact support@parabricks.com for any questions. Exiting...

```

According to the article “[There is no CUDA API to limit memory usage, with or without nvidia-docker.](https://github.com/NVIDIA/nvidia-docker/issues/810)”,

there is a comment:

> There is no CUDA API to limit memory usage, with or without nvidia-docker.

so bad…

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<div class="post-metadata">

**Author:** ![mdemouth](https://sea2.discourse-cdn.com/nvidia/user_avatar/forums.developer.nvidia.com/mdemouth/32/16591_2.png) [@mdemouth](https://forums.developer.nvidia.com/u/mdemouth)\
**Post date:** [November 3, 2020, 10:13am UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024/3 "2020-11-03T10:13:41Z")

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Hi,

we are sorry, but one of the requirements of Clara Parabricks Pipelines is GPU with 12 GB memory RAM or more.

[https://docs.nvidia.com/clara/parabricks/v3.0/text/local\_installation.html](https://docs.nvidia.com/clara/parabricks/v3.0/text/local_installation.html)

Myrieme

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<div class="post-metadata">

**Author:** ![TomNVIDIA](https://sea2.discourse-cdn.com/nvidia/user_avatar/forums.developer.nvidia.com/tomnvidia/32/14181_2.png) [@TomNVIDIA](https://forums.developer.nvidia.com/u/TomNVIDIA)\
**Post date:** [October 12, 2021, 7:46pm UTC](https://forums.developer.nvidia.com/t/nvidia-parabricks-does-pbrun-support-gpu-options/158024/4 "2021-10-12T19:46:09Z")

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