How to run Q-Chem on USC HPCC

First, you need to secure an allocation on HPCC. Check if your group already has an allocation and ask your professor to add you to the list of users. If you do not have one --- request HPC account and allocation (this should be done by the PI). If you are enrolled in Chem545, your name will be added to the class HPCC user list. Once you have the allocation, email to hpc@usc.edu and request to be added to the qchem group. Once this is done, you can submit jobs either by using IQmol graphic interface (which you need to install on your laptop or desktop) or by ssh-ing to HPCC and using a PBS script (this requires a basic knowledge of Unix OS).

Using IQmol

  • Download IQmol graphic interface from the IQmol website.
  • Follow the steps in this tutorial to configure IQmol to submit jobs to HPCC.

From HPCC command-line using PBS

  • Login to USC HPCC using your USC/HPC account.
  • Create your Q-Chem input file:
    my_input.inp
  • Create PBS run script
    qcpbs.run
    with the following content making necessary adjustments to queue, walltime, etc.
    #!/bin/bash
    #PBS -q default
    #PBS -l walltime=00:30:00
    #PBS -l ncpus=1
    
    export QC=/usr/usc/qchem/default
    export QCAUX=$QC/qcaux
    export QCPLATFORM=LINUX_Ix86_64
    export QCRSH=ssh
    export PATH=$QC/bin:$PATH
    export QCSCRATCH=$TMPDIR
    
    cd $PBS_O_WORKDIR
    qchem -nt 1 -save my_input.inp my_output.out
    cp -R "$TMPDIR" "$PBS_O_WORKDIR"
              
  • Submit your PBS job:
    qsub qcpbs.run
  • To run Q-Chem in parallel change
    -nt 1
    to
    -nt N
    in the above script (N is the number of CPU cores; typical values are 4-32). This option should be used only for jobs that take more than 15 min. Consult Q-Chem manual for more information.
  • Note
    -save
    option in the above script: it means that additional files will be copied to your HPCC home, in IQmol's working directory. This option is needed for wave function analysis.

Additional Resources