Using a computer cluster for computer simulations

HPC cluster is necessary when it comes to large scale computer simulations, such as molecular dynamics simulations. For those computing clusters, there are usually two directories: one for login and the other for simulation. It is imperative that simulation must NOT run under the login or home directory, as it would otherwise take up the memory for the operating system.

One needs to have some basic knowledge about Linux systems, as all the operations are done on a Linux system, such as submitting jobs. For a beginner using a windows desktop, it is very recommended to install the wsl-ubuntu (now wsl2) on a windows computer.

To connect to a cluster, one needs to generate a key file:

ssh-keygen -t ed25519 -C "your_email@example.com"

> Enter a file in which to save the key:[Press enter]
> Enter passphrase (empty for no passphrase): [Type a passphrase]
> Enter same passphrase again: [Type passphrase again]

Now there are two files generated (under ~/user/.ssh by default), with one being public and the other private. To get access to a cluster, one needs to generate this local ssh key pair on a local computer. And send the public file (.pub) to the administrator.

Then one can login to a cluster by:

ssh -i /path/to/the/private/key/file user@the.cluster.addr