CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc. In particular it has a wide range of spectroscopic features that link directly to experiment, such as infra-red and Raman spectroscopies, NMR, and core level spectra.
We have the standard (CPU) version of CASTEP (in serial and MPI builds) available on Comet.
Whilst there is a version of CASTEP with GPU acceleration, this was considered a beta release of an older version (23.1), has not been updated, and is restricted to older versions of the Nvidia HPC / CUDA SDK. As such, we have not installed it on Comet.
The commercial BIOVIA Material Studio which incorporates CASTEP does have GPU support, but is not currently licensed for use on Comet.
CASTEP on Comet is provided as an Apptainer container environment - please read the Apptainer guide first. The CASTEP container images are stored in the following location:
/nobackup/shared/containers/castep-25.12.sif - CPU (serial & MPI) versionYou will also find a matching shell script:
/nobackup/shared/containers/castep-25.12.sh
To run CASTEP, simply source the shell script:
$ source /nobackup/shared/containers/castep-25.12.sh
You can then use a helper command container.run to run commands inside the container, without needing pass huge numbers of parameters to the apptainer exec command - this automatically adds bind arguments to let you access /scratch and /nobackup inside the container:
$ source /nobackup/shared/containers/castep-25.12.sh
$ container.run castep.serial -h
You only need to source the shell script once, either at the start of your Comet session, if working interactively, or at the top of your sbatch file if submitting a job.
All of the CASTEP binaries and scripts are available under /opt/castep inside the container:
$ apptainer exec /nobackup/shared/containers/castep-25.12.sif ls /opt/castep/bin
MolPDOS castep2cube castepclean cif2cell den2xsf md2xyz pdb2xtl vasp2pdb
__pycache__ castep2force.py castepconv.py cssr2cell dispersion.pl md_to_phonons.py perl_md.pl xtl2cell
awk_elf_to_xsf castep2ngwst cell2cell cssr2gulp dos.pl mdtep perl_pimd.pl xtl2cssr
bands2dos castep2pdb cell2pdb cube_add elastics.py mode_follow phonon2xyz xtl2pdb
bs_sc2pc castep2shak cell2sgroup cube_info f2py numpy-config phonon_kpoints xtl2sgroup
c2x castep2shx cell2shx cube_subtract generate_strain.py od2od phonons xtl2shx
castep.mpi castep2w90 cell2xsf cube_to_xsf geom2dcd optados pimerge.pl
castep.serial castep2xsf cell2xtl current2nics geom2pdbseq orbitals2bands pot1d
castep2casino castep2xtl cell2xyz den2cube geom2xsf pdb2cell shx2cell
castep2cell castep2xyz celltools den2grd geom2xtl pdb2pdb symmetry_snap
castep2cif castep_GA ceteprouts.pm den2vasp geom2xyz pdb2shak vasp2cell
castep2cssr castep_md_reader.py charge2d den2xplor geom2xyz.pl pdb2shx vasp2cif
$
Within the container, the directory /opt/castep/bin is added to the PATH, so you do not need to prefix it to any commands - see the non-MPI and MPI examples below.
Now you can call the castep.serial binary inside the container. A simple example to show the CASTEP help page is shown below:
$ source /nobackup/shared/containers/castep-25.12.sh
$ container.run castep.serial -h
Usage:
castep <seedname> : Run files <seedname>.cell [and <seedname>.param]
" [-d|--dryrun] <seedname> : 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
$
Call the castep.mpi binary:
$ source /nobackup/shared/containers/castep-25.12.sh
$ container.run castep.mpi -h
Usage:
castep <seedname> : Run files <seedname>.cell [and <seedname>.param]
" [-d|--dryrun] <seedname> : 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
$
This guide is no longer relevant if you source the shell script as detailed above - all of these steps will be performed automatically for you.
By default a container running under Apptainer automatically has access to your home directory - i.e. if
castep tries to read or write files in $HOME, it will be mapped to your real home directory on Comet.
