Crystal

Overview

The CRYSTAL09 program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid HF/DFT approximations.

Version Crystal09 2.0.1 MPP emt64 is installed on the CSF.

Restrictions on use

CRYSTAL09 is protected by a unix group. Only users who belong to a research group which has been granted a license by may be added to the unix group.

Licenses are normally in the name of the Project Investigator or Head of a research group. Members of the research group will be given access but they must confirm that they will abide by the terms and conditions set out in the licence (pdf). The following notes cover the main points of, but are not intended as a replacement for, the license:

You are not permitted to:

• Copy the software or share it with anyone else.
• Modify the software or incorporate it into any other software code without permission of the CRYSTAL authors

You must:

• use the software for not-for profit, non-commercial academic research only.
• cite your usage of the software in your work as per clauses 8, 9 and 10 of the license.

To get access to the software on the CSF we will need proof that your group has a license. Please email its-ri-team@manchester.ac.uk with your details and we will confirm when access has been granted.

Set up procedure

To access the software you must first load the modulefile. This will load the apppropriate compiler, MKL, and MPI modulefiles automatically.

Choose one of the following:

# For multi-core (single compute node) jobs
module load apps/intel-12.0/crystal/c09_201_emt64

# For multi-node (large jobs) 
module load apps/intel-12.0/crystal/c09_201_emt64-ib

Running the application

Please do not run CRYSTAL on the login node. Jobs should be submitted to the compute nodes via batch. There is a script named csf_runmpi09 which is a modified version of the CRYSTAL runmpi09 script that runs your job on the CSF. The script will call mpirun and also copy your input files to the scratch filesystem to run the job from there. Results will be copied back to the current directory. Use of this script is optional but recommended because of the way it ensures all required input files are in place.

The script requires the number of cores you wish to use followed by the CRYSTAL input file (see examples below).

It is permissible to run csf_runmpi09 without any arguments on the login node to print out some help text that indicates which input files it will copy and a few optional environment variables that can be set. However, you must not run a real job on the login node – use a jobscript instead.

Parallel batch job submission

Make sure you have the -ib version of the modulefile (see above) loaded then create a batch submission script (example below). The csf_runmpi09 script is used to start the MPI processes, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd                     # App will run from current directory
#$ -V                       # Inherit current environment for use when job runs
#$ -pe orte-24-ib.pe 48     # Specify a parallel environment and number of cores
                            # NOTE: example uses an IB pe so we must load the c09_201_emt64-ib modulefile

# $NSLOTS is automatically set to the number of cores requested on the -pe line
csf_runmpi09 $NSLOTS inpfilename
    #   
    # inpfilename.d12        CRYSTAL input deck for wave function calculation

Submit the jobscript using:

qsub scriptname

If you want to run the MPPcrystal executable manually, without using the inputfile checking performed by the csf_runmpi09 script then use a jobscript similar to the following:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd                     # App will run from current directory
#$ -V                       # Inherit current environment for use when job runs
#$ -pe orte-24-ib.pe 48     # Specify a parallel environment and number of cores

mpirun -n $NSLOTS MPPcrystal inpfilename
    #   
    # inpfilename.d12        CRYSTAL input deck for wave function calculation

Further info

• The CRYSTAL09 manual is available on the CSF using:

  evince $CRY2K9_ROOT/doc/crystal09_manual.pdf

• CRYSTAL website

Updates

None.