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.

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

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'

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


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'

Available modules: cplex/concert/12.6.0

Available modules: fluent/18.1, fluent/19.2

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

 

 

 

Available modules: isight/2019, isight/2020

Available modules: marc/2017.1

Available modules: matlab/R2018a

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

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.

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

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

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

Available modules: Go/1.12, Go/1.12.1-foss-2018a

Available modules: GROMACS/2018-foss-2018a

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

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: https://www.lammps.org/

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.

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


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

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                                 

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

Available modules: R/3.5.1-foss-2018a

Available modules: Siesta/4.1-b4-intel-2018.4.274