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

2. Subversion Repository  svn co https://repo.chpc.utah.edu/svn/repo/UTAM_repro _research/trunk utam --username=utam2008  password: qUinoa80

3. Repository Snapshots  http://utam.gg.utah.edu/utam_repro_research/ http://utam.gg.utah.edu/utam_repro_research/  username: utam2008  password: qUinoa80  also contains images and intermediate data for student reports

4. Directory Structure

5. Prerequisites  Compiling C++ Library  scons version >= 1.1.0 - required  fftw3 - optional – need to set FFTWHOME  MPI C++ compiler/library – optional  C++ Library Documentation  Doxygen - optional

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

7. 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

8. 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= )

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

10. 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

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

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

13. 3D Modeling  3D domain decomposition object  ability to separate boundary and interior regions  load balancing  3D stencil overlap communication object