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Installation

Learn how to install ST4SD on a variety of platforms

If you are not an administrator then, depending on your user environment, you may not have to install anything. Its recommended you check first steps to determine if you need to do so.

Set Up Local Client

  • For: Researchers & Developers
  • Use When:
    • You want to run workflows on a Kubernetes/OpenShift instance of the workflow stack from your laptop via e.g. a jupyter-notebook
    • You want to develop workflows
    • You want to test writing/running some simple workflows that can run on your laptop/desktop

The local client install only requires st4sd-runtime-core. You can install st4sd-runtime-core directly on your laptop using pip.

Requirements

  • python3
    • We recommend that you use python 3.9 although versions 3.7 through 3.10 should work.

Installing

A simple pip install suffices:

pip install "st4sd-runtime-core[develop]"

Install on OpenShift Local

  • For: Developers
  • Use When
    • You want to test, develop and run small-scale virtual experiments on your laptop.
    • You want to develop or examine the ST4SD micro-services on your laptop

Requirements

  • OpenShift Local is only officially supported on:
    • RedHat Enterprise Linux 7+
    • CentOS 7+
    • The two latest stable Fedora releases
    • Windows 10
    • macOS 11.0 Big Sur or later
  • Ubuntu 18.04 LTS or later and Debian 10 or later are not officially supported and may require manual setup.

We recommend using a x86 device.

You can deploy a small scale version of ST4SD Cloud on your personal device using Red Hat OpenShift Local. To get started with Red Hat OpenShift Local, download the “OpenShift Local” binary (crc) from the Red Hat Console website.

You need a Red Hat account to use OpenShift Local. If you do not have one, you can get one for free on theRed Hat Developerwebsite.

One time Setup

After you install OpenShift Local you will get access to the crc binary. Ensure the crc binary is in your ${PATH} for example when you run crc version in your terminal you get similar output to:

CRC version: 2.22.1+e8068b4
OpenShift version: 4.13.3
Podman version: 4.4.4

Below we use crc in a script to:

  1. create and configure the Virtual Machine that will host OpenShift Local
  2. Set the password of the kubeadmin account to fun - do not use insecure passwords in production.
  3. Deploy ST4SD Cloud on the st4sd-local namespace
  4. Wait for the ST4SD microservices to go online
  5. Open a browser to visit your instance of the Registry UI!
    1. Login as the user developer with the password developer - this is the default non-admin user that crc creates for you.

Copy the text below and execute it in your terminal:

cat <<'EOF'>one_time_setup.sh
set -e
crc config set consent-telemetry no
crc setup
# Increase default resource limits for the Virtual Machine
crc config set cpus 8
crc config set memory 14336
crc config set disk-size 50
# Set the password to "fun" - do not use insecure passwords in production

The script will take 5-15 minutes to complete. While it is building your local ST4SD Cloud deployment, consider exploring the ST4SD Services and ST4SD Registry webpages. You can use the information in there to populate your catalog of experiments and more!

Continue reading if you would like to get more information about the individual steps above.

Setting up your Virtual Machine for OpenShift Local

Red Hat OpenShift Local runs as a Virtual Machine on your device. There is a one-time setup that you need to do using the crc command-line utility that you downloaded in the above step. The default installation of OpenShift Local produces a local OpenShift cluster with:

  • 4 virtual CPU cores,
  • 9 GB of RAM, and
  • 31 GB of storage space

We recommend increasing the defaults with the following:

# one time command
crc setup
# if OpenShift Local is already running, execute "crc stop" first
crc config set cpus 8
crc config set memory 14336
crc config set disk-size 50

Below we also change the default password for the kubeadmin so that the instructions are easier to follow.

# Set the password to "fun" - do not use insecure passwords in production
crc config kubeadmin-password fun

If you ever want to view the credentials for accessing your OpenShift Local instance, you can run

crc console --credentials

Starting and Stopping the OpenShift Local Virtual Machine

Recall that OpenShift Local runs as a small scale Virtual Machine on your personal device. We recommend starting it before you experiment with ST4SD and stopping it when you are done running experiments to release the compute resources that the Virtual Machine is taking up.

