Software

Contents

• Software

  • INSIGNEO-developed software

    • openBF

    • pFIRE

    • Builder2MO

  • INSIGNEO-developed web services

    • CT2S web service

  • Using commercial software

    • Abaqus

    • Amira

    • Solidworks

    • Stata

    • COMSOL

INSIGNEO-developed software

More software than is listed below has been developed by INSIGNEO researchers; this will added in due course.

openBF

openBF is an open-source 1D blood flow solver based on the MUSCL finite-volume numerical scheme, written in Julia and released under the Apache 2.0 free software license.

pFIRE

pFIRE is a parallel application and library for the elastic registration of large images by the method of Barber and Hose (DOI:10.1080/03091900412331289889; DOI:10.1016/j.media.2007.06.011). It is implemented in C++ using the PETSc scientific toolkit to provide parallelised mathematical routines.

• User and developer documentation

• Source code

• Report issues

Example of using pFIRE on the University of Sheffield’s ShARC HPC system:

First, create a pFIRE config file containing e.g.:

fixed = /path/to/Scan1_crop.image
moved = /path/to/Scan2_crop.image
nodespacing = 20
lambda = auto
save_intermediate_frames = true

Let’s assume this file is saved as /path/to/pfire.conf.

Next, create a Grid Engine batch job submission script that runs pFIRE using this config file:

#!/bin/bash
#$ -pe mpi 40
#$ -l h_vmem=50G
#$ -l h_rt=12:00:00
#$ -N my_pfire_job
#$ -M some.user@sheffield.ac.uk
#$ -m bea
#$ -j y

export SPACK_ROOT="/usr/local/community/rse/spack"
export PATH="${SPACK_ROOT}:${PATH}"
source $SPACK_ROOT/share/spack/setup-env.sh

spack load --dependencies pfire@devel+double

mpirun -np $NSLOTS pfire /path/to/pfire.conf

echo -e "\n### HOST INFO ###\n"
cat $PE_HOSTFILE

Let’s assume this file is saved as myjob.qsub. This script:

• Requests 40 CPU cores that don’t all need to be on the same node

• Requests 50GB of RAM per core

• Requests 12 hours of runtime

• Makes a particular build of pFIRE (pfire@devel+double) available for use using the Spack package manager.

• Runs pFIRE on those 40 CPU cores (using MPI) using /path/to/pfire.conf

• Prints out information on the distribution of those CPU cores between cluster nodes before exiting

Finally, submit a job using this submission script by running:

qsub myjob.qsub

NB above we told Spack to load pfire version devel with double-precision floating point support. To see all builds of pFIRE available on ShARC please run the following from a ShARC worker node:

source /usr/local/community/rse/spack/share/spack/setup-env.sh
spack find -v pfire

See the Spack documentation for information on how to identify and distinguish builds of a given software package by:

• version

• build options

• other factors that are less important in this particular case (e.g. compiler, compiler versions, dependencies, dependency versions)

Builder2MO

Builder Mark II - Organ (Builder2MO) is a pre-processor for musculo-skeletal subject-specific models. This freeware allow you to import imaging, gait analysis, EMG, segmentation, and finite element data, and fuse them toward the creation of organ scale subject-specific models of bones, joints, muscles, ligaments, and cartilages.

INSIGNEO-developed web services

CT2S web service

The CT2S (Computed Tomography to Strength) web service provides an estimate of the strength of human bone, using non-invasive medical imaging. A user uploads a computed tomography (CT) scan of the anatomy, and receives back a set of values that characterise the strength of the bone under a series of common loading conditions. This service was developed as part of the MultiSim project.

Using commercial software

Abaqus

The University has a number of licenses for Abaqus but INSIGNEO have purchased 20 additional licenses, the use of which restricted to a specific group of users. These additional licenses are available from the same license server as the University-purchased licenses.

If you would like to be added to the list of users who can use the additional licenses then please contact the INSIGNEO tech team.

Amira

Amira provides for 3D/4D visualisation, processing and analysis functionality. In particular, the software is helpful for image segmentation and registration.

INSIGNEO has one floating license for Amira. In addition, the Integrative Musculoskeletal Biomechanics (IMSB) group has purchased and maintains another floating license. Please contact Dr Enrico Dall’Ara (e.dallara@sheffield.ac.uk) if you would like to discuss getting access to these licenses.

Solidworks

Please contact the INSIGNEO tech team if you want to install/use the SolidWorks computer-aided design (CAD) software.

Stata

Stata is an integrated data science software package which provides tools for data manipulation, visualization, statistics, and reproducible reporting.

INSIGNEO currently has two floating network licenses available for Stata/IC. To discuss access to these licenses please contact Martin Brook (m.l.brook@sheffield.ac.uk) in the first instance.

COMSOL

COMSOL Multiphysics is a cross-platform finite element analysis, solver and multiphysics simulation software.

One network license for COMSOL Multiphysics is available to INSIGNEO members, and an additional license is available for members of the POLARIS group. To discuss access to these licenses please contact Martin Brook (m.l.brook@sheffield.ac.uk) in the first instance.