Microwulf: Uses

Like all Beowulf clusters, Microwulf runs special parallel software -- software that is carefully written to take advantage of a cluster's parallel capabilities. Such software is usually written using the message passing interface (MPI) or the parallel virtual machine (PVM). These libraries provide primitives that processes can use to communicate and synchronize across the network. They also provide a mechanism for executing separate copies of a program (in parallel) on each of a cluster's nodes and/or cores.

There are many free applications that have been written using these libraries for Beowulf clusters. Most have been written by research scientists or engineers to solve particular problems. These include:

• CFD codes, an assortment of programs for computational fluid dynamics
• DPMTA, a tool for computing N-body interactions fastDNAml, a program for computing phylogenetic trees from DNA sequences
• Parallel finite element analysis (FEA) programs, including:
  • Adventure, the ADVanced ENgineering analysis Tool for Ultra large REal world, a library of 20+ FEA modules
  • deal.II, a C++ program library providing computational solutions for partial differential equations using adaptive finite elements
  • DOUG, Domain decomposition On Unstructured Grids
  • GeoFEM, a multi-purpose/multi-physics parallel finite element simulation/platform for solid earth
  • ParaFEM, a general parallel finite element message passing libary
• Parallel FFTW, a program for computing fast Fourier transforms (FFT)
• GADGET, a cosmological N-body simulator
• GAMESS, a system for ab initio quantum chemistry computations
• GROMACS, a molecular dynamics program for modeling molecular interactions, especially those from biochemistry
• MDynaMix, a molecular dynamics program for simulating mixtures
• mpiBLAST, a program for comparing gene sequences
• NAMD, a molecular dynamics program for simulating large biomolecular systems
• NPB 2, the NASA Advanced Supercomputing Division's Parallel Benchmarks suite. These include:
  • BT, a computational fluid dynamics simulation
  • CG, a sparse linear system solver
  • EP, an embarrassingly parallel floating point solver
  • IS, a sorter for large lists of integers
  • LU, a different CFD simulation
  • MG, a 3D scalar Poisson-equation solver
  • SP, yet another (different) CFD simulation
• ParMETIS, a library of operations on graphs, meshes, and sparse matrices
• PVM-POV, a ray-tracer/renderer
• SPECFEM3D, a global and regional seismic wave simulator
• TPM, a collisionless N-body (dark matter) simulator

We are using Microwulf in a variety of ways, including:

• For undergraduate research projects at Calvin College.
• As a high performance computing resource for CS 374: High Performance Computing
• Taking it on the road:
  • to local high schools, to raise interest in computing
  • to conferences, as a model system for "personal" supercomputing
• When not being used for these tasks, Microwulf runs the client for Stanford's Folding@Home project, which helps researchers better understand protein folding, which in turn helps them the causes of (and hopefuly the cures for) genetic diseases. Excess CPU cycles on a Beowulf cluster like Microwulf can be devoted to pretty much any distributed computing project.

Joel Adams > Research > Microwulf > Uses