Using Bee¶

Login¶

There is 1 login node:

Hostname	Node type
`bee`	Bee login node

Host key fingerprint:

Algorithm	Fingerprint (SHA256)
RSA	`SHA256:1GlrJm7DIZ6yJTNTvivsXKBci4+IT31yW8pmpp35NDI`
ECDSA	`SHA256:oHeyvgUhqF3lDaZLtdbjZBoOj8cQbgKNiojfLW9puIA`
ED25519	`SHA256:eywXc/TEtuhxIhle6fvrAzvgba2O30BZkCeXMZO7pJg`

Building dependencies¶

Boost¶

# last update: August 2023
module load gcc/8.4.0 openmpi/4.0.5
mkdir boost-build
cd boost-build
BOOST_VERSION=1.82.0
BOOST_DOMAIN="https://boostorg.jfrog.io/artifactory/main"
BOOST_ROOT="${HOME}/bin/boost_mpi_${BOOST_VERSION//./_}"
mkdir -p "${BOOST_ROOT}"
curl -sL "${BOOST_DOMAIN}/release/${BOOST_VERSION}/source/boost_${BOOST_VERSION//./_}.tar.bz2" | tar xj
cd "boost_${BOOST_VERSION//./_}"
echo 'using mpi ;' > tools/build/src/user-config.jam
./bootstrap.sh --with-libraries=filesystem,system,mpi,serialization,test
./b2 -j 4 install --prefix="${BOOST_ROOT}"

FFTW¶

# last update: August 2023
module load gcc/8.4.0 openmpi/4.0.5
mkdir fftw-build
cd fftw-build
FFTW3_VERSION=3.3.10
FFTW3_ROOT="${HOME}/bin/fftw_${FFTW3_VERSION//./_}"
curl -sL "https://www.fftw.org/fftw-${FFTW3_VERSION}.tar.gz" | tar xz
cd "fftw-${FFTW3_VERSION}"
./configure --enable-shared --enable-mpi --enable-threads --enable-openmp \
    --disable-fortran --enable-avx --prefix="${FFTW3_ROOT}"
make -j 4
make install
make clean

Building software¶

ESPResSo¶

Release 4.2:

# last update: August 2023
module load gcc/8.4.0 openmpi/4.0.5 boost/1.75.0 python/3.8 cmake/3.26.3 \
    py-cython/0.29.21 fftw/3.3.9 cuda/10.2.89 hdf5/1.10.7 py-pip

git clone --recursive --branch 4.2 --origin upstream \
    https://github.com/espressomd/espresso.git espresso-4.2
cd espresso-4.2
python3 -m pip install --user -c "requirements.txt" setuptools numpy scipy vtk h5py
mkdir build
cd build
cp ../maintainer/configs/maxset.hpp myconfig.hpp
sed -i "/ADDITIONAL_CHECKS/d" myconfig.hpp
cmake .. -D CMAKE_BUILD_TYPE=Release -D WITH_CUDA=ON \
    -D WITH_CCACHE=OFF -D WITH_SCAFACOS=OFF -D WITH_HDF5=ON
make -j 4

Release 4.3:

# last update: August 2023
module load gcc/8.4.0 openmpi/4.0.5 cmake/3.26.3 \
    py-cython/0.29.21 hdf5/1.10.7 py-pip
CLUSTER_FFTW3_VERSION=3.3.10
CLUSTER_BOOST_VERSION=1.82.0
export BOOST_ROOT="${HOME}/bin/boost_mpi_${CLUSTER_BOOST_VERSION//./_}"
export FFTW3_ROOT="${HOME}/bin/fftw_${CLUSTER_FFTW3_VERSION//./_}"
export LD_LIBRARY_PATH="${BOOST_ROOT}/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
export LD_LIBRARY_PATH="${FFTW3_ROOT}/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"

git clone --recursive --branch python --origin upstream \
    https://github.com/espressomd/espresso.git espresso-4.3
cd espresso-4.3
sed -ri 's/find_package\(Python 3\.[0-9] REQUIRED/find_package\(Python 3.6 REQUIRED/' CMakeLists.txt
python3 -m pip install --user -c "requirements.txt" setuptools numpy scipy vtk h5py
mkdir build
cd build
cp ../maintainer/configs/maxset.hpp myconfig.hpp
sed -i "/ADDITIONAL_CHECKS/d" myconfig.hpp
cmake .. -D CMAKE_BUILD_TYPE=Release -D ESPRESSO_BUILD_WITH_CUDA=OFF \
    -D ESPRESSO_BUILD_WITH_CCACHE=OFF -D ESPRESSO_BUILD_WITH_WALBERLA=ON \
    -D ESPRESSO_BUILD_WITH_SCAFACOS=OFF -D ESPRESSO_BUILD_WITH_HDF5=ON
make -j 4

Submitting jobs¶

Batch command:

sbatch --job-name="test" --nodes=1 --ntasks=4 --mem-per-cpu=2GB job.sh

Job script:

#!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --output %j.stdout
#SBATCH --error  %j.stderr
module load gcc/8.4.0 openmpi/4.0.5 boost/1.75.0 python/3.8 fftw/3.3.9 cuda/10.2.89
srun --cpu-bind=cores ./pypresso testsuite/python/particle.py