/HIVE

Heterogeneously Integrated Visual-analytic Environment

Primary LanguageJavaScript

#HIVE

HIVE is the acronym for "Heterogeneously Integrated Visualization Environment" and is built on SURFACE.

Build Status

Requirements

  • cmake 2.8 or later
  • Autotools
  • MPI C/C++ compiler(optional for macosx and linux x64 environment)
  • Zoltan v.3.81(Required when you build HIVE with PDMlib support)
  • fpzip 1.0.1(Required when you build HIVE with PDMlib support)
  • cgnslib 3.2.1(Required when you build HIVE with UDMlib support)
  • netcdf4 4.2.1.1(Required when you build HIVE with CDMlib support)
  • HDF5 1.8.10 patch1(Required when you buil HIVE with CDMlib support)
    • Use brew install hdf5 for MacOSX.
  • Fortran compiler(e.g. gfortran. Optional. Required for building OpenMPI and CDMlib)

git clone

$ git clone https://github.com/avr-aics-riken/HIVE.git
$ cd HIVE
$ git submodule update --init

In the later, $HIVE is used for the directory where you cloned HIVE git repository.

Setup

Firstly, HIVE needs to build third party libraries.

K/FX10

Download fpzip, Zoltan and cgnslib and put files into $HIVE/third_party/, then

$ cd $HIVE
$ ./scripts/build_loader_libs_k_cross.sh

Linux

CentOS 6

Assume cmake2.8 and hdf5 has been installed somewhere.

$ cd $HIVE
$ CMAKE_BIN=/path/to/cmake28 ./scripts/build_loader_libs_linux-x64.sh

Ubuntu 14.04

$ sudo apt-get install libhdf5-dev
$ sudo apt-get install gfortran
$ cd $HIVE
$ ./scripts/build_loader_libs_linux-x64.sh

MacOSX(Before Sierra)

MacOSX requires gcc-4.8 and openmpi, also requres homebrew supplied HDF5(gcc4.8 failed to compile HDF5 1.8.10 patch1). (gcc-5 is not supported due to New ABI problem)

Setup

Assume homebrew is installed.

$ brew install gcc48
$ brew install openmpi
$ brew install hdf5
$ export OMPI_CC=gcc-4.8
$ export OMPI_CXX=g++-4.8
$ cd $HIVE
$ ./scripts/build_loader_libs_macosx.sh

macOS Sierra(Work in progress)

For some reason, custom gcc(e.g. gcc installed through homebrew) does not work on Sierra, Thus we forced to use Apple gcc(clang) which does not support OpenMP.

openmpi must be installed with cxx binding, otherwise it fails to compile BCMTools.

Use NetCDF(and HDF5) using homebrew.

Using Apple gcc(clang)

OpenMP feature is not available.

Assume homebrew is installed.

Use gfotran-5 for a fotran compiler.

$ brew install gcc@5
$ brew install openmpi --with-cxx-binding
$ brew install netcdf
$ cd $HIVE
# Edit `netcdf_dir` if requied in `scripts/build_loader_libs_macosx_sierra.sh`, then
$ ./scripts/build_loader_libs_macosx_sierra.sh

Using gcc6

OpenMP available. Some OSX specific feature(e.g. OpenGL) is not available since OSX header assumes clang.

Assume homebrew is installed.

Use gfotran-6 for a fotran compiler.

$ brew install gcc@6
$ brew install netcdf

Install OpenMPI 2.0.2 from source(use gcc6 and enable C++ binding).

$ cd /path/to/openmpi-2.0.2-source
$ CC=gcc-6 CXX=g++-6 ./configure --prefix=/path/to/openmpi --enable-mpi-cxx 
$ make && make install

Use mpicc and mpicxx complied as the above

$ export PATH=/path/to/openmpi/bin:$PATH

$ cd $HIVE
# Edit `netcdf_dir` if requied in `scripts/build_loader_libs_macosx_sierra.sh`, then
$ ./scripts/build_loader_libs_macosx_sierra.sh

How to build HIVE

This is a manual step to build HIVE. Plese see the later section when you want to use predefined cmake build script.

$ cd $HIVE
$ mkdir build
$ cd build

# Build with minimum dependency
$ cmake ../
$ make

# Or enable OpenMP build(optional)
$ cmake ../ -DHIVE_BUILD_WITH_OPENMP=On
# You may run cmake twice to tell OPENMP flag to SURFACE module correctly.
# (This looks like a problem of cmake...)
$ cmake ../ -DHIVE_BUILD_WITH_OPENMP=On
$ make

Build options

Compilers

Use CXX and CC flag to specify custom compiler. e.g.:

CXX=mympicxx CC=mympicc /path/to/cmake ...

