Difference between revisions of "Q-Chem/Example"

From ScientificComputing
Jump to: navigation, search
(Created page with "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),...")
 
 
Line 32: Line 32:
 
Afterwards you can submit the job. Here it is important that you request local scratch space from the batch system and set the variable <tt>QCLOCALSCR</tt> to <tt>$TMPDIR</tt>. 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.
 
Afterwards you can submit the job. Here it is important that you request local scratch space from the batch system and set the variable <tt>QCLOCALSCR</tt> to <tt>$TMPDIR</tt>. 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=$TMPDIR; qchem -nt 2 water.in water.out"'''
+
  [leonhard@euler09 ~]$ '''bsub -n 2 -W 4:00 -R "rusage[mem=1024, scratch=4000]" "export QCLOCALSCR=\$TMPDIR; qchem -nt 2 water.in water.out"'''
 
  Generic job.
 
  Generic job.
 
  Job <33706123> is submitted to queue <normal.4h>.
 
  Job <33706123> is submitted to queue <normal.4h>.
Line 43: Line 43:
 
  [leonhard@euler09 ~]$ '''bjobs'''
 
  [leonhard@euler09 ~]$ '''bjobs'''
 
  No unfinished job found
 
  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.

Latest revision as of 16:37, 7 December 2016

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.