Multiresponse time-to-event Cox proportional hazards model - GPU
Running multisnpnet-Cox_gpu on Nero is very easy.
- First connect to Nero. Detailed instructions can be found here https://github.com/rivas-lab/wiki/wiki/nero-cluster-system. Make sure you connect to Stanford VPN.
- Request compute resources.
srun --pty -p mrivas --mem=770000 --cpus=56 --gres=gpu:8 bash. It's okay if you only request 1 GPU. - Run
ml snpnet_gpu/0.1.0. This will load all dependencies of this package. - Take a look at the file
/local-scratch/mrivas/ruilin/test/test.R. You can simply modify the responseid in this file to analyze different set of phenotypes. You might want to copy that file to a different directory and modify the result and save directories. - Run
Rscript test.R.