Hi all,

I am having a really hard time getting to basecall with my GPU. I am a researcher learning bioinformatics on the side, so I am not super knowledgeable on working with containers/gpu's. I have extensively researched how to get it to work, but I mainly get to articles that are using a container for non-basecalling stuff, so if anyone has Ubuntu and has run basecalling on the GPU, any direction as to how you did it would be extremely AND I MEAN EXTREMELY helpful bc at the moment we have been basecalling with the CPU and its taking over 5hrs to baseball 7gb of Nanopore data!

Below are some commands I have run to check on the drivers, docker, and my comp specs!

ont-guppy version 6.1.1

 - $uname -a

Linux carter-balaj 5.14.0-1032-oem #35-Ubuntu SMP Thu Mar 31 12:49:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

- nvidia-smi

Wed Apr 6 07:54:36 2022
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 470.103.01 Driver Version: 470.103.01 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 Quadro RTX 5000 On | 00000000:91:00.0 On | Off |
| 33% 34C P8 18W / 230W | 493MiB / 16384MiB | 11% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 1807 G /usr/lib/xorg/Xorg 71MiB |
| 0 N/A N/A 3277 G /usr/lib/xorg/Xorg 157MiB |
| 0 N/A N/A 3405 G /usr/bin/gnome-shell 60MiB |
| 0 N/A N/A 4642 G /usr/lib/firefox/firefox 129MiB |
| 0 N/A N/A 4909 G /usr/lib/firefox/firefox 2MiB |
| 0 N/A N/A 6696 G /usr/lib/firefox/firefox 2MiB |
| 0 N/A N/A 6824 G /usr/lib/firefox/firefox 2MiB |
| 0 N/A N/A 6909 G /usr/lib/firefox/firefox 2MiB |
| 0 N/A N/A 8329 G /usr/lib/firefox/firefox 48MiB |
| 0 N/A N/A 39043 G /usr/lib/firefox/firefox 2MiB |



