Quick Links Documentation Notes OpenMP (threaded) Batch job MPI batch job

Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra. The new release of Q-Chem 4.0 represents the state-of-the-art of methodology from the highest performance DFT/HF calculations to high level post-HF correlation methods:

• Dispersion-corrected and double hybrid DFT functionals
• Faster algorithms for DFT, HF and coupled-cluster calculations;
• Structures and vibrations of excited states with TD-DFT;
• Methods for mapping complicated potential energy surfaces;
• Efficient valence space models for strong correlation;
• More choices for excited states, solvation and charge-transfer;
• Effective Fragment Potential and QM/MM for large systems;
• Shared-memory for multicores and implementations for GPU's.

Q-Chem is a licensed product developed by Q-Chem

• Q-Chem 5.0 manual

• Module Name: qchem (see the modules page for more information)
• Q-Chem can use threads or MPI processes to parallelize. Different methods within Q-Chem can utilize one or both kinds of parallelization. See the section on Running Q-Chem in parallel for more information. OpenMP (threads) can utilize multiple cores on a node, but cannot run on multiple nodes.
• After you run 'module load qchem', a set of example input files is available in $QC/samples.
• Reference data in /fdb/qchem/

Create a batch input file (e.g. qchem.sh). For example:

#!/bin/bash
#SBATCH --job-name="QC"
#SBATCH --mail-type=BEGIN,END

module load qchem/4.3

cd /data/$USER/qchem

# copy the sample data to this directory
cp ${QC}/samples/bsse/frgm_mp2_h2o_h2o_h2o.in .

# run qchem
qchem -nt $SLURM_CPUS_PER_TASK  frgm_mp2_h2o_h2o_h2o.in   frgm_mp2_h2o_h2o_h2o.in.out

Submit this job using the Slurm sbatch command. e.g.

sbatch --cpus-per-task=16  --threads-per-core=1 --mem=20g qchem.sh

-nt $SLURM_CPUS_PER_TASK	tells Q-Chem to run $SLURM_CPUS_PER_TASK threads
--cpus-per-task=16	tells Slurm how many CPUs to allocate
--threads-per-core=1	specifies that one thread should be run on each physical core (i.e. ignore hyperthreading). This is usually recommended for cpu-intensive parallel jobs.
--gres=lscratch:100	specifies that 100 GB of local scratch on the node should be allocated to this job. This parameter is required for all Qchem job submissions.

When the qchem module is loaded as part of a batch job, it sets the environment variable $QCLOCALSCR to '/lscratch/$SLURM_JOBID' . This directory is only created if you submit the job with --gres=lscratch:#. (see the User Guide section on using local disk.

Q-Chem can also run MPI . Sample MPI batch script

#!/bin/bash
#SBATCH --job-name="QC"

module load qchem/4.3

cd /data/$USER/qchem

# copy the sample input file to this directory
cp  ${QC}/samples/sp/dft_b5050lyp_c4h6.in .

# run qchem
make-qchem-nodefile
export QCMACHINEFILE=`pwd`/qchem.$SLURM_JOBID.nodes
qchem -np $SLURM_NTASKS  dft_b5050lyp_c4h6.in   dft_b5050lyp_c4h6.in.out
rm $QCMACHINEFILE

Submit this job with:

biowulf% sbatch --ntasks=4 --ntasks-per-core=1  --gres=lscratch:100 qchem.bat

where:

make-qchem-nodefile	a script that writes a file containing a list of nodes to be used
$QCMACHINEFILE	environment variable used by Q-Chem to determine the nodes on which to run
-np $SLURM_NTASKS	tells Q-Chem to run $SLURM_NTASKS MPI processes
--ntasks=4	tells Slurm how many tasks (MPI processes) to run
--ntasks-per-core=1	tells Slurm to run only one task on each physical core (i.e. ignore hyperthreading). This is usually recommended for cpu-intensive parallel jobs.
--gres=lscratch:100	specifies that 100 GB of local scratch on the node should be allocated to this job. This parameter is required for all Qchem job submissions.