Update Quick Start. Update the install_nvidia_docker.sh script.

PiperOrigin-RevId: 321801388
oeh77 · Jul 17, 2020 · 6723c8c · 6723c8c
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diff --git a/docs/deepvariant-quick-start.md b/docs/deepvariant-quick-start.md
@@ -19,9 +19,10 @@ Docker image.
 
 ### Use Docker to run DeepVariant in one command.
 
-In the 0.8 release, we introduced one convenient command that will run through
-all 3 steps that are required to go from a BAM file to the VCF/gVCF output
-files. You can still read about the r0.7 approach in [Quick Start in r0.7].
+Starting from the 0.8 release, we introduced one convenient command that will
+run through all 3 steps that are required to go from a BAM file to the VCF/gVCF
+output files. You can still read about the r0.7 approach in
+[Quick Start in r0.7].
 
 If you want to compile the DeepVariant binaries for yourself, we also have a
 [Dockerfile] that you can use to build your own Docker image. You can read the
@@ -35,7 +36,7 @@ the [External Solutions] section.
 ### Get Docker image
 
 ```bash
-BIN_VERSION="0.10.0"
+BIN_VERSION="rc1.0.0"
 
 sudo apt -y update
 sudo apt-get -y install docker.io
@@ -155,11 +156,11 @@ For more information about `output.visual_report.html`, see the
 
 ## Notes on GPU image
 
-If you are using GPUs, you can pull the GPU version, and make sure to run with
-`nvidia-docker`:
+If you are using GPUs, you can pull the GPU version, and make sure you run with
+`--gpus 1` (because DeepVariant currently can only make use of 1 GPU):
 
 ```
-sudo nvidia-docker run \
+sudo docker run --gpus 1 \
   -v "${INPUT_DIR}":"/input" \
   -v "${OUTPUT_DIR}:/output" \
   google/deepvariant:"${BIN_VERSION}-gpu" \
@@ -238,7 +239,7 @@ Benchmarking Summary:
 [BAM]: http://genome.sph.umich.edu/wiki/BAM
 [BWA]: https://academic.oup.com/bioinformatics/article/25/14/1754/225615/Fast-and-accurate-short-read-alignment-with
 [docker build]: https://docs.docker.com/engine/reference/commandline/build/
-[Dockerfile]: https://github.com/google/deepvariant/blob/r0.10/Dockerfile
+[Dockerfile]: https://github.com/google/deepvariant/blob/r1.0/Dockerfile
 [External Solutions]: https://github.com/google/deepvariant#external-solutions
 [FASTA]: https://en.wikipedia.org/wiki/FASTA_format
 [Quick Start in r0.7]: https://github.com/google/deepvariant/blob/r0.7/docs/deepvariant-quick-start.md

diff --git a/scripts/install_nvidia_docker.sh b/scripts/install_nvidia_docker.sh
@@ -1,11 +1,11 @@
 #!/bin/bash
 # Copyright 2019 Google LLC.
-# This script is used to install `nvidia-docker` on Ubutun 16.04.
+# This script is used to install nvidia docker on Ubutun 16.04.
 # For different Linux distributions and versions, modifications might be needed.
 
 set -euo pipefail
 
-# Installing `nvidia-docker` to use deepvariant_gpu Docker image.
+# Installing nvidia docker to use deepvariant_gpu Docker image.
 # (1) Install nvidia driver:
 # https://github.com/NVIDIA/nvidia-docker/wiki/Frequently-Asked-Questions#how-do-i-install-the-nvidia-driver
 sudo apt-get -qq -y update
@@ -29,33 +29,25 @@ if ! dpkg-query -W cuda-10-0; then
 fi
 
 # (2) Install Docker CE:
-# https://docs.docker.com/install/linux/docker-ce/ubuntu/#install-docker-ce
+# https://docs.docker.com/engine/install/ubuntu/
 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
 sudo apt-key fingerprint 0EBFCD88
 sudo add-apt-repository \
  "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
  $(lsb_release -cs) \
  stable"
 sudo apt-get -qq -y update
-sudo apt-get -qq -y install 'docker-ce=5:18.09.4~3-0~ubuntu-xenial'
-
-# (3) Install nvidia-docker:
-# https://github.com/NVIDIA/nvidia-docker#ubuntu-140416041804-debian-jessiestretch
-# "If you have nvidia-docker 1.0 installed: we need to remove it and all existing GPU containers"
-sudo docker volume ls -q -f driver=nvidia-docker | xargs -r -I{} -n1 sudo docker ps -q -a -f volume={} | xargs -r sudo docker rm -f
-sudo apt-get purge -y nvidia-docker || true
+sudo apt-get -qq -y install docker-ce docker-ce-cli containerd.io
 
+# (3) Install nvidia docker:
+# https://github.com/NVIDIA/nvidia-docker#ubuntu-160418042004-debian-jessiestretchbuster
 # Add the package repositories
-curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | \
-  sudo apt-key add -
-distribution=$(. /etc/os-release;echo "${ID}${VERSION_ID}")
-curl -s -L "https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list" | \
-  sudo tee /etc/apt/sources.list.d/nvidia-docker.list
-sudo apt-get -qq -y update
+distribution=$(. /etc/os-release;echo "$ID$VERSION_ID")
+curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add -
+curl -s -L "https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list" | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
 
-# Install nvidia-docker2 and reload the Docker daemon configuration
-sudo apt-get install -qq -y nvidia-docker2
-sudo pkill -SIGHUP dockerd
+sudo apt-get update && sudo apt-get install -y nvidia-container-toolkit
+sudo systemctl restart docker
 
-# Test nvidia-smi with the latest official CUDA image
-sudo docker run --runtime=nvidia --rm nvidia/cuda nvidia-smi
+#### Test nvidia-smi with the latest official CUDA image
+sudo docker run --gpus 1 nvidia/cuda:10.0-base nvidia-smi