GPU
- accessing gpus is done via the cuda, because its not a cpu there are various driver and dependencies that have to match exactly
- see all nvidia things in your system
ls -la /dev | grep nvidia
Nvidia cuda
- Nvidia cuda allows the user access to the gpus
- First you need to know for what Nvidia drivers your program was designed (e.g. nvidia 384 driver)
- now you need to make sure your nvidia cuda supports this versions
- check here
- some examples:
| CUDA Toolkit | Linux x86_64 Driver Version |
|---|---|
| CUDA 10.0 (10.0.130) | >= 410.48 |
| CUDA 9.2 (9.2.88) | >= 396.26 |
| CUDA 9.1 (9.1.85) | >= 390.46 |
| CUDA 9.0 (9.0.76) | >= 384.81 |
| CUDA 8.0 (8.0.61 GA2) | >= 375.26 |
| CUDA 8.0 (8.0.44) | >= 367.48 |
| CUDA 7.5 (7.5.16) | >= 352.31 |
| CUDA 7.0 (7.0.28) | >= 346.46 |
- e.g. if your program needs 384 since its the latest on xenial you need cuda 9.0
- download the deb file from nvidia
- use Legacy Download for older cuda versions
- use the .deb download on this side end do this (follow site, this is just an example)
sudo dpkg -i cuda-repo-ubuntu1804-10-0-local-10.0.130-410.48_1.0-1_amd64.deb
sudo apt-key add /var/cuda-repo-<press tab>/7fa2af80.pub #this is a file on your computer
sudo apt-get update
sudo apt-get install cuda
Setting up a GPU-machine
- example
gpu-guppy basecaller - available only via xenial (ubuntu 16) and it uses latest xenial-nvidia driver 384
- therefore cuda 9.0 is needed
- cuda is usually installing are drivers
sudo apt-get update
# download and get the cuda 9 deb from nvidia
wget https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda-repo-ubuntu1604-9-0-local_9.0.176-1_amd64-deb
# this gets ubuntu 16.04 64bit linux deb file
# after downloading go to the deb file and do:
sudo dpkg -i cuda-repo-ubuntu1604-9-0-local_9.0.176-1_amd64-deb
sudo apt-key add /var/cuda-repo-9-0-local/7fa2af80.pub
sudo apt-get update
sudo apt-get install cuda
# now guppy basecaller
sudo apt-get update
sudo apt-get install wget lsb-release
export PLATFORM=$(lsb_release -cs)
wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
echo "deb http://mirror.oxfordnanoportal.com/apt ${PLATFORM}-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list
sudo apt-get update
sudo apt-get install ont-guppy