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Newton

The Newton mini-app is a simple yet complete example of using Sensei Python bindings. It solves Newton's law of gravitation using a symplectic integrator. The included initial condition, initializes an area roughly the size of, the solar system with a number of of planets of varying masses at randomly chosen locations. A sun sized body is placed at the center of the domain.

Command line options

usage: newton.py [-h] [--analysis ANALYSIS] [--analysis_opts ANALYSIS_OPTS]
                 [--n_bodies N_BODIES] [--n_its N_ITS] [--dt DT]

optional arguments:
  -h, --help            show this help message and exit
  --analysis ANALYSIS   Type of analysis to run. posthoc,catalyst,configurable
  --analysis_opts ANALYSIS_OPTS
                        A CSV list of name=value pairs specific to each
                        analysis type. cataylst: script=a catalyst Python
                        script. posthoc: mode=pvd|visit,file=file name,dir=
                        output dir freq=number of steps between I/O.
                        configurable: config=xml file
  --n_bodies N_BODIES   Number of bodies per process
  --n_its N_ITS         Number of iterations to run
  --dt DT               Time step in seconds

One uses --analysis to select an analysis, and --analysis_opts to pass analysis specific options in the form of a CSV list to the selcted analysis.

There are three analysis options, catalyst which exercises the CatalystAdaptor, posthoc which exercises the VTKPosthocIO adaptor, and configurable which exercises the ConfigurableAnalysis adaptor. Each of these require some analysis specific options:

Analysis Option Description
catalyst script path to a Catalyst Python script
libsim
configurable config path to a SENSEI ConfigurableAnalysis XML config
posthoc file base output file prefix, step, block and extension are appended to this
dir output directory
mode 0 ParaView compatible output, 1 VisIt compatible output
freq number of steps in between I/O

Catalyst

Building

One needs to point Python to the ParaView install while CMake figures things out. This is because ParaView packages up some common Python modules, such as mpi4py.

# point to ParaView's Python packages
export LD_LIBRARY_PATH=/work/SENSEI/PV/lib/:$LD_LIBRARY_PATH
export PYTHONPATH=/work/SENSEI/PV/lib/site-packages/:/work/SENSEI/PV/lib/:$PYTHONPATH

# configure the build
cmake -DENABLE_PYTHON=ON -DENABLE_CATALYST=ON -DENABLE_CATALYST_PYTHON=ON \
  -DParaView_DIR=/work/SENSEI/PV ../sensei/

Running

One needs to setup Python consistently with the build, and make sure that the Python interpreter can see include ParaView and SENSEI Python modules.

# point to ParaView and SENSEI Python modules
export LD_LIBRARY_PATH=/work/SENSEI/PV/lib/:/work/SENSEI/sensei-build/lib:$LD_LIBRARY_PATH
export PYTHONPATH=/work/SENSEI/PV/lib/site-packages/:/work/SENSEI/PV/lib/:/work/SENSEI/sensei-build/lib:$PYTHONPATH

# run the simulation
mpiexec -np 4 python ../sensei/miniapps/newton/newton.py --analysis=catalyst \
  --analysis_opts=script=../sensei/miniapps/newton/newton_catalyst.py

Libsim

Building

One needs to point SENSEI to VTK and Python built by VisIt.

# point to our VisIt install
VISIT_INSTALL=/work/SENSEI/visit-install/2.13.0/linux-x86_64/
VISIT_DEPS=/work/SENSEI/visit-deps/
VISIT_PYTHON_HOME=${VISIT_DEPS}/visit/python/2.7.11/x86_64/
VISIT_VTK_HOME=${VISIT_DEPS}/visit/vtk/6.1.0/x86_64

# use VisIt's Python. VisIt's VTK should be built in this environment
# as well to ensure that system installs of Python are not accidentally
# linked into VTK
export PYTHONHOME=${VISIT_PYTHON_HOME}
export PYTHONPATH=${VISIT_PYTHON_HOME}/lib/python2.7/site-packages/
export PKG_CONFIG_PATH=${VISIT_PYTHON_HOME}/lib/pkgconfig/
export PATH=${VISIT_PYTHON_HOME}/bin/:$PATH

# use VisIt's VTK
export LD_LIBRARY_PATH=${VISIT_VTK_HOME}/lib/:$LD_LIBRARY_PATH
export PYTHONPATH=${VISIT_VTK_HOME}/lib/python2.7/site-packages/:$PYTHONPATH

# configure the build
cmake -DENABLE_SENSEI=ON -DENABLE_LIBSIM=ON -DENABLE_PYTHON=ON \
  -DVTK_DIR=${VISIT_VTK_HOME}/lib/cmake/vtk-6.1/ -DVISIT_DIR=${VISIT_INSTALL}
  ../sensei

Running

In addition to VisIt's Python and VTK; and SENSEI's Python module, the enviornment must be set up for VisIt. This is easiest done in a launch script that sets up the environment and invokes the given command.

#!/bin/bash

if [[ $# < 1 ]]
then
echo "Usage libsim_launch.sh [arg1 ... argn]"
echo
echo "pass the command to launch in arg1 to argn"
echo
exit -1
fi


VISIT_DEPS=/work/SENSEI/visit-deps/
VISIT_PYTHON_HOME=${VISIT_DEPS}/visit/python/2.7.11/x86_64/
VISIT_VTK_HOME=${VISIT_DEPS}/visit/vtk/6.1.0/x86_64
SENSEI_HOME=/work/SENSEI/sensei-build-libsim


# let VisIt set the environment variables libsim needs
source <(../visit-install/bin/visit -env engine | sed 's/^/export /')

# use VisIt's Python (note VisIt's VTK should be built in this environment)
export PYTHONHOME=${VISIT_PYTHON_HOME}
export PYTHONPATH=${VISIT_PYTHON_HOME}/lib/python2.7/site-packages/
export PKG_CONFIG_PATH=${VISIT_PYTHON_HOME}/lib/pkgconfig/
export PATH=${VISIT_PYTHON_HOME}/bin/:$PATH

# use VisIt's VTK
export LD_LIBRARY_PATH=${VISIT_VTK_HOME}/lib/:$LD_LIBRARY_PATH
export PYTHONPATH=${VISIT_VTK_HOME}/lib/python2.7/site-packages/:$PYTHONPATH

# use SENSEI's Python module
export LD_LIBRARY_PATH=${SENSEI_HOME}/lib:$LD_LIBRARY_PATH
export PYTHONPATH=${SENSEI_HOME}/lib:$PYTHONPATH

# launch the app using the command line
$*

To launch the simulation invoke the launch script with the desired command.

./libsim_launch.sh  mpiexec -np 4 python \
  ../sensei/miniapps/newton/newton.py --analysis=libsim