I recently needed to run a tutorial at a winterschool in computational chemistry. Setting up a an impromptu computing lab can be a bit of a hazzle if:
i) using a local computer lab one is not familar with
ii ) or each student is using their own laptop
It is thus convenient if one could set up a cloud computing solution that one could manage oneself and then the local computer or student-laptop just needs to be able to make an SSH connection to the cloud computing instance.
A cloud computing solution allows one to create as many Linux instances in the cloud as required (e.g. 1 for each student). One can easily create multiple instances simultaneously and then have the students log in to each instance easily via SSH and a private key. The same private key for all students is fine for a 1-day session but for a longer lab one would obviously want to have individual private keys. One can configure each instance regarding OS (e.g. Ubuntu), storage, RAM and CPUs.
However, one must be careful about the cost associated if quality instance machines are needed (CPU/RAM) and how long they run for. I went for Amazon AWS EC2 services.
Useful pages on EC2
https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/concepts.html
https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/EC2_GetStarted.html
AWS info for classrooms:
https://docs.aws.amazon.com/whitepapers/latest/setting-up-multi-user-environments/introduction.html
https://docs.aws.amazon.com/whitepapers/latest/setting-up-multi-user-environments/scenario-1.html
https://docs.aws.amazon.com/whitepapers/latest/setting-up-multi-user-environments/scenario-2.html
Set up
Go to https://aws.amazon.com/pm/ec2/ and click "Create an AWS Account"
Once signed in find the EC2 service page and search for Create/Launch an instance
Select OS, type of instance etc.
Once created, find the page that lists all instances for your account where the instance should be. You can rename the instance (by e.g. student-name)
Warning: Careful to stick with the free-tier instances (should be either t2.micro or t3.micro and it should be labelled clearly) to begin with to avoid any costs upon creating each instance. If you select other instances then you are outside the free-tier and then the more CPU/RAM per instance, the higher the hourly costs.
"Free tier: In your first year includes 750 hours of t2.micro (or t3.micro in the Regions in which t2.micro is unavailable) instance usage on free tier AMIs per month, 30 GiB of EBS storage, 2 million IOs, 1 GB of snapshots, and 100 GB of bandwidth to the internet."
A t2.micro/t3.micro comes instance comes with 2 CPUs which should be sufficient for each student for simple preliminary exercises. It also comes with 1 GB RAM which is hopefully sufficient but could be tricky. If more RAM is required then one needs to go outside the free-tier. Storage also costs (needed for programs and for exercises) so that needs to be taken into account.
Install on each machine
The purpose was to run ASH on each machine, requiring Python,Numpy,OpenMM, xTB and a few other programs.
This was accomplished by copy-pasting the snippet below which should easily install and setup each new machine without any user-intervention needed (takes a few minutes).
#Download Miniforge (mamba,conda)
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
#Install without prompt
sh Miniforge3-Linux-x86_64.sh -b
#Initialize shell
~/miniforge3/bin/mamba init
#Delete
rm Miniforge3-Linux-x86_64.sh
#Reset shell
source ~/.bashrc
#Installation: -y installs without confirm
mamba install -y openmm
mamba install -y xtb-python
mamba install -y pdbfixer
mamba install -y mdtraj
mamba install -y ipython
pip3 install geometric
pip3 install matplotlib
#Delete conda pkgs after installed (4 GB) due to limited space
rm -rf ~/miniforge3/pkgs/*
#ASH
mkdir ~/ASH-code
cd ~/ASH-code
git clone https://github.com/RagnarB83/ash.git
cd ash
git checkout NEW
cd
#PATHS
echo "export PYTHONUNBUFFERED=1" >> ~/.bashrc
echo "export PYTHONPATH=$HOME/ASH-code:$PYTHONPATH" >> ~/.bashrc
source ~/.bashrc
#CALCULATION DIR SETUP
mkdir CALC_DIR
cd CALC_DIR