SCS Clusters

info on scs clusters


Introduction and Access

Lop: 

SCS maintains a computational cluster which is available for use by anyone in the School of Chemical Sciences called lop (DNS lop.scs.illinois.edu.) To get access, fill out the form located here: https://go.scs.illinois.edu/cluster-account . Once you have access, you will log in using your netid and password (The same password used for e-mail, vpn, etc)

Lipid:

Lipid.scs.illinois.edu is also a cluster available for use by all in SCS. Using it requires an SCS account, which can be requested by e-mailing scs-help@illinois.edu. This account is a separate account from your UIUC netid account, though it uses the same login name as your netid. It will be going down before the end of 2020, with its compute being moved over to lop.

Accessing software: 

Some of the software installed will just “work” if you try to run it when logging in (eg. Nwchem). Many packages will require you loading a module first. To do so: 

  1. Type this command to see the available modules to load
    1. module avail
  2. To load a specific module, type the following command (gaussian is used as an example, replace with the one you want)
    1. module load gaussian/g16
  3.  To see which modules you currently have loaded
    1. module list
  4. To unload a module (to load a different version for example). 
    1. module unload gaussian/g16

If there is any software not currently on the cluster that you would like installed, e-mail scs-help@illinois.edu and inquire if that is possible. 

Queues:

Lop:
amd16smt: This queue is composed of dual socket AMD Opteron CPUs with 4 physical cores each with SMT (Simultaneous MultiThreading) enabled yielding 16 cores per node. They each have 64 GB of memory.

gpu: This queue is composed of nodes populated with Nvidia GPUs for use in cuda calculations. Compute-1-20 contains 4xGTX 980s. Compute-1-21 has 4x TITAN X. This queue is only to be used for cuda calculations. Never submit a CPU compute job to this queue.

ib1: This queue is composed of dual socket AMD Opteron CPUs with 4 physical cores each with SMT enabled for 16 total cores. Nodes 2-0 through 2-16 have 64GB of memory while 2-17+ have 32GB. They are connected together via infiniband for multi-node calculations (eg. MPI)

Lipid:
all.q: This queue is composed of dual socket AMD Opteron CPUS with 8 physical cores each with SMT enabled yielding 32 cores per node. They each have 32GB of memory.

gpu: This queue is composed of nodes populated with Nvidia GPUs for use in cuda calculations. Compute-1-0 contains 4xTesla K80s Compute-1-1 also has 4x Tesla k80s This queue is only to be used for cuda calculations. Never submit a CPU compute job to this queue.

Beta: This queue is composed of dual socket Intel Xeon CPUs with 12 physical cores each with HyperThreading disabled for 24 cores total per node. They have 256GB or memory per node.


Quotas:

There is currently a 148 core limit per user enforced on Lop as well as lipid so that no one person can use all the resources on the cluster. In the future, this will be an adaptive quota so that resources are not left idle if only a few people are trying to use them, but for now it is static. If an individual has a pressing need to go above the quota, you can contact us at scs-help@illinois.edu and we will evaluate on a case by case basis.

The command qquota will show how many you are currently using. There is no output if you have no jobs running.

Storage:

Each user has a quota of 250GB on Lop. If more storage is required beyond that (large data sets being calculated for example) contact scs-help@illinois.edu to see if more can be allocated on a case by case basis. Also remember the  Storage Policy - Home Directories from the access form
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.

Software Tutorials: 

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: 

Unix/Linux Primer

Intro to Gaussian Part I

Intro to Gaussian Part II

Simulating Vibrationally-resolved Electronic Spectra Using Gaussian

Determining the pKa of Simple Molecules using Gaussian

X-forwarding

A few software packages have a graphical interface so you will need to set up X forwarding. 

Windows Instructions:

  1. Download and install Xming-mesa (not normal xming). It can be found here: https://sourceforge.net/projects/xming/files/Xming-mesa/
  2. Run the installer
  3. Open NotePad as administrator 
  4. Click on file –> Open in notepad. Open the X0.hosts file in the xming install directory as shown in this picture: scsclusters.png                               
  5. Under localhost on a new line put in 130.126.43.205 (this is the IP for lop). Save the file and close notepad 
  6. Download and install putty found here: https://the.earth.li/~sgtatham/putty/latest/w64/putty-64bit-0.74-installer.msi  
  7. Launch xming
  8. Launch putty
  9. Expand the SSH tree under Connection and click on x11. Click on the box for Enable x11 forwarding
  10. Click on the top option on the right "Session" 
  11. In the Host Name box put lop.scs.illinois.edu then click the Open button
  12. A box will pop up prompting you to "togin as" – put in your netID and hit Enter
  13. It will then prompt you for a password. Use your netID password. Nothing will show as you type, this is standard Unix behavior. 
  14. You will get a prompt. You are now connected to Lop.

Mac Instructions:

  1. Download and install xQuartz 2.7.7 (do not get the latest version) https://dl.bintray.com/xquartz/legacy-downloads/SL/XQuartz-2.7.7.dmg 
  2. Install the downloaded dmg
  3. Run xquartz to start it 
  4. Open up a terminal, located under Applications –> Utilities –> Terminal
  5. In the opened terminal type: ssh -YC netid@lop.scs.illinois.edu 
  6. Put in your netID password when prompted
  7. You are now connected to Lop 









Keywords:lop lipid cluster   Doc ID:104365
Owner:Mark H.Group:University of Illinois School of Chemical Sciences
Created:2020-07-26 22:37 CDTUpdated:2020-10-15 09:35 CDT
Sites:University of Illinois School of Chemical Sciences
CleanURL:https://answers.uillinois.edu/scs-clusters
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