Hi
I am trying out clara-parabricks:4.0.1-1.sif on a g4dn.metal EC2 which has 8 GPUs
This is how I created my sif file:
singularity build clara-parabricks_4.0.1-1.sif docker://nvcr.io/nvidia/clara/clara-parabricks:4.0.1-1
And I get this error when trying to run fq2bam
Bad argument value: Number of GPUs requested (8) is more than number of GPUs (0in the system., exiting.
This is nvidia-smi on the host
nvidia-smi
Sun Jun 4 18:34:55 2023
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.141.03 Driver Version: 470.141.03 CUDA Version: 11.4 |
|-------------------------------+----------------------+----------------------+
| 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 Tesla T4 Off | 00000000:18:00.0 Off | 0 |
| N/A 34C P0 25W / 70W | 13458MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 1 Tesla T4 Off | 00000000:19:00.0 Off | 0 |
| N/A 29C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 2 Tesla T4 Off | 00000000:35:00.0 Off | 0 |
| N/A 30C P8 11W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 3 Tesla T4 Off | 00000000:36:00.0 Off | 0 |
| N/A 28C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 4 Tesla T4 Off | 00000000:E7:00.0 Off | 0 |
| N/A 29C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 5 Tesla T4 Off | 00000000:E8:00.0 Off | 0 |
| N/A 29C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 6 Tesla T4 Off | 00000000:F4:00.0 Off | 0 |
| N/A 29C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 7 Tesla T4 Off | 00000000:F5:00.0 Off | 0 |
| N/A 29C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 7387 C python 13455MiB |
+-----------------------------------------------------------------------------+
This below is from inside the container after invoking it on command like by singularity shell --nv clara-parabricks_4.0.1-1.sif
Singularity> date
Sun Jun 4 18:38:42 EDT 2023
Singularity> nvidia-smi
Sun Jun 4 18:39:50 2023
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.141.03 Driver Version: 470.141.03 CUDA Version: 11.4 |
|-------------------------------+----------------------+----------------------+
| 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 Tesla T4 Off | 00000000:18:00.0 Off | 0 |
| N/A 42C P0 26W / 70W | 13458MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 1 Tesla T4 Off | 00000000:19:00.0 Off | 0 |
| N/A 31C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 2 Tesla T4 Off | 00000000:35:00.0 Off | 0 |
| N/A 32C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 3 Tesla T4 Off | 00000000:36:00.0 Off | 0 |
| N/A 30C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 4 Tesla T4 Off | 00000000:E7:00.0 Off | 0 |
| N/A 31C P8 8W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 5 Tesla T4 Off | 00000000:E8:00.0 Off | 0 |
| N/A 31C P8 11W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 6 Tesla T4 Off | 00000000:F4:00.0 Off | 0 |
| N/A 32C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 7 Tesla T4 Off | 00000000:F5:00.0 Off | 0 |
| N/A 31C P8 9W / 70W | 3MiB / 15109MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 7387 C python 13455MiB |
+-----------------------------------------------------------------------------+
pbrun fq2bam \
> --ref parabricks_sample/Ref/Homo_sapiens_assembly38.fasta \
> --in-fq parabricks_sample/Data/sample_1.fq.gz parabricks_sample/Data/sample_2.fq.gz \
> --out-bam fq2bam_output.bam
[PB Error 2023-Jun-04 18:42:55][ParaBricks/src/pbOpts.cu:132] Bad argument value: Number of GPUs requested (8) is more than number of GPUs (0in the system., exiting.
Would appreciate any help.
Thanks in advance.