install

AWS EC2 Cluster setup for Parallel HDF5 as well as serial HDF5 on Ubuntu 16.04LTS systems

H5CPP for now has a strict C++17 requirements, which in time will be dropped to c++14. The easiest way to start is to obtain a generic ubuntu LTS image then go through the following steps:

GCC-8 from binary, courtesy of Jonathon F

sudo add-apt-repository ppa:jonathonf/gcc-8.1
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install gcc-8 g++-8
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 100 --slave /usr/bin/g++ g++ /usr/bin/g++-8

CMAKE 3.11 the most recent version can be cloned from this github repository

git clone https://github.com/Kitware/CMake.git
cd CMake && ./bootstrap && make
sudo make install

LLVM 7.0.0 and Clang is required to compile and run the h5cpp source code transformation tool. Be certain there is 50GB free disk and 16GB memory space on the system you compiling to prevent spurious error messages in the compile or linking phase. AWS EC2 m3.2xlarge instance has suitable local disk and memory space.

git clone https://git.llvm.org/git/llvm.git/
cd llvm/tools
git clone https://git.llvm.org/git/clang.git/
# begin-optional
cd ../projects
git clone https://git.llvm.org/git/openmp.git/
git clone https://git.llvm.org/git/libcxx.git/
git clone https://git.llvm.org/git/libcxxabi.git/
# end-optional
cd ../../ && mkdir build && cd build
3.0 (quilt)cmake -DCMAKE_INSTALL_PREFIX=/usr/local CMAKE_BUILD_TYPE=MinSizeRel -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_USE_LINKER=gold ../llvm
nohup make -j8&
sudo make install build-essential gcc-8 g++-8

For parellel HDF5 you need a POSIX compliant parallel (duh) filesystem. OrangeFS is a good FSF alternative to commercial solutions. This step is optional, alternative solution is to use single write multiple read SWMR mode where on each computing node you have a dedicated MPI process for IO.

sudo apt-get install -y gcc flex bison libssl-dev libdb-dev linux-source perl make autoconf linux-headers-`uname -r` zip openssl automake autoconf patch g++ libattr1-dev
./configure --with-kernel=/usr/src/linux-headers-$(uname -r) --prefix=/usr/local --enable-shared
make -j4 && sudo make install
make kmod # to build kernel module
sudo make kmod_install
# load module
sudo insmod /lib/modules/4.4.0-1062-aws/kernel/fs/pvfs2/pvfs2.ko

MPI is industry standard for supercomputing and is viable alternative to hadoop on clusters. Be sure to enable grid-engine, and set the C compiler to gcc-5, since it failed with gcc-8 on my install, don't forget to verify SGE grid engine execute ompi_info | grep gridengine

gunzip -c openmpi-3.1.1.tar.gz | tar xf -
cd openmpi-3.1.1
#gcc-8 fails for me July 2018
CC=gcc-5 ./configure --with-sge --with-pvfs2 --prefix=/usr/local
make -j4 && sudo make install

SGE can be downloaded from here: TODO add link

LINALG:

sudo apt install libboost-math-dev # ublas support

The best practice is to install all linear algebra systems from sources, starting with BLAS/LAPACK: INTEL MKL | AMD CML | ATLAS | openBLAS | NETLIB Then following with your C++ LinearAlgebra/scientific library. Be sure that the optimized BLAS/LAPACK is picked up during configuration. In addition to standard functionality you may be interested in SuperLU, Metis, Pardiso, SuiteSparse, UmfPack, Cholmod.

Here is the list of C++ supported Scientific/Linear Algebra libraries: armadillo eigen3 blitz blaze dlib itpp boost: ublas and ETL will be added soon. If I left your favourite out or lacking of functionality please shoot me an email.

DETAILS for intel MKL based system:

download intel MKL from their website, and follow instructions, don't forget to set the variables by adding source /opt/intel/bin/compilervars.sh intel64 to .bashrc.

You will need arpack ``

git clone https://github.com/opencollab/arpack-ng.git
cd arpack-ng
./bootstrap
./configure ## make sure it picks up MKL
make -j4
sudo make install

superLU:

git clone https://github.com/xiaoyeli/superlu.git
cd superlu

armadillo:

./configure -DCMAKE_INSTALL_PREFIX=/usr/local
make && make install

blaze: download from here

./configure -DCMAKE_INSTALL_PREFIX=/usr/local
make && make install

ubuntu 18.04 LTS ami-0d2505740b82f7948

sudo apt install build-essential gcc-8 g++-8
wget http://h5cpp.org/download/hdf5-1.10.4.tar.gz
tar -xvzf tar -xvzf hdf5-1.10.4.tar.gz
cd hdf5-1.10.4 && ./configure --prefix=/usr/local && make -j2 && sudo make install
wget http://h5cpp.org/download/h5cpp_1.10.4.1_amd64.deb
sudo dpkg -i h5cpp_1.10.4.1_amd64.deb