To start the virtual machine type:

crc start
# Use the `oc` command line interface
eval $(cr oc-env)
# Open a browser to login to OpenShift Web Console
crc console
The command crc start prints useful information on the terminal including how to access the OpenShift Web Console as well as the credentials for the kubeadmin and developer users. In our instructions below we login using the kubeadmin user.

To stop the virtual machine type:

crc stop

Installing ST4SD Cloud

When crc start finishes printing information on the terminal, your OpenShift Local cluster has started running. You may now connect using the

kubeadmin account:
# Use the `oc` command line interface
eval $(crc oc-env)
# Ask crc to print the `oc login` commands for you
crc console --credentials
# Now login as the kubeadmin, recall that we set the password to "fun"
oc login -u kubeadmin -p fun https://api.crc.testing:6443
# Open a browser to login to OpenShift Web Console
crc console

Installing

After your OpenShift Local is up and running (i.e. crc start has finished). Follow the instructions on your terminal to login in as an administrator into OpenShift.

  1. Run crc console --credentials to see the oc login commands you can type in your terminal.
  2. Create the project st4sd-local: oc new-project st4sd-local.
  3. Deploy the minimal version of ST4SD: oc apply -f https://raw.githubusercontent.com/st4sd/st4sd-deployment/main/manifests/openshift-local-minimal-release.yaml.
  4. The url to your local instance of ST4SD is https://local.apps-crc.testing
    • You can access your local ST4SD registry-ui at https://local.apps-crc.testing/registry-ui/
    • The very first time you login, OpenShift will inform you that ST4SD wishes to know that you are an authorized user of the system. Accept the OpenShift prompt on your browser.
    • Both default OpenShift accounts (developer and kubeadmin will have access to your ST4SD microservices).
      • By default, the developer account has the password developer.
      • You can print the administrator credentials using crc console --credentials.

You can see the credentials of the default accounts that OpenShift Local creates for you by running crc console --credentials in your terminal.

Install on Kubernetes and OpenShift

  • For: Administrators
  • Use When
    • You want to install an instance of the workflow stack on a k8s/OpenShift cluster

First, add the Simulation Toolkit for Scientific Discovery (ST4SD) operator to the Operator Catalog of your OpenShift cluster:

oc apply -f https://raw.githubusercontent.com/st4sd/st4sd-olm/main/examples/deploy.yaml

Then follow our instructions to configure and install. For comprehensive details on customizing ST4SD deployments using helm post-installation see https://github.com/st4sd/st4sd-deployment.

Install on Classic HPC

  • For: Administrators
  • Use When:
    • You want to run workflows on a classic HPC infrastructure that uses the LSF scheduler

Requirements

The following installation instructions assume you have

  1. Internet access
  2. swig is in your $PATH
    • swig is a program for creating scripting language wrappers. Required for building the LSF wrappers
  3. python3 (3.7 to 3.10) is in your $PATH
  4. The command tox is available
    • Check by typing tox and pressing return

Installing

  1. Clone the ST4SD runtime core repository
    • run git clone https://github.com/st4sd/st4sd-runtime-core.git
  2. cd into the cloned repository
  3. run DEPLOY_VENV=$MYVENV tox -e py37-deploy-lsf --site-packages where
    • $MYVENV is where you want the virtual environment to be created

Learn more

User management

Manage the access permissions of users in your ST4SD Cloud instance using standard Kubernetes mechanisms.

Exploring the Registry UI

Install successful? You can now learn about all the features of our web interface for browsing and examining virtual experiments packages and runs.

Use the APIs

Learn how to use the ST4SD python client API to run, query, and interact with virtual experiments. The APIs also offer access to a trove of experiment metadata and files such as logs and outputs. You can find more examples in our Jupyter Notebooks example repository.

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