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Anastasia Jenkins
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The TCU High-Performance Computing Center The TCU HPCC currently maintains a cluster environment hpcl1.chm.tcu.edu. Work on a second cluster environment is underway. This document details using hpcl1.

Logging In to HPCl1 for the First Time This assumes that you have a new cluster account and a temporary password, and that you are logging in from a TCU-owned Windows desktop on the "lab subnetwork".

1 The TCU High-Performance Computing Center The TCU HPCC currently maintains a cluster environment hpcl1.chm.tcu.edu. Work on a second cluster environment is underway. This document details using hpcl1. Citing the Center Please include the following sentence in any works using center resources. The author[s] acknowledge the TCU High-Performance Computing Center for providing HPC resources. Logging In to HPCl1 for the First Time This assumes that you have a new cluster account and a temporary password, and that you are logging in from a TCU-owned Windows desktop on the "lab subnetwork". Contact the TCU HPC team if you lack any of these things. Connections to the cluster use the PuTTY text terminal. Begin by downloading the executable putty.exe from Save the executable in a shared drive, or on your desktop Double-click the icon to open it. This gives a graphical interface for configuring PuTTY. You will connect via SSH to the cluster IP address, I recommend saving this address using "Save Session" 1

I also recommend adjusting the default colors, using the Window->Colours dialog.

Type in your username, an d hit return. Type in your temporary password, and hit return again.

This "terminal" window is where you will do almost all of your work. It is similar to the terminal on Mac OS X or the Windows DOS terminal.

2 I also recommend adjusting the default colors, using the Window->Colours dialog. I use white for the background, black for the foreground and bold foreground: Once you click "Open", you should get a new terminal window. Type in your username, an d hit return. Type in your temporary password, and hit return again. The cursor will not move as you type in your password, and you will not see your password on the screen. This "terminal" window is where you will do almost all of your work. It is similar to the terminal on Mac OS X or the Windows DOS terminal. The first thing you need to do is to change your temporary password. This is done with Unix command "passwd". Type in passwd and hit return: Follow the instructions for typing in your temporary password, then a new password. Because of technical issues, you'll need to the TCU HPC team whenever you change your password. We'll run 2

a script to propagate that password across the compute nodes. After you've changed your password, open a new PuTTY window, and log in again using your new password.

3 a script to propagate that password across the compute nodes. After you've changed your password, open a new PuTTY window, and log in again using your new password. If the new password works, then you can continue. If you get stuck, Ctrl-c will typically kill any running commands. The next thing you need to do is get familiar with the Unix command line. This is where you make directories, traverse directories, open files, and so on. I recommend working through an online tutorial, such as This should take about an hour. You'll also want to get familiar with editing text documents. We use the vi text editor. This follows a different model from standard Windows text editors, and takes some getting used to. I recommend working through an online tutorial, such as Once you've completed Graphics It is often useful to open new windows from the terminal. We do this using X11 forwarding. To do this, first download the Xming X server for Windows from onto your Windows desktop. You will need administrator access to install it. Once it is installed, Xming will be in the Windows start menu. Click on it to start Xming. Xming runs in the background and displays X11-forwarded images from PuTTY. You will not typically see any evidence that Xming is running. You can check it by clicking the lower-right corner of the Windows desktop: The resulting pop-up window should show the Xming logo. Next, you need to enable X11 forwarding in your SSH connection. Do this via the SSH->X11 option in the PuTTY configuration GUI. I recommend re-saving your PuTTY session after making this change. After this, you should be able to open X11 images from the terminal. 3

Running Gaussian Calculations The cluster is often used to run Gaussian calculations. Here I'll illustrate calculating the Hartree-Fock/6-31+G(d,p) vibrational spectrum of formaldehyde.

4 Running Gaussian Calculations The cluster is often used to run Gaussian calculations. Here I'll illustrate calculating the Hartree-Fock/6-31+G(d,p) vibrational spectrum of formaldehyde. Start by running the command "tcsh", to set up the Gaussian environment variables. Then, open the GaussView viewer with command gv. I recommend running it in the background with command & Set up the calculation as usual, and save it as formaldehyde.com Then, open formaldehyde.com in vi: 4

5 Add lines at the top of the file specifying 4 GB memory and 4 shared processors. (You can also do this from GaussView) Next, you'll use a Perl script to submit this calculation to the "queue" of jobs running on the cluster. Here we'll run on the newest Generation 9 nodes, using the number 9 as the second argument to our script. You can check the status of your queued jobs using command qstat: Here the job is running with status "R", as job ID You can check the status of other peoples' jobs using the command showq. Once the job is complete, it will disappear from the list of queued jobs. You can view the results in GaussView by opening log file formaldehyde.log The cluster has three main queues gen6, gen8, and gen9 corresponding to the three generations of nodes present. Generation 6 is the slowest, generation 9 is the fastest. By default, the submit script will not re-run a.com file if the corresponding.log file already exists. If you Running Other Calculations To run other kinds of jobs, you'll need to understand the job queueing system. Every substantial job on the cluster must be run on the compute nodes, and must be queued through the Torque/MOAB job queueing system. This is done by writing portable batch script (pbs) files for each job. PBS files are submitted with command msub. The pbs file for the aforementioned formaldehyde calculation is reproduced below. The job sets up environment variables, prepares a temporary directory, and runs the Gaussian 09 executable g09 on input file formaldehyde.com. #PBS -N formaldehyde #PBS -S /bin/tcsh #PBS -q gen9 #PBS -l walltime=100:00:00 5

6 #PBS -l nodes=1:ppn=4 #PBS -l mem=4gb setenv NPROCS `wc -l < $PBS_NODEFILE` echo "This job has allocated $NPROCS processors" cd $PBS_O_WORKDIR setenv g09root /opt/temp/g09-b1 source $g09root/g09/bsd/g09.login rm -rf /tmp/g09-$pbs_jobid-formaldehyde mkdir /tmp/g09-$pbs_jobid-formaldehyde setenv GAUSS_SCRDIR /tmp/g09-$pbs_jobid-formaldehyde $g09root/g09/g09 <formaldehyde.com >formaldehyde.log rm -rf /tmp/g09-$pbs_jobid-formaldehyde Writing PBS scripts is a nontrivial task. I recommend contacting the TCU HPC team before starting to run any new piece of code. ================== Notes for administrators. Every new user needs to be added to the queues using qmgr Every new Gaussian user needs to be added to the gaussian group Every change in a user's password or group membership must be propagated to compute nodes using run make -C /var/yp Every change in a user's group membership or queue access requires the user to log out and log back in again. 6

New User Tutorial. OSU High Performance Computing Center

New User Tutorial. OSU High Performance Computing Center New User Tutorial OSU High Performance Computing Center TABLE OF CONTENTS Logging In... 3-5 Windows... 3-4 Linux... 4 Mac... 4-5 Changing Password... 5 Using Linux Commands... 6 File Systems... 7 File