In-situ Workflow Autotuner

1. Scenario 1 for ADIOS1-coupled Applications

1.1 Quick start

cd scenario-1
./build-all.sh
source env_all.sh

1.2 Manually setup Environments step by step

cd scenario-1
export ROOT=$PWD/install
mkdir -pv $ROOT

(1) Load modules

module unload intel-mkl/2017.3.196-v7uuj6z
module load intel/17.0.4-74uvhji
module load intel-mpi/2017.3-dfphq6k
module load cmake/3.12.2-4zllpyo
module load jdk/8u141-b15-mopj6qr
module load tcl/8.6.6-x4wnbsg

(2) Download and install FlexPath

mkdir korvo_build
cd korvo_build
wget https://gtkorvo.github.io/korvo_bootstrap.pl
perl ./korvo_bootstrap.pl stable $ROOT/korvo

Edit korvo_build_config

korvogithub configure --disable-shared
korvogithub cmake -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS=-fPIC -DCMAKE_CXX_FLAGS=-fPIC -DTARGET_CNL=1 -DPKG_CONFIG_EXECUTABLE=IGNORE

Then, build the static libraries of korvo (used by ADIOS)

perl ./korvo_build.pl

Edit korvo_build_config

korvogithub configure
korvogithub cmake

Then, build the dynamic libraries of korvo (used by LAMMPS)

perl ./korvo_build.pl

Set environmental variable.

export KORVO_HOME=$ROOT/korvo
export PATH=$KORVO_HOME/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$KORVO_HOME/lib

(3) Download ADIOS 1 from https://users.nccs.gov/~pnorbert/adios-1.13.1.tar.gz and install ADIOS 1

tar -zxvf adios-1.13.1.tar.gz
export LIBS=-pthread
cd adios-1.13.1
./configure --prefix=$ROOT/adios --with-flexpath=$ROOT/korvo CFLAGS="-g -O2 -fPIC" CXXFLAGS="-g -O2 -fPIC" FCFLAGS="-g -O2 -fPIC"
make -j 8
make install
export ADIOS_HOME=$ROOT/adios
export PATH=$ADIOS_HOME/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ADIOS_HOME/lib

(4) Download, compile and test the application Heat-transfer and Stage-write

Download coupled applications Heat-transfer and Stage-write with commit hash of e2353b06d0ded82ff00402e072987b7c1ed506a9:

git clone https://github.com/CODARcode/Example-Heat_Transfer.git

Modify Example-Heat_Transfer/Makefile and Example-Heat_Transfer/stage_write/stage_write to use compilers mpicc and mpif90, and compile:

cd Example-Heat_Transfer
make
cd Example-Heat_Transfer/stage_write
make
cd Example-Heat_Transfer

Test in two terminal windows:

mpiexec -n 12 ./heat_transfer_adios2 heat 4 3 40 50 6 5

mpiexec -n 3 ./stage_write/stage_write heat.bp staged.bp FLEXPATH "" MPI ""

Copy/link the configuration file heat_transfer.xml:

mkdir -pv experiment
ln -s heat_transfer.xml experiment/heat_transfer.xml

(5) Download and install Swift/T

Download and Install Ant:

wget https://www.apache.org/dist/ant/binaries/apache-ant-1.10.10-bin.tar.gz
tar -zxvf apache-ant-1.10.10-bin.tar.gz -C $ROOT
export ANT_HOME=$ROOT/apache-ant-1.10.10
export PATH=$ANT_HOME/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ANT_HOME/lib

Download Swift/T (branch tong01 with commit hash of de99add30a64622a65f603e304f22f57ed3e20d4):

git clone https://github.com/swift-lang/swift-t.git
cd swift-t
git checkout tong01

Generate the compiling script:

dev/build/init-settings.sh

Set the installation path SWIFT_T_PREFIX=$ROOT/swift-t-install in the file dev/build/swift-t-settings.sh and compile/install Swift/T:

dev/build/build-swift-t.sh
export SWIFT_T_HOME=$ROOT/swift-t-install
export PATH=$SWIFT_T_HOME/turbine/bin:$SWIFT_T_HOME/stc/bin:$PATH

(6) Compile and test the application LAMMPS and Voro++

Request accessing the source code https://github.com/CODARcode/Example-LAMMPS.git

Download:

git clone https://github.com/CODARcode/Example-LAMMPS.git

Compile LAMMPS:

cd Example-LAMMPS/lammps/src
make yes-kspace yes-manybody yes-molecule yes-user-adios_staging
make mpi -j8
make mpi -j8 mode=shlib

Compile Voro++-0.4.6:

cd Example-LAMMPS/voro++-0.4.6/src
make -j8 CXX=mpicxx CFLAGS=-fPIC

Compile adios_integration (timeout_sec in voro_adios_omp_staging.h can be set.):

cd Example-LAMMPS/adios_integration
make -j8

Edit swift-liblammps/build.sh to set MPICC as $( which mpicc ) and compile swift-liblammps

cd Example-LAMMPS/swift-liblammps
sed -i 's/^MPICC=$( which cc )$/MPICC=$( which mpicc )/' build.sh
./build.sh

Compile swift-all:

cd ../swift-all
./build-16k.sh

(7) Download and install Conda

wget https://repo.anaconda.com/archive/Anaconda2-5.3.1-Linux-x86_64.sh
chmod +x Anaconda2-5.3.1-Linux-x86_64.sh
./Anaconda2-5.3.1-Linux-x86_64.sh -p $ROOT/anaconda2
export PATH=$ROOT/anaconda2/bin:$PATH
conda create -n codar python=2.7
export PATH=$ROOT/anaconda2/envs/codar/bin:$PATH

(8) Reconfigure Swift/T with Python and Rebuild/reinstall Swift/T

Edit swift-t/swift-t-settings.sh to set ENABLE_PYTHON as 1 and PYTHON_EXE as the path of python executable and rebuild Swift/T:

dev/build/build-swift-t.sh