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README.md

SENSEI

The SENSEI project takes aim at a set of research challenges for enabling scientific knowledge discovery within the context of in situ processing at extreme-scale concurrency. This work is motivated by a widening gap between FLOPs and I/O capacity which will make full-resolution, I/O-intensive post hoc analysis prohibitively expensive, if not impossible.

We focus on new algorithms for analysis, and visualization - topological, geometric, statistical analysis, flow field analysis, pattern detection and matching - suitable for use in an in situ context aimed specifically at enabling scientific knowledge discovery in several exemplar application areas of importance to DOE. Complementary to the in situ algorithmic work, we focus on several leading in situ infrastructures, and tackle research questions germane to enabling new algorithms to run at scale across a diversity of existing in situ implementations.

Our intent is to move the field of in situ processing in a direction where it may ultimately be possible to write an algorithm once, then have it execute in one of several different in situ software implementations. The combination of algorithmic and infrastructure work is grounded in direct interactions with specific application code teams, all of which are engaged in their own R&D aimed at evolving to the exascale.

Quick links
Project Organization
Build and Install
Using the SENSEI Library

Project Organization

SENSEI library

The SENSEI library contains core base classes that declare the AnalysisAdaptor API which is used to interface to in situ infrastructures and implement custom analyses; the DataAdaptor API which AnalysisAdaptors use to access simulation data in a consistent way; and a number of implementations of both. For more information see our SC16 paper.

DataAdaptors

Class Description
DataAdaptor Base class declaring data adaptor API
VTKDataAdaptor Implementation for use with VTK data sets. This adaptor can be used to pass VTK data sets from the simulation to the Analysis.
ADIOSDataAdaptor Implementation that serves up data from ADIOS. For use in an ADIOS End point.

AnalysisAdaptors

Class Description
AnalysisAdaptor Base class declaring analysis adaptor API
ADIOSAnalysisAdaptor Implementation for using ADIOS from your simulation.
LibsimAnalysisAdaptor Implementation for using Libsim from your simulation.
CatalystAnalysisAdaptor Implementation for using Catalyst from your simulaiton.
Autocorrelation Implementation that computes autocorrelation
Histogram Implementation that computes histograms.
PosthocIO Implementation that writes uniform meshes using VTK or MPI I/O. This was used in year II miniapp campaign.
VTKPosthocIO Implementation that writes VTK data sets using VTK XML format to the ".visit" format readable by VisIt, or ".pvd" format readable by ParaView.
ConfigurableAnalysis Implementation that reads an XML configuration to select and configure one or more of the other analysis adaptors. This can be used to quickly switch between the analysis adaptors at run time.

Mini-apps

SENSEI ships with a number of mini-apps that demonstrate use of the SENSEI library with custom analyses and the supported in situ infrastructures. When the SENSEI library is enabled the mini-apps will make use of any of the supported in situ infrastructures that are enabled. When the SENSEI library is disabled mini-apps are restricted to the custom analysis such as histogram and autocorrelation.

More information on each mini-app is provided in the coresponding README in the mini-app's source directory.

  • Parallel3D The miniapp from year I generates data on a uniform mesh and demonstrates usage with in situ infrasturctures and histogram analysis.

  • Oscillators The miniapp from year II generates time varying data on a uniform mesh and demonstrates usage with in situ infrasturctures, histogram, and autocorrelation analyses.

  • Newton This Python n-body miniapp demonstrates usage of in situ infrastructures and custom analyses from Python.

End points

End points are programs that receive and analyze simulation data through ADIOS. The end point reads data being serialized by the ADIOS analysis adaptor and pass it back into a SENSEI bridge for further analysis.

Build and Install

The SENSEI project uses CMake 3.0 or later. The CMake build options allow you to choose which of the mini-apps to build as well as which frameworks to enable. It is fine to enable multiple infrastructures, however note that Catalyst and Libsim are currently mutually exclusive options due to their respective use of different versions of VTK.

Typical build procedure

$ mkdir build
$ cd build
$ ccmake .. # set one or more -D options as needed
$ make
$ make install

