Installed software
This page lists the major software packages which are installed on Lovelace.
Commercial Software Packages
Please note that the HPC Service does not provide licenses for anything other than the Intel development tools. For other packages it is imperative that you ensure you will have access to enough license tokens to be able to run your planned work.
Abaqus
Available modules: abaqus/2017.1, abaqus/2019, abaqus/2020
Example submission script:
#!/bin/bash
#PBS -N abaqus
#PBS -q compute
#PBS -l walltime=5:00:00
#PBS -l nodes=1:ppn=40
#PBS -A projectcode
module purge
module load abaqus/2019
# You can specify an alternative license server in abaqus_v6.env in
# your home directory
export NCPUS=`wc -l < $PBS_NODEFILE`
cd $PBS_O_WORKDIR
abaqus job=testjob cpus=$NCPUS parallel=domain domains=$NCPUS double=both int
CFX
Available modules: cfx/18.1, cfx/19.2
Example submission script:
#!/bin/bash -l
#PBS -q compute
#PBS -N test
#PBS -l walltime=100:00:00
#PBS -l nodes=2:ppn=40
#PBS -A projectcode
cd $PBS_O_WORKDIR
module purge
module load cfx/19.2
nodes=`cat $PBS_NODEFILE`
nodes=`echo $nodes | sed -e 's/ /,/g'`
export CFX5RSH=ssh
cfx5solve -def wakes_speed1_173.def -par-dist $nodes -start-method 'HP MPI Distributed Parallel'
COMSOL
Available modules: comsol/5.3, comsol/5.5, comsol 5.6
Example submission script:
#!/bin/bash
#PBS -N comsol
#PBS -q compute
#PBS -l walltime=4:00:00
#PBS -l nodes=1:ppn=40
#PBS -A projectcode
module purge
module load comsol/5.5
cd $PBS_O_WORKDIR
export NCPUS=`wc -l < $PBS_NODEFILE`
comsol -nn $NCPUS --nnhost $PBS_NUM_NODES -np $PBS_NUM_PPN mkl batch -inputfile cylinder_flow.mph
CST
Available modules: cst/2019
Example submission script:
#!/bin/bash
#PBS -N CST
#PBS -q vis
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=40
#PBS -A projectcode
module purge
module load cst/2019
cd $PBS_O_WORKDIR
export NCPUS=`wc -l < $PBS_NODEFILE`
# Single node version
cst_design_environment -numthreads=$PBS_NUM_PPN -c -r 'Metallic Test.cst'
CPLEX
Available modules: cplex/concert/12.6.0
Fluent
Available modules: fluent/18.1, fluent/19.2
Intel Development Tools
Intel compilers: intel/compiler/64/2018/18.0.5, intel/compiler/64/2019/2.187, intel/compiler/64/2019/5.041, intel/compiler/64/2019/19.0.2
Intel MPI: intel/mpi/64/2018/4.274, intel/mpi/64/2019/2.187, intel/mpi/64/2019/5.041
Intel MKL: intel/mkl/64/2018/4.274, intel/mkl/64/2019/2.187, intel/mkl/64/2019/5.041
Intel DAAL: intel/daal/64/2018/4.274, intel/daal/64/2019/2.187, intel/daal/64/2019/5.041
Intel IPP: intel/ipp/64/2018/4.274, intel/ipp/64/2019/2.187, intel/ipp/64/2019/5.041
Intel TBB: intel/tbb/64/2018/4.274, intel/tbb/64/2019/2.187, intel/tbb/64/2019/5.041
Intel ITAC: intel/itac/2018/4.025, intel/itac/2019/2.187, intel/itac/2019/5.041
The 32-bit versions are also available but we advise against using them:
Intel compilers (32 bit): intel/compiler/32/2018/18.0.5, intel/compiler/32/2019/19.0.2
Intel MPI (32 bit): intel/mpi/32/2018/4.274
Intel TBB (32 bit): intel/tbb/32/2018/4.274
Isight
Available modules: isight/2019, isight/2020
MARC
Available modules: marc/2017.1
MATLAB
Available modules: matlab/R2018a
STAR-CCM+
Available modules: lboro/starccm+/13.02.013, lboro/starccm+/14.02.012
Example submission script:
#!/bin/bash -l
#PBS -q compute
#PBS -N test
#PBS -l walltime=1:00:00
#PBS -l nodes=2:ppn=40
#PBS -A projectcode
cd $PBS_O_WORKDIR
module purge
module load lboro/starccm+/14.02.012
export NCPUS=`wc -l < $PBS_NODEFILE`
starccm+ -batch -np $NCPUS -machinefile $PBS_NODEFILE -rsh ssh 20141111.sim
sleep 60
VASP - Vienna Ab initio Simulation Package
This software is only available to specific research groups.
Available modules: VASP/5.4.4-intel-2018.4.274
Example submission script:
#!/bin/bash
#PBS -A projectcode
#PBS -N test
#PBS -q compute
#PBS -l nodes=4:ppn=40
#PBS -l walltime=100:00:00
newgrp yourvasplicensegroup
cd $PBS_O_WORKDIR
module purge
module load VASP/5.4.4-intel-2018.4.274
mpirun -np 160 vasp_std
Open Source Software Packages
Only major packages are listed here, many utilities are not listed.
