PAAKAT -- Insitu analysis

Motivation

Scalable, Data analysis, Visualization

Table of contents

1. Compilation
   1. VTK / PARAVIEW / CATALYST
2. PAAKAT

---

Compilation

Compilation is divided in three main steps :

1. VTK / PARAVIEW / CATALYST
2. PAAKAT

The Visualization Tookit (VTK) is used to manipulation and displaying of scientific data.

Paraview is a data analysis and visualization application.

ParaView Catalyst (Catalyst) is an in situ use case library

NEK5K is a fast and scalable high-order solver for computational fluid dynamics

PAAKAT is an adaptador.

1. VTK / PARAVIEW / CATALYST

CATALYST uses the scaling capabilities of VTK and ParaView to suppor the in situ use case.

Three levels of compilation are here considered :

I. Full Paraview

II. Partial Paraview

III. Decaf Paraview

Full Paraview manipulates and displays scientific data through the use of a python or C++ VTK API

Partial Paraview can manipulate and/or display scientific data through the use of the C++ VTK API
The use of python is optional.

Decaf Paraview manipulates scientific data through the use of the C++ VTK API.

This last option has been chosen in order to encourage scalability and portability of the code.

Decaf Compilation

1.III. Decaf Paraview

a. Download ParaView Source Code

git clone https://github.com/jmake/DecafPV560.git 

b. CMake configuration

>> cmake ../SRC  \
    -DCMAKE_INSTALL_PREFIX=EXECS01 \
    -DPARAVIEW_BUILD_QT_GUI=OFF \
    -DCMAKE_CXX_FLAGS=-fpermissive \
    -DCMAKE_CXX_COMPILER=CC  \
    -DCMAKE_C_COMPILER=cc \
    -DCMAKE_Fortran_COMPILER=ftn \
    -DPARAVIEW_USE_ICE_T=OFF \
    -DPARAVIEW_USE_MPI=ON \
    -DBUILD_SHARED_LIBS=OFF \
    -DVTK_Group_ParaViewRendering=OFF \
    -DVTK_USE_X=OFF \
    -DVTK_OPENGL_HAS_OSMESA=OFF \
    -DVTK_OPENGL_HAS_EGL=OFF \
    -DModule_vtkIOExport=OFF \
    -DVTK_BUILD_ALL_MODULES_FOR_TESTS=OFF \
    -DVTK_Group_Rendering=OFF \
    -DVTK_Group_StandAlone=OFF \
    -DVTK_Group_MPI=ON \
    -DModule_vtkCommonCore=ON \
    -DModule_vtkFiltersGeneral=ON \
    -DVTK_RENDERING_BACKEND=None \
    -DPARAVIEW_ENABLE_VTK_MODULES_AS_NEEDED=FALSE \
    -DModule_vtkVTKm=ON \
    -DModule_vtkAcceleratorsVTKm=ON \
    -DModule_vtkPVVTKExtensionsDefault=ON \
    -DPARAVIEW_ENABLE_COMMANDLINE_TOOLS=OFF \
    -DPARAVIEW_CURRENT_CS_MODULES= 

c. Checking

>> ccmake .

 CMAKE_BUILD_TYPE                 Debug
 MACOSX_APP_INSTALL_PREFIX        WHERE/WILL/BE/INSTALLED
 ...
 PARAVIEW_ENABLE_CATALYST         ON
 PARAVIEW_ENABLE_PYTHON           OFF  
 PARAVIEW_ENABLE_QT_SUPPORT       OFF
 ...
 MPIEXEC_EXECUTABLE               mpiexec
 ...
 PARAVIEW_USE_MPI                 ON 

d. Compilation

-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Cray Programming Environment 2.6.0 C
...
-- Cray Programming Environment 2.6.0 CXX
...
-- Could not use git to determine source version, using version 5.6.0
-- The Fortran compiler identification is GNU 7.3.0
 ... 
-- Found MPI_C: /opt/cray/pe/craype/2.6.0/bin/cc  
-- Found MPI_CXX: /opt/cray/pe/craype/2.6.0/bin/CC  
-- Found MPI_Fortran: /opt/cray/pe/craype/2.6.0/bin/ftn  
...
-- Configuring done
-- Generating done
-- Build files have been written to: ... 

[  0%] Built target ParaViewData
[  0%] Built target H5make_libsettings
[  1%] Built target verdict
[  1%] Built target VTKData
...
[ 88%] Built target vtkIOMPIParallel
...
[100%] Built target vtkPVCatalyst
...
[100%] Built target vtkPVVTKExtensionsDefault

Beskow, 16cores, ~5 min (2019)
Nord, 16cores, ~7 min (2020Jul)
Juwels, 16 cores, ~20 min (2020Nov)