 - $ dpkg -l | grep -I nvidia

ii libaccinj64-10.1:amd64 10.1.243-3 amd64 NVIDIA ACCINJ Library (64-bit)
 ii libcublas10:amd64 10.1.243-3 amd64 NVIDIA cuBLAS Library
ii libcublaslt10:amd64 10.1.243-3 amd64 NVIDIA cuBLASLt Library
ii libcudart10.1:amd64 10.1.243-3 amd64 NVIDIA CUDA Runtime Library
ii libcufft10:amd64 10.1.243-3 amd64 NVIDIA cuFFT Library
ii libcufftw10:amd64 10.1.243-3 amd64 NVIDIA cuFFTW Library
ii libcuinj64-10.1:amd64 10.1.243-3 amd64 NVIDIA CUINJ Library (64-bit)
ii libcupti-dev:amd64 10.1.243-3 amd64 NVIDIA CUDA Profiler Tools Interface development files
ii libcupti-doc 10.1.243-3 all NVIDIA CUDA Profiler Tools Interface documentation
ii libcupti10.1:amd64 10.1.243-3 amd64 NVIDIA CUDA Profiler Tools Interface runtime library
ii libcurand10:amd64 10.1.243-3 amd64 NVIDIA cuRAND Library
ii libcusolver10:amd64 10.1.243-3 amd64 NVIDIA cuSOLVER Library
ii libcusolvermg10:amd64 10.1.243-3 amd64 NVIDIA cuSOLVERmg Library
ii libcusparse10:amd64 10.1.243-3 amd64 NVIDIA cuSPARSE Library
ii libnppc10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives core runtime library
ii libnppial10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Arithmetic and Logic
ii libnppicc10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Color Conversion
ii libnppicom10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Compression
ii libnppidei10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Data Exchange and Initialization
ii libnppif10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Filters
ii libnppig10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Geometry transforms
ii libnppim10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Morphological operations
ii libnppist10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Statistics
ii libnppisu10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Support
ii libnppitc10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives lib for Image Threshold and Compare
ii libnpps10:amd64 10.1.243-3 amd64 NVIDIA Performance Primitives for signal processing runtime library
ii libnvgraph10:amd64 10.1.243-3 amd64 NVIDIA Graph Analytics library (nvGRAPH)
ii libnvidia-cfg1-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA binary OpenGL/GLX configuration library
ii libnvidia-common-470 470.103.01-0ubuntu0.20.04.1 all Shared files used by the NVIDIA libraries
ii libnvidia-compute-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA libcompute package
ii libnvidia-compute-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVIDIA libcompute package
ii libnvidia-container-tools 1.9.0-1 amd64 NVIDIA container runtime library (command-line tools)
ii libnvidia-container1:amd64 1.9.0-1 amd64 NVIDIA container runtime library
ii libnvidia-decode-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA Video Decoding runtime libraries
ii libnvidia-decode-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVIDIA Video Decoding runtime libraries
ii libnvidia-encode-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVENC Video Encoding runtime library
ii libnvidia-encode-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVENC Video Encoding runtime library
ii libnvidia-extra-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 Extra libraries for the NVIDIA driver
ii libnvidia-fbc1-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA OpenGL-based Framebuffer Capture runtime library
ii libnvidia-fbc1-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVIDIA OpenGL-based Framebuffer Capture runtime library
ii libnvidia-gl-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA OpenGL/GLX/EGL/GLES GLVND libraries and Vulkan ICD
ii libnvidia-gl-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVIDIA OpenGL/GLX/EGL/GLES GLVND libraries and Vulkan ICD
ii libnvidia-ifr1-470:amd64 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA OpenGL-based Inband Frame Readback runtime library
ii libnvidia-ifr1-470:i386 470.103.01-0ubuntu0.20.04.1 i386 NVIDIA OpenGL-based Inband Frame Readback runtime library
ii libnvidia-ml-dev 10.1.243-3 amd64 NVIDIA Management Library (NVML) development files
ii libnvjpeg10:amd64 10.1.243-3 amd64 NVIDIA JPEG library (nvJPEG)
ii libnvrtc10.1:amd64 10.1.243-3 amd64 CUDA Runtime Compilation (NVIDIA NVRTC Library)
ii libnvtoolsext1:amd64 10.1.243-3 amd64 NVIDIA Tools Extension Library
ii libnvvm3:amd64 10.1.243-3 amd64 NVIDIA NVVM Library
ii nvidia-compute-utils-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA compute utilities
ii nvidia-container-toolkit 1.9.0-1 amd64 NVIDIA container runtime hook
ii nvidia-cuda-dev 10.1.243-3 amd64 NVIDIA CUDA development files
ii nvidia-cuda-doc 10.1.243-3 all NVIDIA CUDA and OpenCL documentation
ii nvidia-cuda-gdb 10.1.243-3 amd64 NVIDIA CUDA Debugger (GDB)
ii nvidia-cuda-toolkit 10.1.243-3 amd64 NVIDIA CUDA development toolkit
ii nvidia-dkms-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA DKMS package
ii nvidia-docker2 2.10.0-1 all nvidia-docker CLI wrapper
ii nvidia-driver-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA driver metapackage
ii nvidia-kernel-common-470 470.103.01-0ubuntu0.20.04.1 amd64 Shared files used with the kernel module
ii nvidia-kernel-source-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA kernel source package
ii nvidia-opencl-dev:amd64 10.1.243-3 amd64 NVIDIA OpenCL development files
ii nvidia-prime 0.8.16~0.20.04.2 all Tools to enable NVIDIA's Prime
ii nvidia-profiler 10.1.243-3 amd64 NVIDIA Profiler for CUDA and OpenCL
ii nvidia-settings 470.57.01-0ubuntu0.20.04.3 amd64 Tool for configuring the NVIDIA graphics driver
ii nvidia-utils-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA driver support binaries
ii nvidia-visual-profiler 10.1.243-3 amd64 NVIDIA Visual Profiler for CUDA and OpenCL
ii screen-resolution-extra 0.18build1 all Extension for the nvidia-settings control panel
ii xserver-xorg-video-nvidia-470 470.103.01-0ubuntu0.20.04.1 amd64 NVIDIA binary Xorg drive

Installation Guide followed (NVIDIA Drivers and Docker were previously set by someone else)

https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#ubuntu-installation