use on HPCs

This page shows how to compile TomoATT on a few HPCs which we have been using.
If you have any experience on compiling TomoATT on other HPCs, your contribution on this page is highly appreciated. So please feel free to contact us.

Gekko @ NTU

1. Load necessary modules and select GNU compilers

module purge && module load cmake gnu/gcc-9.3.0

2. compiler openmpi and HDF5 with parallel option

./install_mpi_and_hdf5_local.sh
will create openmpi and hdf5 executables in external_libs/local_mpi_hdf5/bin

3. Compile TomoATT

# make a build directory
mkdir build

# compile TomoATT
cd build
CC=/usr/local/gcc-9.3.0/bin/gcc CXX=/usr/local/gcc-9.3.0/bin/g++ cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5

make -j16

Then the executable TOMOATT is created in the build directory.

Fugaku @ RIKEN

0. start interactive job on Fugaku (for accessing arch64 environment)

pjsub --interact -g hp<project_id> -L "node=1" -L "rscgrp=int" -L "elapse=1:00:00" --mpi "max-proc-per-node=12" --sparam "wait-time=600" -x PJM_LLIO_GFSCACHE=/vol0004 --no-check-directory     

1. Load necessary modules

# prepare spack env
. /vol0004/apps/oss/spack/share/spack/setup-env.sh
# load Fujitsu mpi
spack load /jfzaut5
# or load gnu 11.2.0
spack load /nphnrhl /cvur4ou

2. Download hdf5 source code and compile it

# every file will be placed in external_libs
cd ./external_libs

# make a local install pass
mkdir local_mpi_hdf5

# download hdf5 source
wget https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/snapshots/v112/hdf5-1.12.2-1.tar.gz

#Extract the downloaded directory
tar -xvf hdf5-1.12.2-1.tar.gz && cd hdf5-1.12.2-1

# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
CC=mpifcc CFLAGS="-Nclang" CXX=mpiFCC CXXFLAGS="-Nclang" ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5

# make
make -j12 && make install

# now hdf5 executables are in external_libs/local_mpi_hdf5/bin

or with gnu 11.2.0

# download hdf5 source
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.13/hdf5-1.13.2/src/hdf5-1.13.2.tar.gz
#Extract the downloaded directory
tar -xvf hdf5-1.13.2.tar.gz
cd hdf5-1.13.2
# Configure the code. (the pathes to mpicc, mpicxx should vary on the environment)
CC=mpicc CXX=mpic++ ./configure --enable-parallel --enable-unsupported --enable-shared --enable-cxx --prefix=$(pwd)/../local_mpi_hdf5
# make
make -j12 && make install

3. Compile TomoATT

# cd to TomoATT directory
cd ../..

# make a build directory
mkdir build

# compile TomoATT
cd build

CC=mpifcc CXX=mpiFCC cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5
# or for gnu 11.2.0
cmake .. -DCMAKE_PREFIX_PATH=$(pwd)/../external_libs/local_mpi_hdf5

make -j12

4. terminalte interactive job

Ctrl + D