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SENSEI

This is the Sensei repository for the code for all the miniapps and analysis routines.

Repository Organization

- CMake/

  This contains CMake files e.g. mpi.cmake, FindADIOS.cmake, etc.

- sensei/

  This contains the source code for the all files under the 'sensei' namespace
  including the core components, DataAdaptor.[h,cxx], AnalysisAdaptor.[h,cxx],
  as well as example analysis adaptor implementations such as Histogram.[h,cxx].

  All classes within this directory are under the 'sensei' namespace and application
  code can include these header using fully qualified paths e.g.

    #include <sensei/DataAdaptor.h> // for sensei::DataAdaptor declaration.
    #include <sensei/AnalysisAdaptor.h> // for sensei::AnalysisAdaptor declaration.

  Adaptor implementations that depend on insitu frameworks are contained within
  directories specific for that framework under this directory.

- sensei/adios/

  Contains source code for all files under the 'sensei::adios' namespace.
  This houses sensei::DataAdaptor and sensei::AnalysisAdaptor implementations that read and write
  data using ADIOS APIs, namely, 'sensei::adios::DataAdaptor' and
  'sensei::adios::AnalysisAdaptor'.

- sensei/catalyst/

  Contains source code for all files under the 'sensei::catalyst' namespace.
  This houses sensei::catalyst::AnalysisAdaptor which implements 'sensei::AnalysisAdaptor'
  interface to use Catalyst for the analysis. Since in Catalyst, analysis is performed
  via pipelines, this directory contains instances of pipelines (e.g. sensei::catalyst::Slice).

- sensei/libsim

  Contains source code for all files under the 'sensei::libsim' namespace.
  This houses the Libsim analysis adaptor for making slice images, etc.

- miniapps/

  All miniapps generated for various bechmarks and testing is included in this directory.
  Each miniapp includes both the expository implementation
  independent of Sensei infrastructure as well as a version that uses Sensei.

- miniapps/parallel3d/

  Code for miniapp from year I.

- miniapps/oscillators/

  Core for miniapp from year II.

- endpoints/

  Code for executables that act as analysis endpoints for frameworks like ADIOS (ADIOSAnalysisEndPoint.cxx)
  and GLEAN. These executables (will) use the sensei::adios::DataAdaptor and sensei::glean::DataAdaptor
  to ingest data from these frameworks back to Sensei for further analysis.

- utils/
    - diy/
    - grid/
    - opts/
    - pugixml/

  Various utility code used by the various analysis implementations.

- configs/

  Sample configuration XML files demonstrating how a configurable analysis pipeline
  can be setup.

Build instructions

The project uses CMake 3.0 or later. The options provided allow you to choose which of the miniapps to build as well as which frameworks to enable.

When ENABLE_SENSEI is off, none of the insitu frameworks are useable. However, miniapps are trypically instrumented with a prototype analysis code e.g. 3D_Grid is set up to compute histograms while oscillators is set up to do an autocorrelation analysis (if SENSEI_EXT_DIR is set).

When ENABLE_SENSEI, the miniapps take in an configuration xml that is used to configure analysis via Sensei infrastructure. Looks at the 3dgrid.xml, oscillator.xml and adiosendpoint.xml for examples of these config files.

Let's look at the various CMake flags and how they affect the generated build.

  • ENABLE_SENSEI: (ON/OFF) Set to ON to enable Sensei. Thus, when ENABLE_SENSEI is OFF, miniapps will only support the one insitu analysis routine they were hardcoded for. If ON, you will need to set the VTK_DIR to point to an existing VTK build since Sensei depends on vtkCommonDataModel module for its data model and adaptor classes.

  • VTK_DIR: Path to VTKConfig.cmake file. When building with libsim or Catalyst, you should point this to the VTK build used/included by the two frameworks.

You can choose which miniapp to build using the following flags.

  • ENABLE_PARALLEL3D: (ON/OFF) Set to ON to build the parallel_3d miniapp from miniapp campaign #1. This miniapp can do histogram analysis if ENABLE_SENSEI is OFF. If ENABLE_SENSEI is ON, this will use the Sensei bridge along with data and analysis adaptors to do the analysis specified in the configuration XML.

  • ENABLE_OSCILLATORS: (ON/OFF) Set to ON to build the oscillators miniapp from miniapp campaign #2. If ENABLE_SENSEI is OFF, this miniapp can do autocorrelation analysis alone (if SENSEI_EXT_DIR is set). If ENABLE_SENSEI is ON, this miniapp supports the histogram, autocorrelation (if SENSEI_EXT_DIR is set), catalyst-slice, etc. as specified in a configuration xml.