Build Options

Build Option Default Description
ENABLE_SENSEI ON Enables the core SENSEI library. Requires VTK. When this is disabled, the included mini-apps will run fixed analyses. When enabled, the mini-apps will pass data through SENSEI and the analysis may be configured at run-time. This allows SENSEI overhead to be characterized.
ENABLE_PYTHON OFF Enables Python bindings. Requires VTK, Python, Numpy, mpi4py, and SWIG.
ENABLE_VTK_GENERIC_ARRAYS OFF Enables use of VTK's generic array feature.
ENABLE_CATALYST OFF Enables the Catalyst analysis adaptor. Depends on ParaView Catalyst. Set ParaView_DIR.
ENABLE_CATALYST_PYTHON OFF Enables Python features of the Catalyst analysis adaptor.
ENABLE_ADIOS OFF Enables ADIOS adaptors and endpoints. Set ADIOS_DIR.
ENABLE_LIBSIM OFF Enables Libsim data and analysis adaptors. Requires Libsim. Set VTK_DIR and LIBSIM_DIR.
ENABLE_VTK_IO OFF Enables adaptors to write to VTK XML format.
ENABLE_VTK_MPI OFF Enables MPI parallel VTK filters, such as parallel I/O.
ENABLE_VTKM ON Enables analyses that use VTKm directly instead of via VTK.
ENABLE_PARALLEL3D ON Enables the parallel 3D mini-app.
ENABLE_OSCILLATORS ON Enables the oscillators mini-app.
VTK_DIR Set to the directory containing VTKConfig.cmake.
ParaView_DIR Set to the directory containing ParaViewConfig.cmake.
ADIOS_DIR Set to the directory containing ADIOSConfig.cmake
LIBSIM_DIR Path to libsim install.

For use with ADIOS

cmake -DENABLE_SENSEI=ON -DENABLE_ADIOS=ON -DVTK_DIR=[your path] -DADIOS_DIR=[your path] ..

Can be used with either ParaView_DIR when configuring in conjunction with Catalyst, or VTK_DIR otherwise.

For use with Libsim

cmake -DENABLE_SENSEI=ON -DENABLE_LIBSIM=ON -DVTK_DIR=[your path] -DLIBSIM_DIR=[your path] ..

VTK_DIR should point to the VTK used by Libsim.

For use with Catalyst

cmake -DENABLE_SENSEI=ON -DENABLE_CATALYST=ON -DParaView_DIR=[your path] ..

Optionally, -DENABLE_CATALYST_PYTHON=ON will enable Catalyst Python scripts. Note that a development version of ParaView is required when building with both ENABLE_CATALYST and ENABLE_VTKM are enabled as released versions of ParaView (5.5.2 and earlier) do not include a modern-enough version of vtk-m.

Enable writing to Visit ".visit" format or ParaView ".pvd" format

cmake -DENABLE_SENSEI=ON -DENABLE_VTK_IO=ON  -DVTK_DIR=[your path] ..

Can be used with either ParaView_DIR or VTK_DIR.

For use with VTK-m

cmake -DENABLE_SENSEI=ON -DENABLE_VTKM=ON -DVTK_DIR=[your path] ..

Note that a development version of VTK is required when building with both ENABLE_SENSEI and ENABLE_VTKM are enabled as released versions of VTK (8.1.1 and earlier) do not include a modern-enough version of vtk-m.

Enabling Python bindings

In essence this is as simple as adding -DENABLE_PYTHON=ON. However, VTK (or ParaView when used with Catalyst) needs to be built with Python enabled, and NumPy, mpi4py, and SWIG are required. Note that there are some caveats when used with Catalyst and Libsim. These are described in more detail in the Newton mini app README.

Using the SENSEI library

To use SENSEI from your CMake based project include the SENSEI CMake config in your CMakeLists.txt.

find_package(SENSEI REQUIRED)

add_executable(myexec ...)
target_link_libraries(myexec sensei ...)

Additionally, your source code may need to include senseiConfig.h to capture compile time configuration.

Included Software and Software Dependencies

The SENSEI framework includes the following software:

  • DIY2, Copyright (c) 2015, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).
  • {fmt}, Copyright (c) 2012-2016, Victor Zverovich.
  • pugixml, Copyright (c) 2006-2016 Arseny Kapoulkine.

The SENSEI framework makes use of (links to) the following software:

  • ADIOS, Copyright (c) 2008 - 2009. UT-BATTELLE, LLC. Copyright (c) 2008 - 2009. Georgia Institute of Technology.
  • ParaView/Catalyst, Copyright (c) 2005-2008 Sandia Corporation, Kitware Inc. Sensei requires ParaView v5.5.1 or later when ENABLE_CATALYST is on and a development version (v5.6.0 or later) when both ENABLE_CATALYST and ENABLE_VTKM are on.
  • VisIt/libsim, Copyright (c) 2000 - 2016, Lawrence Livermore National Security, LLC.
  • VTK, Copyright (c) 1993-2015 Ken Martin, Will Schroeder, Bill Lorensen. Sensei can use VTK provided separately or the VTK included with VisIt/libSim (VTK v6.1 when ENABLE_LIBSIM is on) or ParaView/Catalyst (VTK v8.1 when ENABLE_CATALYST is on). If VTK is provided separately and both ENABLE_VTK and ENABLE_VTKM are on, Sensei requires a development version (VTK v9.0 or later).
  • VTKm, Copyright (c) 2014-2018 NTESS, SNL, LANL, UT-Battelle, Kitware, UC Davis. A development version is currently required as packaging infrastructure has recently changed.

For full license information regarding included and used software please refer to the file THIRDPARTY_SOFTWARE_LICENSES.