Getting Started in the York Lab
Learning objectives
Getting started in the York Lab
Tutorial
Starting From Scratch
Welcome to York Lab! This document has some introductory “how to”s and “what to”s regarding getting started in the lab.
Software York Lab members use everyday include:
You’ll be heavily reading, writing, and running bash scripts, with eventual python scripts.
You’ll be using VMD heavily for visualizing structures and trajectories.
In order to submit jobs to clusters you’ll be using Slurm scheduling mostly.
You’ll be writing papers, and any other lab related document that goes through Darrin using LaTeX.
You’ll be using git version tracking software for essential shared libraries and software used in the group as well as manuscripts etc.
You’ll be mostly using Amber simulation package – eventually will have to compile and use different versions of the software.
Local HPC resources: Getting an Amarel account:
We often run jobs on a local computing cluster called Amarel. To request access, fill out this form with your rutgers email:
In addition to filling out this form, to receive access to the York group owned nodes and software packages you need to email OARC (help@oarc.rutgers.edu) and cc Darrin to request access to lbsr group on Amarel.
External HPC resources: Getting an Expanse/Frontera Account
We also have access to external HPC resources. Currently these include:
Read HPC Resource Info page for details.
Getting on the IQB Building Mailing Lists:
Our building manager Hank (Henry Wojciechowski) recommended signing up for these:
The building one is important since we get updates on building closures, technical problems etc.
People in CCB get automatically added to their mailing lists but If you would like to be added reach out to Loretta Lupo in CCB: lal275@chem.rutgers.edu
Public key info for adding new machines to our git network:
If your workstation isn’t setup to communicate with our local git repository hosted on Riesling, the following needs to be done. To check whether it is set up type:
mrgit --list
If It’s not showing a list of our repositories then you’re probably not setup.
Newer OSs no longer supports rsh keys so going forward we will be using the default setting of ssh-keygen. First generate a key:
ssh-keygen -t
then allow it to be used by
echo "PubkeyAcceptedKeyTypes +ssh-rsa" > ~/.ssh/config
then set the permissions
chmod 600 ~/.ssh/config
Most recent need was ~/.ssh/config to have:
HostKeyAlgorithms +ssh-rsa
PubkeyAcceptedKeyTypes +ssh-rsa
DO NOT CHANGE THE PUBLIC KEY OF YOUR WORKSTATION ONCE IT HAS ACCESS TO OUR GIT REPO
Once you have your public key setup, email/send your ~/.ssh/id_rsa.pub (as an attachment to avoid linebreaks from copy-paste) to solen.
Once you are added to user list do the following to get our git repo initiated on your machine:
mkdir -p ~/devel/git/Admin; cd ~/devel/git/Admin
git clone git@riesling.rutgers.edu:Admin/shell-admin
mkdir -p ~/devel/git/Management; cd ~/devel/git/Management
git clone git@riesling.rutgers.edu:Management/Git
Then copy the example bashrc in shell-admin as your bashrc:
cp devel/git/Admin/shell-admin/example-bashrc ~/.bashrc
New Lab Member Info for Website
Send the following to Solen:
A photo
- info:
Education
Email
Office info (I can put that in for you)
If you have linkedIn, orcid, google scholar and/or twitter pages that you want shown on your profile.
About me section: A brief description of what you are interested and currently working on. It can be very broad, and we can always update it later.
Country or State you grew up in or feel connected to as you are “from” there. This is simply to show the diversity in the group, and it’s more in terms of land & culture than about race or anything else, that’s why we have the landshaped flags. If you have a preferred land shaped flag for your country/state feel free to attach that as well (otherwise I’ll just find something on google).
Remote Work
Virtual Office
We’re using MS Teams as our virtual office, so we’re online when we would have been in the office etc. That way if anyone has questions for anyone or Darrin wants to reach someone we’re all there. So we expect everyone to be online (i.e. not offline) when they’re working. Most projects have their own channel, and we use the general channel for things that concern everyone. Please adjust your notifications so that you don’t miss what’s going on in channels you are a part of.
Virtual workstation
We use linux workstations in the lab. You will be assigned a workstation from the lab to which you’ll connect remotely. To do so you will need a linux-based environment. If you have a mac laptop you can simply use the terminal app, if you’re on windows you’ll need additional software such as cygwin, putty, or mobaXterm. Windows 10 and 11 come with “ubuntu on Windows” and win 11 version seems to work pretty well. You can also look into setting up a virtual linux environment on your machine using VirtualBox (depending on your machine’s specifications it might not yield practical). One other software is NoMachine - this enables you to visually manipulate the remote desktop, the efficiency of this depends heavily on your network speed. If you choose to use this your workstation in lab needs the “server” version installed, and your laptop needs client version. Information on configuring the client can be found at the end of this document.
Connecting to Your Linux Machine via SSH
Our linux workstations are all available on the Rutgers network (off-campus, you need to use the VPN, see below). To log in to them via ssh, you can connect as follows.
ssh [username]@[computername].rutgers.edu
Or you might not need the rutgers.edu bit.
ssh [username]@[computername]
Remote Access Outside of Campus
In order to remotely connect to any machine on the Rutgers network from outside of the Rutgers network (i.e. off campus) you’ll need vpn access. Please go through soc.rutgers.edu for information regarding getting setup with remote access, but in short you will need DUO mobile app on your phone/tablet and will need to go through two-step verification every time you want to connect.
Configuring New Machine for remote desktop visualization:
When you add a new machine on your end you need the following settings:
nx server
host: [computerName].rutgers.edu (port stays same, udp box checked)
password
Don’t use a proxy (I know it’s counterintuitive)
name: whatever you choose
In your first connection it’ll ask username and password, after that the user name will come filled in and you will only have to enter password.