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Access to the cluster

ssh username@211.86.151.102

Compilation instructions

Before you start compiling Nektar++, you need to load the following modules

module load cmake/3.19.0 intel/2019.update5  \
hpcx/2.9.0/intel-2019.update5 mkl/2019.update5 \
gcc/10.3.0 boost/1.71.0/intel-2019.update5

The following environment variable can be defined to help cmake find the correct boost version

export BOOST_HOME=/opt/boost/1.71.0/intel-2019.update5

Download the source code

git clone https://gitlab.nektar.info/nektar/nektar.git nektar++

Create the build directory

cd nektar++
mkdir build
cd build

run cmake

CC=mpicc CXX=mpicxx
cmake -DNEKTAR_USE_MPI=ON -DNEKTAR_USE_MKL=ON \
-DNEKTAR_USE_SYSTEM_BLAS_LAPACK=OFF \
-DNEKTAR_USE_FFTW=ON -DNEKTAR_USE_HDF5=ON \
-DTHIRDPARTY_BUILD_BOOST=OFF \
-DTHIRDPARTY_BUILD_HDF5=ON  \
-DNEKTAR_ENABLE_SIMD_AVX512=ON  \
-DCMAKE_CXX_FLAGS=-mavx512f\ -mfma  \
-DTHIRDPARTY_BUILD_FFTW=ON  \
-DTHIRDPARTY_BUILD_BLAS_LAPACK=OFF   ..

Then unload gcc

module unload gcc/10.3.0

Then run

make -j4 install

Submit jobs

Create an interactive job on the compute node in the test queue

salloc -p test -N 1 -n 1 --qos=testqos

Submit a job using sbatch, sbatch job.sub, with a job.sub file

#!/bin/sh

#SBATCH -J gear2D
#SBATCH -o job-%j.log
#SBATCH -e job-%j.err
#SBATCH -n 40
#SBATCH --time=0:05:0

echo Time is `date`
echo Directory is $PWD
echo This job runs on the following nodes:
echo $SLURM_JOB_NODELIST
echo This job has allocated $SLURM_JOB_CPUS_PER_NODE cpu cores.

module load cmake/3.19.0
module load intel/2019.update5
module load hpcx/2.9.0/intel-2019.update5
module load mkl/2019.update5
module load gcc/10.3.0
export NEK_DIR=/home/ses/agao20/code/nektar++/build2
export NEK_BUILD=$NEK_DIR/dist/bin
export LD_LIBRARY_PATH=/gpfs/opt/gcc/10.3.0/lib64:/lib64:$NEK_DIR/ThirdParty/dist/lib:$NEK_DIR/dist/lib64:$LD_LIBRARY_PATH

MPIRUN=mpirun #Intel mpi and Open MPI
$MPIRUN $NEK_BUILD/IncNavierStokesSolver gear.xml condition.xml  -i Hdf5 -v &> runlog

References

https://www.nektar.info/nektar-on-archer2/
https://www.nektar.info/nektar-ic-hpc/