Options

-DLUA_USE_READLINE=Off -DLUA_USE_CURSES=Off : disable link with curses and readlines in lua

HIVE_BUILD_UNIT_TEST OFF CACHE BOOL "Build unit test?"
HIVE_BUILD_K_CROSS_COMPILE OFF CACHE BOOL "Build for K/FX10 target with corss compiling?"
HIVE_BUILD_WITH_MPI OFF CACHE BOOL "Build with MPI support?"
HIVE_BUILD_WITH_OPENMP OFF CACHE BOOL "Build with OpenMP support?"
HIVE_BUILD_SCREEN_PARALLEL OFF CACHE BOOL "Build with screen parallel support?(Also need to enable HIVE_BUILD_WITH_MPI option)"
HIVE_BUILD_WITH_CDMLIB OFF CACHE BOOL "Build with CDMlib support?(Also need to enable HIVE_BUILD_WITH_MPI option)"
(You may need manually add `sz` to NETCDF_LIBS in hrender/CMakeList.txt, depending on your system)
HIVE_BUILD_WITH_PDMLIB OFF CACHE BOOL "Build with PDMlib support?"
HIVE_BUILD_WITH_HDMLIB OFF CACHE BOOL "Build with HDMlib support?"
HIVE_BUILD_WITH_UDMLIB OFF CACHE BOOL "Build with UDMlib support?"
HIVE_BUILD_WITH_BCMTOOLS OFF CACHE BOOL "Build with BCMTools support?(Also need to enable HIVE_BUILD_WITH_MPI option)"
HIVE_BUILD_WITH_COMPOSITOR OFF CACHE BOOL "Build with 234Compositor support?(Also need to enable HIVE_BUILD_WITH_MPI option)"
HIVE_BUILD_WITH_PMLIB OFF CACHE BOOL "Build with PMlib support?(Also need to enable HIVE_BUILD_WITH_MPI option)"
SANITIZE_ADDRESS=On/Off : Enable/Disable Address sanitizer(HiveCore/Modules/SURFACE). Default = off.
BUILD_SHARED_LIBS=On/Off : Build HiveCore as module(.so) or static.

K/FX10

Optionally edit ./scripts/cmake_k_cross.sh, then

$ cd $HIVE 
$ mkdir build
$ ./scripts/cmake_k_cross.sh
$ cd build
$ make

Known issues

hrender must be build with BUILD_SHARED_LIBS OFF. Module build is not supported on K/FX10 platform at this time(causes runtime libstdc++ exception due to linkage/shared_lib problem)

Linux

Intel Compiler

Optionally edit ./scripts/cmake_linux-x64-all-icc.sh, then

$ cd $HIVE 
$ mkdir build
$ ./scripts/cmake_linux-x64-all-icc.sh
$ cd build
$ make

GCC

Optionally edit ./scripts/cmake_linux-x64-all.sh, then

$ cd $HIVE 
$ mkdir build
$ ./scripts/cmake_linux-x64-all.sh
$ cd build
$ make
Address sanitizer

HiveCore, Modules and SURFACE can be built with address sanitizer(ASAN) support. We recommend to use recent clang compiler(gcc 4.8+ works, but clang has much better ASAN support)

Plese set clang compiler to cmake and mpi(e.g. through CC/CXX environment), then add -DSANITIZE_ADDRESS=On to cmake flag.

MacOSX OpenMP + MPI build(Before Sierra)

$ cd $HIVE
$ mkdir build
$ ./scripts/cmake_macosx_mpi.sh
$ cd build
$ make

macOS Sierra

$ cd $HIVE
$ ./scripts/cmake_macosx_mpi_sierra.sh
$ cd build
$ make

Setup node.js for HIVE UI

$ cd $HIVE
$ cd build/bin/HIVE_UI
$ npm install

Run HIVE UI

$ cd $HIVE
$ cd build/bin/HIVE_UI
$ node server.js

Setup SceneNodeEditor

$ cd $HIVE
$ cd build/bin/SceneNodeEditor
$ npm install

Run SceneNodeEditor

$ cd $HIVE
$ cd build/bin/SceneNodeEditor
$ node server.js

Data loaders and formats

  • HDMlib

    • float precision voxel type(scalar and vector)
    • double precision voxel type(scalar and vector)
      • Convert to float precision for internal representation

  • UDMlib

    • triangle element
    • quad element
    • tetra element
    • pyramid element
    • prism element
    • hexahedron element
    • custom attributes
      • float and vec3 type

  • CDMlib

    • float precision voxel type(scalar and vector)
    • double precision voxel type(scalar and vector)
      • Convert to float precision for internal representation
    • non-uniform spacing
    • NetCDF4 format support

  • PDMlib

    • particle data
    • custom attributes
      • float, vec2, vec3, vec4 and uint type