However the /nobackup directory is not included by default. If you want castep to read or write data to or from your project directory, prefix the apptainer exec call as follows:
$ apptainer exec --bind /scratch:/scratch --bind /nobackup:/nobackup /nobackup/shared/containers/castep-25.12.sif castep.serial
With this bind option,
castep can read and write all of your normal group folders and files under the /nobackup directory, in addition to anything in your $HOME. The example run file linked above shows an example of the use of these bind options.
Please note that due to limitations in compatibility between the CASTEP source code and more modern releases of the Python build tools (e.g. meson and similar), it has not been possible to install the CASTEP to Python API integration features (e.g. from make castep_python).
Important!
The following sections are only relevant to Comet RSE staff or those needing to build CASTEP from source themselves. Users of CASTEP should ignore this section.
Build requirements
autoconfbuild-essentialcmakef90wrap - Python modulegcc-14 and gfortran-14gitgziplibsymspg-devmesonnumpy - Python modulelibgomp1openmpi-bin, openmpi-common and libopenmpi-devmpi4py - Python modulePyCifRW - Python modulepython3 and python3-pipply - Python modulescipy - Python moduletarwget
Some of these need to be installed manually as part of the base OS or container environment, a small number of the Python modules are automatically installed by pip which is called during the make install phase of the compilation of CASTEP. Some additional Python modules are not installed automatically by CASTEP and need to be added prior to the make check or make install phase.
Compiler settings for anything built from source in this CASTEP environment use the settings below, ensuring optimal execution on the AMD Epyc architecture. Note that the OPENBLAS_TARGET variable is the recommended setting for OpenBLAS on AMD Zen 4 (and higher) processors - it is not a mistake:
export CFLAGS="-O3 -march=znver5 -pipe"
export OPENBLAS_TARGET=SKYLAKEX
This simple script, castep_cpu_build.sh, maps the current directory (which should contain CASTEP-25.12.tar.gz - this is not provided freely due to licensing terms) and calls the apptainer build command using the definition file, castep_cpu_build.def, provided below.
Build script:
#!/bin/bash
echo "Loading modules..."
module load apptainer
echo "OK"
echo ""
echo "Building container..."
export APPTAINER_TMPDIR=/scratch
# You **must** provide the CASTEP-25.12.tar.gz file in a directory
# and then specify it in the bind parameter to apptainer as below.
# By default we try to find it in the same directory as this script.
CASTEP_TAR_FOLDER=`pwd`
if [ -s "$CASTEP_TAR_FOLDER/CASTEP-25.12.tar.gz" ]
then
echo "- Found: $CASTEP_TAR_FOLDER/CASTEP-25.12.tar.gz"
else
echo "- ERROR: $CASTEP_TAR_FOLDER/CASTEP-25.12.tar.gz not found"
exit 1
fi
apptainer build --bind=$CASTEP_TAR_FOLDER:/mnt castep.sif castep_cpu_build.def 2>&1 | tee castep.log
Container definition file:
