Contacts

Find a list of contact persons here.

Summary

Domain

Cardiovascular.

Description

We are carrying out rapid, patient specific simulations of bloodflow in intracranial cerebral aneurysms to assess the short and long range effects of their treatment via the introduction of a stent or flow diverter. The simulations are to be executed over a full range of physiological states to inform clinicians about the long term consequences of their choice of treatment.

Scientific articles and documentation

 

HemeLB user’s guide

 

Computational requirements

Programming language: C++
Dependencies: cmake, parmetis, tinyXML, boost, MPI, ctemplate, cppunit.
Memory requirements: 1-2G per rank depending on sparsity and problem size.
Disk requirements: HDF5 is required for some features.
Complimentary tools:

Type of software license

Open.

Performance and HPC profile

Systems on which the software is deployed

LRZ SuperMUC, Prometheus (PLGrid), Eagle (PLGrid), Inula (PLGrid), ARCHER (EPCC).

Parallelism

Type of parallelism: MPI
Scalability: Typical runs 7200 cores / 300 nodes. Large runs 60000 cores / 2500 nodes.

Mode of operation

One single extreme parallel run for each problem required.

I/O, as relevant to CompBioMed Application Pipeline

Input

Format: STL (for surface geometry), XML (config file), GMY (HemeLB own format)
Coming from: The XML and GMY are generated from the STL using the HemeLB setup tool.
Disk use: GMY is the only large file, and it is typically 100M to 2G in size.

Output

Format: Own format, XTR.
Used by: ParaView.
Disk use: Depends on geometry size/output frequency. Can be between 500Mb and 20G.

Benchmarks and examples

Instructions for running on dedicated platforms