UTAM REPRODUCIBLE RESEARCH AND C++ LIBRARIES Samuel Brown – February 6, 2009

Subversion Repository  svn co _research/trunk utam --username=utam2008  password: qUinoa80

Repository Snapshots   username: utam2008  password: qUinoa80  also contains images and intermediate data for student reports

Directory Structure

Prerequisites  Compiling C++ Library  scons version >= required  fftw3 - optional – need to set FFTWHOME  MPI C++ compiler/library – optional  C++ Library Documentation  Doxygen - optional

Environment Setup  Option 1:  cd utam  source utamvars.[c]sh  Option 2:  export UTAMHOME=/path/to/utam  source $UTAMHOME/utamvars.sh

Reproducibility  Report directories contain a latex file and uniform python script for generating results and compiling report  run.py: python only, does not use scons  generates and runs shell scripts interactively  simple mechanisms for downloading data and controlling computation with sources and targets

run.py Process( cmds=[ ], sources=[ ], targets=[ ], docmds=1, // check for targets or force/skip wdir=, // working directory bdir=, // batch directory sdir=, // source directory pbs=, // submit to cluster? nodes=, ppn=, walltime=, datapath=, scratchpath=, clean=, ktemps=, kbatch= )

C++ Compilation  Compilation must take place from $UTAMHOME/src/ucsl  Top-level SConstruct should be customized to your system  cd $UTAMHOME/src/ucsl  scons

SConstruct Customization USE_MPI=True BGP=False INTEL=False SANDDUNE=False HMM=False PS3D=False TEP=False if(BGP): UCPPFLAGS = ['-O5'] CC = 'bgxlc' CXX = 'bgxlc++' MPICC = 'mpixlc' MPICXX = 'mpixlcxx' BUILD_SERIAL = False USE_FFTW = True USE_THREAD = False

C++ Library Basic Objects  Parameter Initialization  Memory Abstractions  Traces  Axes  Planes  Volumes

C++ Library  Task-specific File I/O  Trace files  Volume files  Coordinate file

3D Modeling  3D domain decomposition object  ability to separate boundary and interior regions  load balancing  3D stencil overlap communication object