4.5.0-1 : Haplotype Caller : Number of GPUs requested (2) is more than number of GPUs (0) in the system., exitin

Healthcare & Life Sciences Parabricks
,
1

Hi Parabricks Team,

I’ve successfully used apptainer + pb to execute pb_run fastq2bam . It created my bam files and now I want to use pb_run haplotypecaller. But I get the following error:

[PB Error 2025-Sep-05 18:17:13][src/haplotype_vc.cpp:843] Number of GPUs requested (2) is more than number of GPUs (0) in the system., exiting.

my comand was:

nvidia-smi 1>&2

pbrun haplotypecaller \
    --num-gpus 2 \
    --ref Homo_sapiens_assembly38.fasta \
    --in-bam "name.cram" \
    --gvcf \
    --out-variants "name.g.vcf.gz" \
    --tmp-dir TMP \
    --logfile name.hc.log \

the stderr is:

INFO:    underlay of /etc/localtime required more than 50 (79) bind mounts
INFO:    underlay of /usr/bin/nvidia-smi required more than 50 (374) bind mounts
Fri Sep  5 18:17:12 2025       
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 575.51.03              Driver Version: 575.51.03      CUDA Version: 12.9     |
|-----------------------------------------+------------------------+----------------------+
| 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-PCIE-40GB          On  |   00000000:21:00.0 Off |                    0 |
| N/A   30C    P0             33W /  250W |       0MiB /  40960MiB |      0%      Default |
|                                         |                        |             Disabled |
+-----------------------------------------+------------------------+----------------------+
|   1  NVIDIA A100-PCIE-40GB          On  |   00000000:81:00.0 Off |                    0 |
| N/A   30C    P0             33W /  250W |       0MiB /  40960MiB |      0%      Default |
|                                         |                        |             Disabled |
+-----------------------------------------+------------------------+----------------------+
                                                                                         
+-----------------------------------------------------------------------------------------+
| Processes:                                                                              |
|  GPU   GI   CI              PID   Type   Process name                        GPU Memory |
|        ID   ID                                                               Usage      |
|=========================================================================================|
|  No running processes found                                                             |
+-----------------------------------------------------------------------------------------+
[PB Info 2025-Sep-05 18:17:13] ------------------------------------------------------------------------------
[PB Info 2025-Sep-05 18:17:13] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2025-Sep-05 18:17:13] ||                              Version 4.5.0-1                             ||
[PB Info 2025-Sep-05 18:17:13] ||                         GPU-GATK4 HaplotypeCaller                        ||
[PB Info 2025-Sep-05 18:17:13] ------------------------------------------------------------------------------
[PB Error 2025-Sep-05 18:17:13][src/haplotype_vc.cpp:843] Number of GPUs requested (2) is more than number of GPUs (0) in the system., exiting.

I don’t know much about working with GPUs. Can you please tell me what I’m doing wrong ?

thanks !

P.

PS: I saw Error with clara-parabricks:4.0.1-1 fq2bam - Bad argument value: Number of GPUs requested is more than number of gpus in system but it doesn’t help