Bootstrap: docker
From: ubuntu:noble
####################################################################
#
# CASTEP 25.12
#
# NOTE 1: This build is for the CPU-only version of CASTEP.
#
# NOTE 2: This build relies on CASTEP-25.12.tar.gz being mounted
# in a folder at /mnt/ at the time this build file is run. Check
# castep_cpu_build.sh to see how this is accomplished.
#
# NOTE 3: The CASTEP source code, whilst free, is *not* freely
# distributed. See https://www.castep.org/get_castep
#
####################################################################
%post
# Prevent interactive prompts
export DEBIAN_FRONTEND=noninteractive
####################################################################
#
# Basic system packages
#
####################################################################
# Update & install only necessary packages
apt-get update
apt-get install -y apt-utils wget autoconf cmake build-essential tar git aptitude python3-pip gcc-14 gfortran-14 openmpi-bin openmpi-common libopenmpi-dev libgomp1 autoconf libsymspg-dev meson vim
ln -s /usr/bin/python3 /usr/bin/python
# Clean up APT cache to save space
apt-get clean
# Dependency for some castep python scripts
pip3 install f90wrap --break-system-packages
pip3 install numpy --break-system-packages
pip3 install scipy --break-system-packages
# Remove any Python cache files after pip
pip3 cache purge
#####################################################################
#
# This is all the custom stuff needed to build CASTEP
#
#####################################################################
# This flag needs to be set to indicate which CPU architecture we
# are optimising for. You cannot build for AMD on an Intel host,
# as several of the 'make install' steps for FFTW3, OpenBLAS etc
# attempt to execute code built during the install... and Intel
# won't understand certain AMD opcodes and vice versa.
AMD_ARCH=0
if [ "$AMD_ARCH" = "1" ]
then
# Compiling on AMD Epyc
export BASE_CFLAGS="-O3 -march=znver5 -pipe"
# On Zen5 arch, OpenBLAS suggests using Skylake-X support
export OPENBLAS_TARGET=SKYLAKEX
export MAKE_JOBS=8
else
# Compiling on Intel Skylake+ - 12/13th gen core processors or higher - no AVX-512 support
export BASE_CFLAGS="-O3 -march=skylake -pipe"
# Target OpenBLAS to not use AVX-512 support
export OPENBLAS_TARGET=HASWELL
export MAKE_JOBS=8
fi
export FFTW_CFLAGS="$CFLAGS -fopenmp"
export CFLAGS="$BASE_CFLAGS"
echo ""
echo "Post-OS-install setup for CASTEP"
echo "================================"
# A download place for external libraries
mkdir -p /src/zipped
echo ""
echo "1. Building optimised OpenBLAS"
echo "=============================="
cd /src/zipped/ && \
wget https://github.com/OpenMathLib/OpenBLAS/releases/download/v0.3.31/OpenBLAS-0.3.31.tar.gz && \
cd /src && \
tar -xzf zipped/OpenBLAS-0.3.31.tar.gz && \
cd /src/OpenBLAS-0.3.31 && \
CC=gcc-14 make -j$MAKE_JOBS TARGET=$OPENBLAS_TARGET && \
make install && \
ln -s /opt/OpenBLAS/lib/libopenblas.so /opt/OpenBLAS/lib/libblas.so && \
ln -s /opt/OpenBLAS/lib/libopenblas.so /opt/OpenBLAS/lib/liblapack.so && \
echo "/opt/OpenBLAS/lib" > /etc/ld.so.conf.d/openblas.conf
if [ "$AMD_ARCH" = "1" ]
then
# This is for AMD arch only
echo ""
echo "2. Building AMD optimised FFTW3"
echo "==============================="
cd /src/zipped && \
wget https://github.com/amd/amd-fftw/archive/refs/tags/5.2.tar.gz && \
cd /src && \
tar -xzf zipped/5.2.tar.gz && \
cd /src/amd-fftw-5.2 && \
export OMPI_CC=gcc-14 && \
CC=gcc-14 CFLAGS=$FFTW3_CFLAGS AMD_ARCH=znver5 F77=gfortran-14 ./configure \
--enable-shared \
--enable-openmp \
--enable-mpi \
--enable-threads \
--enable-amd-opt \
--with-g77-wrappers \
--prefix=/opt/fftw3 && \
make -j$MAKE_JOBS && \
make install && \
echo "/opt/fftw3/lib" > /etc/ld.so.conf.d/fftw3.conf
else
# This is for non-AMD arch
echo ""
echo "2. Building FFTW3 (non-AMD)"
echo "==========================="
cd /src/zipped && \
