Installation guide

BioTuring ecosystem - GPU enterprise version installation guide

1. Pre-Installation Requirements

Before installing the BioTuring Ecosystem, some pre-installation steps are required:

• The system has one or multiple NVIDIA GPU(s) (at least 16 GB memory per GPU) - with Turing architecture or above.
• The system is running Ubuntu 20.04 or above.
• SSL certificate and a domain name for users to securely access the platform on the web browser.
• Please contact support@bioturing.com to get the token for your company.

Note: The ideal system that we recommend for most companies is AWS g5.8xlarge

2. Installation

Note: We suggest starting from scratch to avoid package/driver conflicts.

0. Update the system:

sudo apt update && sudo apt upgrade -y
sudo apt install build-essential wget curl gnupg lsb-release ca-certificates xfsprogs -y

1. Install NVIDIA CUDA Toolkit 11.7.

Run the commands below to install NVIDIA CUDA Toolkit 11.7 on Ubuntu 20.04.x:

wget https://developer.download.nvidia.com/compute/cuda/11.7.1/local_installers/cuda_11.7.1_515.65.01_linux.run
sudo sh cuda_11.7.1_515.65.01_linux.run

2. Install docker.

curl https://get.docker.com | sh
sudo systemctl --now enable docker

3. Install the NVIDIA container toolkit.

distribution=$(. /etc/os-release;echo $ID$VERSION_ID) \
  && curl -fsSL https://nvidia.github.io/libnvidia-container/gpgkey | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-container-toolkit-keyring.gpg \
  && curl -s -L https://nvidia.github.io/libnvidia-container/$distribution/libnvidia-container.list | \
    sed 's#deb https://#deb [signed-by=/usr/share/keyrings/nvidia-container-toolkit-keyring.gpg] https://#g' | \
    sudo tee /etc/apt/sources.list.d/nvidia-container-toolkit.list
sudo apt update
sudo apt install nvidia-docker2
sudo systemctl restart docker

4. Make sure that /dev/shm size is at least half of physical memory.
   To change the configuration for /dev/shm, add one line to /etc/fstab. For example, if the system has 128 GB of physical memory:

tmpfs /dev/shm tmpfs defaults,size=64g 0 0

Run the command below to make the change immediately:

sudo mount -o remount /dev/shm

5. Prepare an SSL certificate with two files named exactly: tls.crt and tls.key. And put them in the /config/ssl folder. For example:

sudo mkdir -p /config/ssl
sudo mv tls.crt /config/ssl
sudo mv tls.key /config/ssl

6. Create default directories to store user data. We highly recommend using persistent storage for these directories. In the commands below, we use an empty EBS volume.

sudo mkfs -t ext4 /dev/nvme2n1
sudo mkdir /data
sudo mount /dev/nvme2n1 /data
sudo mkdir /data/app_data
sudo mkdir /data/user_data

7. Pull the BioTuring Ecosystem image.

sudo docker pull bioturing/bioturing-ecosystem:2.0.6

8. Run the docker image.

docker run -it -d \
    -e WEB_DOMAIN='<yourcompany.com>' \
    -e BIOTURING_TOKEN='<your token from BioTuring>' \
    -e SSO_DOMAINS='<your company email address, example: @bioturing.com>' \
    -e ON_BIOTURING_K8S='FALSE' \
    -e K8S_BUFFER_PATH='' \
    -e N_TQ_WORKERS='4' \
    -e K8S_TQ_ADDR='' \
    -e K8S_LENS_TQ_ADDR='' \
    -v /data/user_data:/data/user_data \
    -v /data/app_data:/data/app_data \
    -v /config/ssl:/config/ssl \
    --name bioturing-ecosystem \
    --gpus all \
    --shm-size=64gb \
    -p 443:443 \
    -p 80:80 \
    bioturing/bioturing-ecosystem:2.0.6

Wait for a few minutes for the platform to download all of the required services.
After that, the BioTuring ecosystem is up and running.

3. Notices

3.1. Security

• The BioTuring Ecosystem uses HTTPS protocol to securely communicate over the network.
• All of the users need to authenticate using a BioTuring account or the company's SSO to access the platform.
• We highly recommend setting up a private VPC network for IP restriction.
• The data stays behind the company firewall.

3.2. Data visibility

• Data can be uploaded to Personal Workspace or Data Sharing group.
• In the Personal Workspace, only the owner can see and manipulate the data she/he uploaded.
• In the Data Sharing group, only people in the group can see the data.
• In the Data Sharing group, only people with sufficient permissions can manipulate the data.