RPI CSCI-6360 Parallel Programming & Computing 2014: Group Project
If you wish to contribute to this code, please fork this repository (http://github.com/fifthblackbird/PPCproject) into your GitHub account before cloning.
This is a group project intended to implement POSIX threads and to improve MPI-IO performance in MMSP (http://github.com/mesoscale/mmsp).
The code depends on the Mesoscale Microstructure Simulation Project (MMSP) libraries [1].
The source directory contains code for grain growth simulations using a sparse phase-field model [2] and a Potts Monte Carlo model [3].
Before building this code, download the MMSP source code and create symbolic links to MMSP/include and MMSP/algorithms.
E.g., if you store MMSP in ~/Downloads/mmsp, run
ln -s ~/Downloads/mmsp/include source/include
ln -s ~/Downloads/mmsp/algorithms source/algorithms
In source/, the Make commands default to the phase-field model:
e.g., make or make parallel will build graingrowth.out or parallel_GG.out, respectively, both of which depend on graingrowth.cpp.
To compile the Monte Carlo version, append "mc" to the commands:
e.g., make mc or make parallelmc will build graingrowth.out or parallel_MC.out, respectively, both of which depend on graingrowth_MC.cpp.
To build this code on an IBM Blue Gene/Q supercomputer, make sure the IBM xl_r compiler and zlib library are available.
On the Rensselaer Polytechnic Institute BG/Q, AMOS, module load xl_r experimental/zlib.
Then, make bgq or make bgqmc.
The recommended mode for this program is using --nonstop, which will intialize and coarsen a simulation domain. e.g., use
mpirun -np 6 ./parallel_GG.out --nonstop 3 voronoi.000.dat 200 200 4
to initialize and save a startup file (voronoi.000.dat) and a checkpoint file after 200 steps (voronoi.200.dat), using six MPI ranks with 4 pthreads each.
Make sure you have hardware support for 24 threads before running this command!
Note that AMOS is big-endian. Most consumer PCs are little-endian.
If you have downloaded a binary data file generated using MMSP on AMOS, make wrongendian and run it on the file.
Afterwards, you can use standard MMSP utilities (e.g., mmsp2vti) to export a file for visualization.
References:
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J. Gruber and T. Keller. The Mesoscale Microstructure Simulation Project. http://github.com/mesoscale/mmsp
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I. Steinbach and F. Pezzolla. "A Generalized Field Method for Multiphase Transformations Using Interface Fields." Physica D 134 (1999) 385-393. DOI: 10.1016/S0167-2789(99)00129-3
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S.A. Wright, S.J. Plimpton, T.P. Swiler, R.M. Fye, M.F. Young, and E.A. Holm. "Potts-model grain growth simulations: Parallel algorithms and applications." SAND Report (1997) 1925.