CASTEP¶

Licensing¶

Only licensed users of CASTEP are entitled to use it and license details are available on CASTEP’s website. Access to CASTEP on the system is controlled using a Unix group. That is, only members of the castep group can access and run the program. To be added to this group, you will need to contact research-it@sheffield.ac.uk and provide evidence of your eligibility to use CASTEP.

Interactive Usage¶

The serial version of CASTEP should be used for interactive usage. After connecting to iceberg (see Establishing a SSH connection), start an interactive session with the qrsh or qsh command. Make the serial version of CASTEP available using one of the following commands:

module load apps/intel/15/castep/16.11-serial
module load apps/intel/15/castep/16.1-serial
module load apps/intel/15/castep/8.0-serial

The CASTEP executable is called castep.serial so if you execute:

castep.serial

You should get the following:

Usage:
castep <seedname>                : Run files <seedname>.cell [and <seedname>.param]
  "    [-d|--dryrun] <seedanme>  : Perform a dryrun calculation on files <seedname>.cell
  "    [-s|--search] <text>      : print list of keywords with <text> match in description
  "    [-v|--version]            : print version information
  "    [-h|--help] <keyword>     : describe specific keyword in <>.cell or <>.param
  "         "      all           : print list of all keywords
  "         "      basic         : print list of basic-level keywords
  "         "      inter         : print list of intermediate-level keywords
  "         "      expert        : print list of expert-level keywords
  "         "      dummy         : print list of dummy keywords

If, instead, you get:

-bash: castep.serial: command not found

It is probably because you are not a member of the castep group. See Licensing for details on how to be added to this group.

Interactive usage is fine for small CASTEP jobs such as the Silicon example given at http://www.castep.org/Tutorials/BasicsAndBonding

To run this example, you can do:

# Get the files, decompress them and enter the directory containing them
wget http://www.castep.org/files/Si2.tgz
tar -xvzf ./Si2.tgz
cd Si2

# Run the CASTEP job in serial
castep.serial Si2

# Read the output using the more command
less Si2.castep

CASTEP has a built in help system. To get more information on using castep use:

castep.serial -help

Alternatively you can search for help on a particular topic:

castep.serial -help search keyword

or list all of the input parameters:

castep.serial -help search all

Batch Submission - Parallel¶

The parallel version of CASTEP is called castep.mpi. To make the parallel environment available, use one of the following module commands:

module load apps/intel/15/castep/16.11-parallel
module load apps/intel/15/castep/16.1-parallel
module load apps/intel/15/castep/8.0-parallel

As an example of a parallel submission, we will calculate the bandstructure of graphite following the tutorial at http://www.castep.org/Tutorials/BandStructureAndDOS

After connecting to iceberg (see Establishing a SSH connection), start an interactive session with the qrsh or qsh command. Download and decompress the example input files with the commands

wget http://www.castep.org/files/bandstructure.tgz
tar -xvzf ./bandstructure.tgz

Enter the directory containing the input files for graphite:

cd bandstructure/graphite/

Create a file called submit.sge that contains the following:

#!/bin/bash
#$ -pe openmpi-ib 4    # Run the calculation on 4 CPU cores
#$ -l rmem=4G          # Request 4 GB of real memory per core
module load apps/intel/15/castep/16.11-parallel

mpirun castep.mpi graphite

Submit it to the system with the command:

qsub submit.sge

After the calculation has completed, get an overview of the calculation by looking at the file graphite.castep:

more graphite.castep

Installation Notes¶

These are primarily for system administrators.

Version 16.11¶

Serial (no MPI) and parallel (MPI) builds were compiled. Both builds were compiled with Intel compiler 15.0.3 (including the Intel MKL 2015.3 for BLAS and FFT routines). The parallel build was compiled using OpenMPI 1.10.0.

Both builds were installed using this script Note that this compiles both builds in /data/$USER as the build directory must be availble to all cluster nodes to allow for subsequent Testing of the parallel build. ~2.2 GB of free space is required.

The non-MPI build modulefile was installed as /usr/local/modulefiles/apps/intel/15/castep/16.11-serial
The MPI build modulefile was installed as /usr/local/modulefiles/apps/intel/15/castep/16.11-parallel

Version 16.1¶

The jump in version numbers from 8 to 16.1 is a result of CASTEP’s change of version numbering. There are no versions 9-15.