CMake
Available modules:
CMake/3.7.2-GCCcore-6.4.0
CMake/3.7.2-intel-2018.4.274
CMake/3.7.2-intel-2019.2.187
CMake/3.8.0-GCCcore-6.4.0
CMake/3.8.0-intel-2018.4.274
CMake/3.8.0-intel-2019.2.187
CMake/3.8.1-GCCcore-6.4.0
CMake/3.8.1-intel-2018.4.274
CMake/3.8.1-intel-2019.2.187
CMake/3.9.1-foss-2018a
CMake/3.9.1-GCCcore-6.4.0
CMake/3.9.1-intel-2018.4.274
CMake/3.9.1-intel-2019.2.187
CMake/3.9.5-GCCcore-6.4.0
CMake/3.10.0-intel-2018.4.274
CMake/3.10.0-intel-2019.2.187
CMake/3.10.1-foss-2018a
CMake/3.10.1-GCCcore-6.4.0
CMake/3.10.1-GCCcore-8.2.0
CMake/3.10.2-GCCcore-6.4.0
CMake/3.10.2-GCCcore-8.2.0
CMake/3.11.4-GCCcore-6.4.0
CMake/3.11.4-GCCcore-8.2.0
CMake/3.12.1-GCCcore-6.4.0
CMake/3.13.3-GCCcore-8.2.0
CP2K
Available modules: CP2K/6.1-foss-2019a, CP2K/6.1-intel-2018.4.274, CP2K/7.1-intel-2018.4.274
Example submission script:
#!/bin/bash
#PBS -N test
#PBS -l walltime=02:00:00
#PBS -l nodes=1:ppn=40
#PBS -q vis
#PBS -A projectcode
module purge
module load CP2K/6.1-foss-2019a
cd $PBS_O_WORKDIR
export NCPUS=`wc -l < $PBS_NODEFILE`
mpirun -np $NCPUS cp2k.popt -i Si.inp -o Si.out
DLPOLY
Modules available: DL_POLY_Classic/1.9-intel-2018.4.274
Example submission script:
#!/bin/bash
#PBS -N DL_POLY
#PBS -l nodes=1:ppn=40
#PBS -l walltime=03:00:00
#PBS -A projectcode
module purge
module load DL_POLY_Classic/1.9-intel-2018.4.274
cd $PBS_O_WORKDIR
mpirun DLPOLY.X
Go
Available modules: Go/1.12, Go/1.12.1-foss-2018a
GROMACS
Available modules: GROMACS/2018-foss-2018a
Julia
Available modules: Julia/1.5.1-foss-2018a-linux-x86_64
Description: The Julia programming language.
Web site: https://julialang.org/
Example submission script:
#!/bin/bash
#PBS -N julia-test
#PBS -l nodes=1:ppn=40
#PBS -l walltime=03:00:00
#PBS -A projectcode
module load Julia/1.5.1-foss-2018a-linux-x86_64
cd $PBS_O_WORKDIR
export JULIA_NUM_THREADS=$PBS_NUM_PPN
julia test.julia
LAMMPS
Available modules: LAMMPS/3Mar2020-intel-2018.4.274-Python-3.7.0
Description: LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
Website:
Example submission script:
#!/bin/bash
#PBS -N LAMMPS-eam-N1
#PBS -l nodes=2:ppn=40
#PBS -l walltime=02:00:00
#PBS -A projectcode
module purge
module load LAMMPS/3Mar2020-intel-2018.4.274-Python-3.7.0
export NCPUS=`wc -l < $PBS_NODEFILE`
export OMP_NUM_THREADS=2
cd $PBS_O_WORKDIR
mpirun -np $NCPUS -ppn 40 lmp_mpi -sf intel -pk intel 0 omp 2 -in in.eam -log none
This example runs 40 MPI processes, each of which is two-way threaded via OpenMP.
OpenFOAM
Available modules:
OpenFOAM/v1712-intel-2018.4.274, OpenFOAM/v1812-intel-2018.4.274, OpenFOAM/v1912-intel-2018.4.274
OpenFOAM/2.4.0-intel-2018.4.274, OpenFOAM/2.4.0-intel-2019.2.187, OpenFOAM/4.1-intel-2018.4.274, OpenFOAM/5.0-intel-2018.4.274, OpenFOAM/7-intel-2018.4.274
Example submission script:
#!/bin/bash
#PBS -l walltime=1:00:00
#PBS -N moto
#PBS -q compute
#PBS -l nodes=2:ppn=40
#PBS -A projectcode
cd $PBS_O_WORKDIR
module purge
module load OpenFOAM/7-intel-2018.4.274
source $FOAM_BASH
mpirun -np 80 pisoFoam -parallel
ParaView
Available modules: ParaView/5.2.0-intel-2018.4.274-mpi, ParaView/5.4.1-foss-2018a-mpi, ParaView/5.4.1-intel-2018.4.274-mpi
Python
Available modules:
Python/2.7.14-foss-2018a
Python/2.7.14-GCCcore-6.4.0-bare
Python/2.7.14-intel-2018.4.274-bare
Python/2.7.14-intel-2018.4.274
Python/2.7.14-intel-2019.2.187-bare
Python/2.7.14-intel-2019.2.187
Python/2.7.15-foss-2018a
Python/2.7.15-GCCcore-8.2.0
Python/2.7.15-intel-2019.2.187
Python/3.6.6-foss-2018a
Python/3.6.6-intel-2018.4.274
Python/3.7.0-foss-2018a
Python/3.7.0-intel-2018.4.274
Python/3.7.2-GCCcore-8.2.0
QuantumESPRESSO
Available modules: QuantumESPRESSO/6.1-intel-2018.4.274, QuantumESPRESSO/6.3-intel-2018.4.274
Example submission script:
#!/bin/bash -l
#PBS -q compute
#PBS -N espresso
#PBS -l walltime=00:20:00
#PBS -l nodes=1:ppn=40
#PBS -A projectcode
module purge
module load QuantumESPRESSO/6.1-intel-2018.4.274
cd $PBS_O_WORKDIR
mpiexec -np 40 bands.x < test.in
R
Available modules: R/3.5.1-foss-2018a
Siesta
Available modules: Siesta/4.1-b4-intel-2018.4.274