Parabricks GPU request

Healthcare Parabricks
1

Hi, I am having trouble trying to request GPU access to run Parabricks.
I keep getting the error “Number of GPUs requested (8) is more than number of GPUs (1) in the system. Exiting …”
Here are the resources I tried to allocate:

#!/bin/bash
#SBATCH --job-name=bwa-seq4
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64gb
#SBATCH --time=0:200:00
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH --mail-user=xxx@ufl.edu
#SBATCH --error=Bwa_seq4_%A.err
#SBATCH --output=Bwa_seq4_%A.out
#SBATCH --account=reed
#SBATCH --qos=reed
#SBATCH --partition=gpu
#SBATCH --gpus=1
#SBATCH --constraint=rtx6000

I have access to 274GB of MEM and 78 CPUs in our HPC. I also tried the command NVIDIA_VISIBLE_DEVICES=“1” before the pbrun command. Nothing seems to work to override the default 8 GPU request.
Does this means I need to have access to 8 GPUs to run parabricks?

2

Hi,

to be able to run with specific GPUs on a multi GPU system you need to provide options : --num-gpus NUM_GPUS and --gpu-devices GPU_DEVICES.

Please refer to help or documentation for more information about those options.

Myrieme

3

Thank you so much! It worked after adding --num-gpus with the pbrun