Paton Lab Computing Resources

Here is an overall list of computing resources available to students in the Paton lab

But first, here are some tips for accessing these computers:

• ssh is a fundamental command used to virtually log into a system

• $USER in all these example commands should be replaced with your username on these computers

• You will need to create accounts on all of these computers to gain access

• I recommend setting up aliases in your ~/.bashrc or ~/.bash_profile or ~/.zshrc

  • Aliases can be used as short cuts for bash commands

  • Using aliases to log into different computers can save time and confusion

Expanse and Bridges2

We typically apply for an ACCESS grant each year to get compute time on the Expanse and Bridges2 clusters.

The following aliases will allow you to type expanse or bridges2 into your terminal and immediately ssh to that computer.

alias expanse='ssh $USER@login.expanse.sdsc.edu'
alias bridges2='ssh $USER@bridges2.psc.edu'

Note

You will still have to type in a password, but this will allow you to avoid typing the long hostname each time you want to access another computer.

Before you can access either of these computers, you will have to create accounts for both expanse and bridges2, as well as ACCESS in order to use the resources.

Note

Make sure you know your username on each of these computers, as it may be different than what you normally use depending on how the account is created.

You can follow these websites to make accounts on Expanse, Bridges2, and ACCESS.

Additionally, you will need to fill out this form to gain access to Gaussian, or email them for help.

You should also get in contact with an ACCESS admin in the group (Mihai, Graham & Abhijeet as of June 2023) to be added to the allocations group for the lab.

Alpine

As CSU students, we have access to a shared cluster Alpine with CU Boulder (hosted in Boulder, CO).

In order to gain access to Alpine follow this link Each time you log onto Alpine, you will need to run the command module load slurm/alpine. More information can be found here.

Note

We have access to Alpine as CSU students, not through an ACCESS allocation. Because of this, make sure that you are logging in with your CSU information, not your ACCESS information.

The alias to log in to Alpine is:

alias alpine='ssh $USER@colostate.edu@login.rc.colorado.edu'

You will be required to log in using your CSU NetID information (username and password), as well as sign in with Duo. There are two ways to sign in with Duo to this computer: type your_password then enter in the 6-digit pin on the Duo app, or type your_password,push which will send a Duo push notification to your phone.

Note

Let's say that for illustrative purposes that your password is 123456 and that you want a Duo push. Then you will type 123456,push.

Before you can use Gaussian on Alpine, you will need to email rc-help@colorado.edu to be added to rpatongrp@colostate.edu (just send them your username).

You should also add the following to your ~/.bashrc or ~/.bash_profile or ~/.zshrc on Alpine for additional group-specific messages:

# Get group aliases and functions
export RSP=rpaton@colostate.edu
export PROJECTS=/projects/$RSP
if [ -d $PROJECTS/bin ] ; then
    PATH=$PATH:$PROJECTS/bin
    export PATH
fi
if [ -f $PROJECTS/bin/.bashrc ]; then
    source $PROJECTS/bin/.bashrc
fi

ACME

ACME is a shared computer between the Paton and Kim labs. This computer has a queueing system (SLURM) to allow for easy use for all students of the Theory Suite. There are also a number of premade submission scripts on ACME that are available to help with running jobs.

Here is the alias for ACME:

alias acme='ssh $USER@acme.chem.colostate.edu'

To gain access to ACME, contact an admin to make an account. The current admin for the Paton group is Abhijeet, and from the Kim group you can go to Sabari, or Collin (October 2024).

There are sample input files for many of the software that we use on ACME. If you would like to see example calculation input files, you can copy the folder /opt/apps/example_jobs/ into your home directory to see the format of different input files. Currently there are examples for CREST, Gaussian, MILO, QChem, ORCA, NCI, and xTB.

Local Resources

The Paton lab also has a number of local machines available to students to use. These machines do not have a queueing system like ACME of the HPCs, but are useful for different tasks you may have.

Here are aliases to the local CSU resources:

alias subzero='ssh $USER@subzero.chem.colostate.edu'
alias fireball='ssh $USER@fireball.chem.colostate.edu'
alias dynamo='ssh $USER@dynamo.chem.colostate.edu'
alias buzzsaw='ssh $USER@buzzsaw.chem.colostate.edu'
alias skymarshal='ssh $USER@skymarshal.chem.colostate.edu'
alias drstrange='ssh $USER@drstrange.chem.colostate.edu'

To get accounts on these computers, you will need to contact an admin. For the Paton lab, this is Abhijeet or Alex (October 2024).