wget https://www.fftw.org/fftw-3.3.10.tar.gz && \
cd /src && \
tar -zxf zipped/fftw-3.3.10.tar.gz && \
cd /src/fftw-3.3.10
export OMPI_CC=gcc-14 && \
CC=gcc-14 CFLAGS=$FFTW3_CFLAGS F77=gfortran-14 ./configure \
--enable-shared \
--enable-openmp \
--enable-mpi \
--enable-threads \
--with-g77-wrappers \
--prefix=/opt/fftw3 && \
make -j$MAKE_JOBS && \
make install && \
echo "/opt/fftw3/lib" > /etc/ld.so.conf.d/fftw3.conf
fi
echo ""
echo "3. Building Lapack"
echo "=================="
cd /src/zipped && \
wget https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.12.0.tar.gz && \
cd /src && \
tar -xzf zipped/v3.12.0.tar.gz && \
cd /src/lapack-3.12.0 && \
mkdir build && \
cd build && \
CC=gcc-14 FC=gfortran-14 cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=/opt/lapack .. && \
CC=gcc-14 FC=gfortran-14 cmake --build . -j --target install && \
echo "/opt/lapack/lib" > /etc/ld.so.conf.d/lapack.conf && rm /etc/ld.so.cache && ldconfig
echo ""
echo "4. Building CASTEP"
echo "=================="
# Unpack the source tarball
cd /src && \
tar -xzf /mnt/CASTEP-25.12.tar.gz
# We have to do a little bit of symlinking here, as CASTEP assumes it is installing to /usr/local ...
mkdir -p /opt/castep/bin
mkdir -p /opt/castep/lib
mkdir -p /opt/castep/local
ln -s /opt/castep/bin /opt/castep/local/bin
ln -s /opt/castep/lib /opt/castep/local/lib
# Step in to the source tree
cd /src/CASTEP-25.12
mkdir -p bin/linux_x86_64_gfortran10--serial
mkdir -p bin/linux_x86_64_gfortran10--mpi
# Edit the build rules to ensure we are
# linking to the correct location for the installed LAPACK libs
echo ""
echo "4.1 Editing obj/platforms/linux_x86_64_gfortran10.mk"
echo "================================================"
cp -v obj/platforms/linux_x86_64_gfortran10.mk obj/platforms/linux_x86_64_gfortran10.mk.old && \
cat obj/platforms/linux_x86_64_gfortran10.mk.old | \
sed 's/MATH_LIBS = -llapack -lblas/MATH_LIBS = -L\/opt\/lapack\/lib -llapack -lblas/g' > obj/platforms/linux_x86_64_gfortran10.mk
# Edit optimisation rules for AMD Zen 5
echo ""
echo "4.2 Editing cmake/buildflags_gnu.cmake"
echo "=================================="
cp -v cmake/buildflags_gnu.cmake cmake/buildflags_gnu.cmake.old
if [ "$AMD_ARCH" = "1" ]
then
cat cmake/buildflags_gnu.cmake.old | \
sed 's/march=mavx/march=znver5/g' | \
sed 's/march=native/march=znver5/g' > cmake/buildflags_gnu.cmake
else
cat cmake/buildflags_gnu.cmake.old | \
sed 's/march=mavx/march=skylake/g' | \
sed 's/march=native/march=skylake/g' > cmake/buildflags_gnu.cmake
fi
# Edit include path for Source/Utility/FreeIPC_c.c
# This has an incorrect header include path "mpi.h" where it should have <openmpi/mpi.h>
echo ""
echo "4.3 Editing Source/Utility/FreeIPC_c.c"
echo "======================================"
cp -v Source/Utility/FreeIPC_c.c Source/Utility/FreeIPC_c.c.old
cat Source/Utility/FreeIPC_c.c.old | sed 's/include "mpi.h"/include <openmpi\/mpi.h>/g' > Source/Utility/FreeIPC_c.c
echo ""
echo "4.4 Now build/install CASTEP main binaries - SERIAL version"
echo "==========================================================="
# We call the compile and 'install' in one, to share the same flags - this is the serial version
make -j$MAKE_JOBS install FFT_THREAD=true GRIMMED3=compile GRIMMED4=compile DL_MG=compile INSTALL_DIR=/opt/castep/bin CFLAGS="$BASE_CFLAGS" CC=gcc-14 BUILD=fast MATHLIBS=openblas MATHLIBDIR=/opt/OpenBLAS/lib FFT=fftw3 FFTLIBDIR=/opt/fftw3/lib
echo ""
echo "4.5 Now install CASTEP tools - SERIAL version"
echo "============================================="
make install-tools
echo ""
echo "4.6 Now check CASTEP - SERIAL version"
echo "====================================="
make check
##################################################################################################
echo ""
echo "4.7 Now build/install CASTEP main binaries - MPI version"
echo "========================================================"
