hi,
I have UBUNTU 20.04 and two Gpus P40 .Getting the following error below when running parabricks with mode pbrun "f2qbam. "
I am using the parabricks container on singularity and testing with the files that i got in nvidia tutorials , Homo_sapiens_assembly38.fasta
#Calling the singularity run with --nv parameter
bin/singularity run --nv parabricks/clara-parabricks_4.0.1-1.sif pbrun fq2bam --num-gpus 2 --ref ~/local/src/singularity-ce/parabricks/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta --in-fq ~/local/src/singularity-ce/parabricks/parabricks_sample/Data/sample_1.fq.gz ~/local/src/singularity-ce/parabricks/parabricks_sample/Data/sample_2.fq.gz --out-bam ~/local/src/singularity-ce/parabricks/outputdir/fq2bam_output.bam
Always on the same error mensage :
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for /home/danilo_barboza/local/src/singularity-
ce/parabricks/parabricks_sample/Data/sample_1.fq.gz and /home/danilo_barboza/local/src/singularity-
ce/parabricks/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
g 1 b 0 B 1 P 8 s 1 r 0 o 2 m 1 z 4 f 2 v 0 M 2 X 0 name /home/danilo_barboza/local/src/singularity-ce/parabricks/outputdir/fq2bam_output.bam
/usr/local/parabricks/binaries//bin/bwa mem /home/danilo_barboza/local/src/singularity-ce/parabricks/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta /home/danilo_barboza/local/src/singularity-ce/parabricks/parabricks_sample/Data/sample_1.fq.gz /home/danilo_barboza/local/src/singularity-ce/parabricks/parabricks_sample/Data/sample_2.fq.gz @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1 -Z ./pbOpts.txt
[PB Info 2023-Mar-22 22:52:43] ------------------------------------------------------------------------------
[PB Info 2023-Mar-22 22:52:43] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Mar-22 22:52:43] || Version 4.0.1-1 ||
[PB Info 2023-Mar-22 22:52:43] || GPU-BWA mem, Sorting Phase-I ||
[PB Info 2023-Mar-22 22:52:43] ------------------------------------------------------------------------------
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[PB Info 2023-Mar-22 22:53:03] GPU-BWA mem
[PB Info 2023-Mar-22 22:53:03] ProgressMeter Reads Base Pairs Aligned
For technical support visit Help - NVIDIA Docs
Exiting…
Could not run fq2bam
Exiting pbrun …
INFO: Cleaning up image…
Memory
$ cat /proc/meminfo
MemTotal: 1056256480 kB
MemFree: 47753832 kB
MemAvailable: 993996072 kB
Buffers: 3202116 kB
Cached: 933634784 kB
SwapCached: 4841092 kB
CPU
[sudo] password for danilo_barboza:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 224
On-line CPU(s) list: 0-223
Thread(s) per core: 2
Core(s) per socket: 28
Socket(s): 4
NUMA node(s): 4
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
GPUS
±----------------------------------------------------------------------------+
| NVIDIA-SMI 510.39.01 Driver Version: 510.39.01 CUDA Version: 11.6 |
|-------------------------------±---------------------±---------------------+
| 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 P40 Off | 00000000:25:00.0 Off | 0 |
| N/A 49C P0 114W / 250W | 2342MiB / 23040MiB | 79% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
| 1 Tesla P40 Off | 00000000:5B:00.0 Off | 0 |
| N/A 22C P8 9W / 250W | 2MiB / 23040MiB | 0% Default |
| | | N/A |
±------------------------------±---------------------±---------------------+
±----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 1624076 C java 2340MiB |
Please helpp