info on scs clusters
Introduction and Access
While some of the software installed will just “work” if you try to run it when logging in, most packages will require you to load a module first. To do so:
- Type this command to see the available modules to load
- To load a specific module, type the following command (gaussian is used as an example, replace with the one you want)
module load gaussian/g16
- If you get a message such as "ERROR: Module 'X' depends on one of the modules 'Y" you need to load module(s) Y first.
- To see which modules you currently have loaded
- To unload a module (to load a different version for example).
module unload gaussian/g16
If there is any software not currently on the cluster that you would like installed, e-mail firstname.lastname@example.org and inquire if that is possible.
Queues on Lop:
qquotawill show how many cores you are currently using. NOTE: There is no output if you have no jobs running.
Any job running on the cluster for longer than 7 days is subject to termination without warning. We will attempt to contact the user ahead of time to see if an extension can be worked out but if it is time sensitive this may not be possible. If you have a job or two that you need to run for an extended period of time, contact email@example.com to request an exception. This exception WILL NOT be granted for more than two jobs at a time.
Students in courses are treated differently from SCS students, staff and faculty. Their access to Lop will be revoked after the end of finals for a semester and all data will be deleted. If a student wishes to keep anything, said student must remove it from lop before the end of the semester.
Below, find various links to tutorials for software on the cluster. Many of these are out of date but we are working to make them current:
Tutorial - Quantum Chemistry - Simulating Vibrationally-resolved Electronic Spectra Using Gaussian
Determining the pKa of Simple Molecules using Gaussian
Referencing for Research:
When writing a paper from research done using the SC Cluster, please add a statement similar to "We are grateful to the School of Chemical Sciences Computing for support and access to the SCS HPC Cluster."
A few software packages have a graphical interface so you will need to set up X forwarding.
MobaXterm seems to work best right after install with little configuration. https://mobaxterm.mobatek.net/ Just install, put lop.scs.illinois.edu into the quick connect box and you're off. See below for instructions on getting Xming to work, though it hasn't been as reliable since end of 2020.
- Download and install Xming-mesa (not normal xming). It can be found here: https://sourceforge.net/projects/xming/files/Xming-mesa/
- Run the installer
- Open NotePad as administrator
- Click on file –> Open in notepad. Open the X0.hosts file in the xming install directory as shown in this picture:
- Under localhost on a new line put in 22.214.171.124 (this is the IP for lop). Save the file and close notepad
- Download and install putty found here: https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.74-installer.msi
- Launch xming
- Launch putty
- Expand the SSH tree under Connection and click on x11. Click on the box for Enable x11 forwarding
- Click on the top option on the right "Session"
- In the Host Name box put lop.scs.illinois.edu then click the Open button
- A box will pop up prompting you to "togin as" – put in your netID and hit Enter
- It will then prompt you for a password. Use your netID password. Nothing will show as you type, this is standard Unix behavior.
- You will get a prompt. You are now connected to Lop.
- Download and install xQuartz 2.7.7 (do not get any other version, they don't seem to work with Gaussview)
- Install the downloaded dmg
- Reboot your computer entirely
- Log back in after reboot and launch xQuartz. DO NOT RUN UPDATES. always decline.
- If an xterm window did not open when you launched Quartz, right click/control click on it in the Dock and launch xterm
- In the opened xterm type: ssh -X firstname.lastname@example.org
- Put in your netID password when prompted
- This will give errors about unable to connect. This is fine, this step seems to possibly set something in the user profile
- load the gaussian module (module load gaussian/g16) and then type gv. This will fail saying cannot connect to x-server
- type exit to disconnect
- type ssh -Y email@example.com
- load the gaussian modjule and launch gv. This should bring up the Gaussview window properly.
- If it does not work, open a new xterm window. In this window type the following (without the quotes) "xhost +local:" then repeat steps 6-12
- If the above steps do not work, try making a brand new account on your mac and follow the above steps under it to see if it works there
- If it still does not work, contact firstname.lastname@example.org