# We call the compile and 'install' in one, to share the same flags - this is the MPI version
# It has to be compiled independently of the serial version as several of the libs it creates
# and links to are different in parallel mode.
make -j$MAKE_JOBS FFT_THREAD=true GRIMMED3=compile GRIMMED4=compile DL_MG=compile INSTALL_DIR=/opt/castep/bin CFLAGS="$BASE_CFLAGS" CC=gcc-14 BUILD=fast COMMS_ARCH=mpi SUBARCH=mpi MATHLIBS=openblas MATHLIBDIR=/opt/OpenBLAS/lib FFT=fftw3 FFTLIBDIR=/opt/fftw3/lib
cp -v obj/linux_x86_64_gfortran10--mpi/castep.mpi /opt/castep/bin
##################################################################################################
#########################################
#
# The make castep_python process does not work!!!
#
# Modern versions of Python (3.12+) build extensions with f2py using
# 'meson' rather than 'distutils' ... unfortunately meson insists on
# variables/variable names *not* having a '-' in them... and one of the
# libraries that f2py wants to link with castep_python is libmctc-lib.a ...
# which turns into -lmctc-lib, as well as the variable name mctc-lib
# ... and meson promptly chokes on it.
#
# As documented here: https://github.com/mesonbuild/meson/issues/9754
#
# Runing 'make castep_python' gets you an error like this:
# =======================
# The Meson build system
# Version: 1.3.2
# Source dir: /tmp/tmprbqjfprk
# Build dir: /tmp/tmprbqjfprk/bbdir
# Build type: native build
#
# meson.build:41:0: ERROR: Assignment target must be an id.
# mctc-lib = declare_dependency(link_args : ['-lmctc-lib'])
# ^
# A full log can be found at /tmp/tmprbqjfprk/bbdir/meson-logs/meson-log.txt
# =======================
#
# Only way around this is to hack the source to rename libmctc-lib.a into
# something like libmctc_lib.a ...
#
# Suspect that this part of CASTEP hasn't been tested in some time.
#
#########################################
#echo ""
#echo "4.8 Build the CASTEP Python interface"
#echo "====================================="
#make castep_python
#pip3 install -e obj/linux_x86_64_gfortran10--mpi/
#make check-python
# Production binaries don't need extra debug
# information - strip it to make them smaller
cd
echo ""
echo "5. Removing CASTEP debugging symbols"
echo "===================================="
/bin/file /opt/castep/bin/* | grep "ELF 64-bit" | awk -F: '{print $1}' | while read BIN_FILE
do
strip -g $BIN_FILE
done
# Remove all src packages
echo ""
echo "6. Cleaning up downloaded src tree"
echo "=================================="
rm -rf /src
pip3 cache purge
echo ""
echo "7. All done"
%environment
export PYTHONPATH=/opt/castep/lib/python3.12/dist-packages
export PATH=/opt/castep/bin:/opt/fftw3/bin:/opt/OpenBLAS/bin:/usr/bin:/usr/local/bin:/usr/sbin:/usr/local/sbin:$PATH
export LD_LIBRARY_PATH=/opt/OpenBLAS/lib:/opt/fftw3/lib:/opt/castep/lib:/opt/lapack/lib
export CFLAGS="-O3 -march=znver5 -pipe"
export CC=gcc-14
export FC=gfortran-14
export OMPI_CC=gcc-14
%runscript
ls /opt/castep/bin