To use analysis routines from Catalyst, you can use the following flags.

  • ENABLE_CATALYST: (ON/OFF) Set to ON to enable analysis routines that use Catalyst. This option is only available when ENABLE_SENSEI is ON. This builds an analysis adaptor for Sensei that invokes Catalyst calls to do the data processing and visualization. When set to ON, you will have to point ParaView_DIR to a ParaView (or Catalyst) build containing ParaViewConfig.cmake file.

  • ENABLE_ADIOS: (ON/OFF) Set to ON to enable ADIOS components. When enabled, this generates a ADIOSAnalysisEndPoint that can be used as an endpoint components that reads data being serialized by the ADIOS analysis adaptor and pass it back into a Sensei bridge for further analysis. ADIOSAnalysisEndPoint itself can be given configuration XML for select analysis routines to run via Sensei infrastructure.

  • ENABLE_LIBSIM: (ON/OFF) Set to ON to enable Libsim components. In addition, you must set LIBSIM_DIR so it points to the location of the installed LIBSIMConfig.cmake file to locate Libsim and set up its dependencies. When these settings are enabled/set, the Libsim analysis adaptor will be built.

  • SENSEI_EXT_DIR: Path to the sensei-ext repository. Optionally set to include non-public extensions to the sensei codebase.

Typical build usage:

make build
cd build
ccmake .. # set cmake options as needed
make

All executables will be generated under bin.

Miniapps/Executables

Details on each of the miniapps are as follows:

  • Parallel3D

    Usage (ENABLE_SENSEI=ON):
    ./bin/3D_Grid -g 4x4x4 -l 2x2x2 -f config.xml
        -g global dimensions
        -l local (per-process) dimensions
        -f Sensei xml configuration file for analysis
    
    Usage (ENABLE_SENSEI=OFF):
    ./bin/3D_Grid -g 4x4x4 -l 2x2x2 -b 10
        -g global dimensions
        -l local (per-process) dimensions
        -b histogram bins
  • Oscillators

    Usage (ENABLE_SENSEI=ON):
    ./bin/oscillator [OPTIONS] OSCILLATORS.txt
    Options:
        -b, --blocks INT      number of blocks to use [default: 1]
        -s, --shape POINT     domain shape [default: 64 64 64]
        -t, --dt FLOAT        time step [default: 0.01]
        -f, --config STRING   Sensei analysis configuration xml (required)
        --t-end FLOAT         end time [default: 10]
        --sync                synchronize after each time step
       -h, --help             show help
    
    Usage (ENABLE_SENSEI=OFF, ENABLE_SENSEI_EXT=<not set>):
    ./bin/oscillator [OPTIONS] OSCILLATORS.txt
    Options:
        -b, --blocks INT             number of blocks to use [default: 1]
        -s, --shape POINT            domain shape [default: 64 64 64]
        -t, --dt FLOAT               time step [default: 0.01]
        --t-end FLOAT                end time [default: 10]
        --sync                       synchronize after each time step
        -h, --help                   show help
    
    Usage (ENABLE_SENSEI=OFF, ENABLE_SENSEI_EXT=<set to valid dir>):
    ./bin/oscillator [OPTIONS] OSCILLATORS.txt
    Options:
        -b, --blocks INT             number of blocks to use [default: 1]
        -s, --shape POINT            domain shape [default: 64 64 64]
        -t, --dt FLOAT               time step [default: 0.01]
        -w, --window UNSIGNED LONG   analysis window [default: 10]
        -k, --k-max UNSIGNED LONG    number of strongest autocorrelations to report [default: 3]
        --t-end FLOAT                end time [default: 10]
        --sync                       synchronize after each time step
        -h, --help                   show help
  • ADIOSAnalysisEndPoint

    Usage (ENABLE_SENSEI=ON):
    ./bin/ADIOSAnalysisEndPoint[OPTIONS] input-stream-name
    Options:
       -r, --readmethod STRING   specify read method: bp, bp_aggregate, dataspaces, dimes, or flexpath  [default: bp]
       -f, --config STRING       Sensei analysis configuration xml (required)
       -h, --help                show help
    
    Usage (ENABLE_SENSEI=OFF):
    <NOT AVAILABLE>

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.
  • VisIt/libsim, Copyright (c) 2000 - 2016, Lawrence Livermore National Security, LLC.
  • VTK, Copyright (c) 1993-2015 Ken Martin, Will Schroeder, Bill Lorensen.

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