Serial (1 CPU core) and Parallel versions of CASTEP were compiled. Both versions were compiled with version 15.0.3 of the Intel Compiler Suite and the Intel MKL versions of BLAS and FFT were used. The parallel version made use of OpenMPI 1.8.8

The Serial version was compiled and installed with

module load compilers/intel/15.0.3
install_dir=/usr/local/packages6/apps/intel/15/castep/16.1
mkdir -p $install_dir

tar -xzf ./CASTEP-16.1.tar.gz
cd CASTEP-16.1

#Compile Serial version
make INSTALL_DIR=$install_dir  FFT=mkl MATHLIBS=mkl10
make INSTALL_DIR=$install_dir  FFT=mkl MATHLIBS=mkl10 install install-tools

The directory CASTEP-16.1 was then deleted and the parallel version was installed with

#!/bin/bash
module load libs/intel/15/openmpi/1.8.8
#The above command also loads Intel Compilers 15.0.3
#It also places the MKL in LD_LIBRARY_PATH

install_dir=/usr/local/packages6/apps/intel/15/castep/16.1

tar -xzf ./CASTEP-16.1.tar.gz
cd CASTEP-16.1

#Workaround for bug described at http://www.cmth.ph.ic.ac.uk/computing/software/castep.html
sed 's/-static-intel/-shared-intel/' obj/platforms/linux_x86_64_ifort15.mk -i

#Compile parallel version
make COMMS_ARCH=mpi  FFT=mkl MATHLIBS=mkl10
mv ./obj/linux_x86_64_ifort15/castep.mpi $install_dir

CASTEP Version 8

The Serial version was compiled and installed with

module load compilers/intel/15.0.3
install_dir=/usr/local/packages6/apps/intel/15/castep/8.0

tar -xzf ./CASTEP-8.0.tar.gz
cd CASTEP-8.0

#Compile Serial version
make INSTALL_DIR=$install_dir  FFT=mkl MATHLIBS=mkl10
make INSTALL_DIR=$install_dir  FFT=mkl MATHLIBS=mkl10 install install-tools

The directory CASTEP-8.0 was then deleted and the parallel version was installed with

#!/bin/bash
module load libs/intel/15/openmpi/1.8.8
#The above command also loads Intel Compilers 15.0.3
#It also places the MKL in LD_LIBRARY_PATH

install_dir=/usr/local/packages6/apps/intel/15/castep/8.0
mkdir -p $install_dir

tar -xzf ./CASTEP-8.0.tar.gz
cd CASTEP-8.0

#Compile parallel version
make COMMS_ARCH=mpi  FFT=mkl MATHLIBS=mkl10
mv ./obj/linux_x86_64_ifort15/castep.mpi $install_dir

Modulefiles¶

Testing¶

Version 16.1 Serial

The following script was submitted via qsub from inside the build directory:

#!/bin/bash
#$ -l rmem=10G
module load compilers/intel/15.0.3

cd CASTEP-16.1/Test
../bin/testcode.py -q  --total-processors=1 -e /home/te1st/CASTEP/CASTEP-16.1/obj/linux_x86_64_ifort15/castep.serial -c simple -v -v -v

All but one of the tests passed. It seems that the failed test is one that fails for everyone for this version since there is a missing input file. The output from the test run is on the system at /usr/local/packages6/apps/intel/15/castep/16.1/CASTEP_SERIAL_tests_09022016.txt

Version 16.1 Parallel

The following script was submitted via qsub from inside the build directory

#!/bin/bash
#$ -pe openmpi-ib 4
#$ -l rmem=10G
module load libs/intel/15/openmpi/1.8.8

cd CASTEP-16.1/Test
../bin/testcode.py -q  --total-processors=4 --processors=4 -e /home/te1st/CASTEP/CASTEP-16.1/obj/linux_x86_64_ifort15/castep.mpi -c simple -v -v -v

Version 8 Parallel The following script was submitted via qsub

#!/bin/bash
#$ -pe openmpi-ib 4
module load libs/intel/15/openmpi/1.8.8

cd CASTEP-8.0
make check COMMS_ARCH=mpi  MAX_PROCS=4 PARALLEL="--total-processors=4 --processors=4"

All tests passed.