Q-Chem/Example

As an example Q-Chem job, we are running an single point Hartree-Fock calculation for a water molecule on two cores using an aug-cc-pVQZ basis set. The input file (water.in), looks like

[leonhard@euler09 ~]$ ls water.in 
water.in
[leonhard@euler09 ~]$ cat water.in 
$molecule
   0  1
   O
   H1  O  oh
   H2  O  oh  H1  hoh

   oh  =   1.2
   hoh = 120.0
$end

$rem
   JOBTYPE       sp             Single Point energy
   METHOD        hf             Hartree-Fock
   BASIS         aug-cc-pVQZ    Basis set
$end

$comment
HF/aug-cc-pVQZ water single point calculation
$end

As a first step, you need to load the modules required for running Q-Chem.

[leonhard@euler09 ~]$ module load new gcc/4.8.2 qchem/4.3_SMP
Now run 'qchem-init' to initialize your environment for Q-Chem
[leonhard@euler09 ~]$ qchem-init

Afterwards you can submit the job. Here it is important that you request local scratch space from the batch system and set the variable QCLOCALSCR to $TMPDIR. This will make sure that temporary files are saved on the local hard drive of the compute node, which gives a better performance compared to using a storage system that is attached via network to the cluster.

[leonhard@euler09 ~]$ bsub -n 2 -W 4:00 -R "rusage[mem=1024, scratch=4000]" "export QCLOCALSCR=\$TMPDIR; qchem -nt 2 water.in water.out"
Generic job.
Job <33706123> is submitted to queue <normal.4h>.
[leonhard@euler09 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33706123   leonhard   PEND  normal.4h  euler09                 *water.out Dec  7 17:16
[leonhard@euler09 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33706123   leonhard   RUN   normal.4h  euler09     2*e1155     *water.out Dec  7 17:16
[leonhard@euler09 ~]$ bjobs
No unfinished job found
[leonhard@euler09 ~]$ grep "Total energy" water.out 
 Total energy in the final basis set = -75.9698992838

The resource usage summary of the job can be found in the corresponding LSF log file.