Here is the CPU information for ACME and the local linux machines:

acme.chem.colostate.edu acme (20 x 32 cpus)
dynamo.chem.colostate.edu dynamo (2 x 24 cpus)
buzzsaw.chem.colostate.edu buzzsaw (2 x 24 cpus)
fireball.chem.colostate.edu fireball (2 x 24 cpus)
subzero.chem.colostate.edu subzero (2 x 24 cpus)
skymarshal.chem.colostate.edu skymarshal (1 x AMD Ryzen Threadripper PRO 7985WX 64-Cores)
drstrange.chem.colostate.edu drstrange (2 x NVIDIA RTX A6000 GPUs | AMD Ryzen Threadripper PRO 5975WX 32-Cores)

On the linux machines, it may also be helpful to test to see what software is correctly installed/called. To check this make sure that this line is included in your .bashrc:

export PATH=$PATH:/usr/local/patonlab/python:/usr/local/patonlab/autotest

then create an empty folder (probably called autotest), go into the folder, and type the command

AUTOTEST

Running this command goes through several useful packages that are installed on these machines and submits a quick test job to ensure that they are working. If everything is working and set up correctly, you should get a result that looks something like:

!  Gaussian 16 is working properly
!  NBO7 is working properly
!  Orca is working properly in serial
!  Orca is working properly in parallel
!  QChem is working properly
normal termination of xtb
!  XTB is working properly
!  CREST is working properly
!  NCIPLOT is working properly
!  COSMOTHERM is working properly
ridft ended normally
!  TURBOMOLE is working properly in parallel

If you get an error for one of the packages, it is most likely a problem with the path set for that program in your .bashrc, and you should correct/add the path and run AUTOTEST again.

When you are finished testing the programs, you can delete the files with the command

AUTOTEST_CLEAN

RStor File Storage

The Paton group also has a file backup system called RStor. This storage is a good way to put files for any completed projects, as well as any large datasets that you may have created or are using. Here are instructions for how to access this drive and add files.

Warning

This is a private drive only for students in the Paton group at CSU. For this reason, you will need to email IT Support (Ross Madden) and cc Rob so that they can invite you to the drive. Until then, you will be unable to access the drive.

How you set up the drive on your personal computer might be different based on if you have a Mac or a PC. I will include instructions for both here to be followed after you have been added as a user.

Warning

In order to access this drive, you have to be on campus or using the VPN.

Mac Instructions

To access the drive on your Mac, you have two options. First, you can directly click this link: smb://campusrstor1.onefs.colostate.edu/natsci/patonlab

Otherwise, you can click on your desktop/background, then at the top of your screen click Go then Connect to Server... in the pull-down menu. This will take you to a finder page titled "Connect to Server". Type in smb://campusrstor1.onefs.colostate.edu/natsci/patonlab in the space and hit Connect. This will now prompt you to log in using your CSU login information, possibly preceeding your username with COLOSTATE\.

Warning

Make sure that this login information matches how you log into RamWeb. The username for this drive will be your CSU username, regardless of what your username on your laptop is. If your CSU username is CamRam but your laptop knows you as CoolCam, you will need to update the username field to read CamRam or COLOSTATE\CamRam.

Once you've logged in, you should be in a Finder window called patonlab. This is the RStor drive, you're in! From here, you can also open a terminal window to this folder directly from the Finder window, and you'll be able to use the drive to store your files. Otherwise, you can type cd /Volumes/patonlab/ in any terminal window to access the RStor drive.

PC Instructions

The first step to accessing the drive on a Windows computer is opening the File Explorer and going to This PC. If your computer is Windows 10, click Map Network Drive while in the File tab. If your computer is Windows 11, click the three dots on the top right ribbon (under the search bar), then click Map Network Drive.

Once on this page, choose an empty drive (probably T: or Z:). in the Folder box, type \\campusrstor1.onefs.colostate.edu\natsci\patonlab. Now, a popup window should appear asking for your login information. You will log in with your CSU information, the CSU net ID preceeded by COLOSTATE\ and your password like you would use for RamWeb or email.

Note

Your username for this is going to be COLOSTATE\your_csu_netID and the password is your normal CSU password

Warning

You may need to alter auto-fill settings here to ensure that the login information is correct. For example, if your computer knows you as CoolCam, it might try to fill that in automatically instead of your CSU net ID CamRam. Make sure that you change this to the correct information.

Once you've logged in this way, you should be all set to use and access all of the files in the drive. If you run into any issues setting it up, just follow this link for instructions, or email IT Support (Ross Madden).

Transferring Files to RStor

Note

Once you are logged in, you should see two folders, "Completed_projects" and "Users"

There are a few ways to transfer files into this backup drive. The first is to just drag-and-drop files using the Finder or File Explorer windows. The next is to transfer files using the terminal. My preference is rsync, so I will go over how to transfer files to the drive this way. You can also you scp.

Moving files into this drive works the same as any rsync command, where you specify which files you're moving and where you plan to move them to. I recommend that you always pull the files from any other computer/HPC to you while you are in the RStor drive on the terminal. For this, you will use:

rsync -azvp --progress '<USERNAME>@<COMPUTER>:/location/of/files/to/store' .

Warning

Some of the computers or HPCs have unexpected hostnames, or <COMPUTER> in my above example. You want to include the hostname you use when you ssh into the computer, not the output when you run the hostname command. For example, Alpine is login.rc.colorado.edu, not loginXX. Also, make sure that <USERNAME> is what you use to login to the computer, so for Alpine your username is Your-CSU-ID@colostate.edu instead of just Your-CSU-ID.

From here, type in your password for the computer you are moving files from (Alpine in my example) to start moving files. This command takes files from a specified folder (/location/of/files/to/store) and transfers them to the current working directory (.), so make sure the current working directory is where you want the files to go before running this command.