View it on HackMD This note serves the following purpose: As the onboard training for anyone using a command-line interface for their work, with most examples on our group workstation and a few examples on Sherlock. It provides best practices for writing code and using a command-line interface to run code. As the reference note for fundamental technical issues or additional tips for enhancing the personal workflow. As the reference note for the future administrator to understand the system setup. The note is the main page and contains links to additional references. The main page aims at onboard newcomer, so they can grasp the essential concepts and start using the workstation ASAP. Other references teach one how to achieve specific things in a step-by-step way.

MTIgcm is a software package written largely in Fortran 90 that has been used for decades in Atmospheric and Oceanic science to run idealized forward models of weather or climate phenomena. The documentation is quite good, but seeing as I don't know what I'm doing on Sherlock or with Fortran, I figure that I'll make this HackMD file as I go. Step 1: Compile Here is a script written by Rob King that is saved as build_mitgcm.sh. Fortran is a language that requires the code is first compiled, and then it is run. As such, it is a two step process. This code accomplishes the first step. It does not use MPI, but Niall may change this when necessary. Additionally, it assumes that you have downloaded MITgcm to your home directory. If you have not, change line 35 to reflect where you have downloaded MITgcm. #!/bin/bash #SBATCH -p serc #SBATCH -c 16 #SBATCH --mem 8G #SBATCH --time 00:30:00

This note serves the following purpose: As the protocol for the group computer manager to add a new user to the group workstation and to the group storage cluster. :::info Before you get started, make sure that the new user has already received an account and a password from Stanford that way they can be added to the group storage cluster. And if you are outside Stanford, make sure you are using the Cisco VPN.<!--(https://workcontinuity.princeton.edu/remoteaccess).--> ::: :::info Note, the inequality symbols <insert something meaningful> are meant to indicate that you insert the answer to the question/phrase in the expression. The inequality symbols should not be entered in as part of the bash command itself.

=== A reference for Lai Research Group Computing Infrastructure === The IP address of the workstation is sdss-yaolai.stanford.edu. 1. Contact Yao for applying an account of the workstation > 2. Within Princeton network, or access internet via [Princeton VPN service](https://informationsecurity.princeton.edu/connecting-to-princeton-n) --> For commandline (CLI) usage, it provides SSH login via: ssh <your_account_name>@sdss-yaolai.stanford.edu

Summarize the current performance issues on scaling up the PINN method to real-world data. The number of collocation points we are targeting is about $10^8$ data points. The settings: We assume using $10^8$ collocation points, the same number as data points. We use a model that is larger than the typical models we use (8 layers with 128 nodes each, and a final layer with 4 nodes as output) We run the expeirments with $2\times10^3$ iterations and multiply the number to make estimatation on $10^5$ iterations, which is also larger than typical one we use. The optimizer we use is Adam. L-BFGS is roughly 2x times slower than Adam Tests on the Della, using the IceShelf2D project at commit 172caf.

Author: Niall Coffey, Josh Rines First of all, many questions can be answered at MATLAB on the HPC Clusters. This short page is meant to give quick tips for using MATLAB on Princeton HPC clusters. I recommend writing the code outside of the Della GUI, and then uploading and running parallelized code on the Della GUI. Access - 2 Options: GUI or no GUI GUI Click, sign in with your NetID, interface the directory from Files tab, launch sessions from My Interactive Sessions tab. You may also interface the directory by SSHing in with ssh netid@della.princeton.edu and entering your password. I discovered this by a typo when trying to access MATLAB on the HPC Clusters, GUI on Tigressdata. Since I don't actually know where tigressdata is stored (you cannot access it from mydella.princeton.edu), if you use ssh -X <netID>@della.princeton.edu, and move to the folder of interest, you can run the Matlab GUI with seemingly no wait time or session end time (this comes with former method as you specify the number of hours you want). I've attached a screenshot below of what it looks like to show that the graphics aren't too bad.

sudo apt-get install xrdp sudo apt-get install xfce4 sudo ufw allow 3389. We do not use ssh to login, since it's more cumbersome to user Add exec startxfce4 into /etc/xrdp/startwm.sh Set allow_channels=false in /etc/xrdp/xrdp.ini to avoid strange thinclient_drives directory under $HOME, reference Change the default terminal emulator: sudo update-alternatives --config x-terminal-emulator, reference Performance issue Change crpt_level to low

A summary on how to launch a Jupyter notebook with specific Conda environment file. Before you start, make sure to download and install Anaconda. Also, you have to download our project from the GitHub page. The project contains the environment files we use. Two environments (TensorFlow 1/ TensorFlow 2) we are using for this class: TensorFlow 2 (Mac, Win) TensorFlow 1 (Mac, Win) Using Jupyter Locally Launch TerminalFor Windows, you must use Anaconda Prompt For Mac, use the regular terminal

=== A reference for Lai Research Group Computing Infrastructure === This guide teaches how to use Visual Studio Code to develop code on our workstation. :::success Our training session recording might help ::: 1. Install

There is very detailed documentation available: https://www.sherlock.stanford.edu/docs/. Help is available here: https://www.sherlock.stanford.edu/docs/user-guide/troubleshoot/. Getting into Sherlock Official documentation: https://www.sherlock.stanford.edu/docs/getting-started/connecting/#login Use ssh on the command line to access the Sherlock cluster: ssh username@sherlock.stanford.edu Use your SUnet password to log in; it will require Duo authentication.

Version control means managing the changes of files in an organized way. Version control tool is the software to aid the process. In this short tutorial, we'll introduce concepts of version control and the primary usage of Git. Going through the tutorial, you will be able to properly manage code using the essential features of Git. Before we start, you need to create an empty directory and transform it into a Git-managed project. I use ~/Document/git-test as an example. Inside the directory, execute: `git init The command will create a hidden directory .git under the current working directory: