Tips on using HPCC

Login to HPCC

From Windows

You need to download and install SSH client.
For example this one: Bitvise Tunneller

After installation open the program and use the following settings:
Host: hpc-login2.usc.edu
Port: 22
Username: your USC account name used for the USC e-mail
Password: your password for the USC account

After you login to HPC you will see two windows:
black one is called terminal and used to type commands
second window is a graphical interface for SFTP that allows you to copy files from you local machine to HPC

From Linux

ssh username@hpc-login2.usc.edu
where 'username' is your USC account name and hpc-login2 states for the 64-bit systems.

Use simple shell script

- Download qchempbs.sh script to the folder with your input file.

- Check that file have a permission to be executed (when you do "ls -l" it should show x in file permissions)

- If permissions are incorrectd do
chmod +x qchempbs.sh

- Now you can simply run qchem by typing:
./qchempbs.sh you_input_filename batch_name your_job_name
where 'batch_name' defines how long your job will run and can be one of the following:
  • blitz - 10 min
  • quick - 30 min
  • normal - 5 hours
  • big - 24 hours
Remember, that the less time you ask the fater you job will go through the queue. But if you requested time is not enough to finish the job it will be killed.

-Check the status:
qstat -u your_username

That is it!

Old method

Below is the description of th eold method. Don't do use unless you want to experiment and customize the script and clearly understand what are you doing.

Setup Q-Chem enviroment

-Download qsetup4_sing and qsetup_scr files to your home directory
-In qsetup4_sing in line
setenv QCSCRATCH /scratch/khistyae
change khistyae to your username

Run Q-chem

-Download samplejob.pbs as a template for your pbs-files
-Specify recources that you need, your working directory and you input and output filenames
-Submit the job:
qsub samplejob.pbs
-Check the status:
qstat -u your_username


For more information read this presentation



Our group project directoty is:
/home/rcf-proj/aik