From 52fe12eacde52f68a86e3fde29733bbee77536c9 Mon Sep 17 00:00:00 2001 From: chunlin Date: Mon, 3 Apr 2023 08:58:48 +0000 Subject: [PATCH 1/2] =?UTF-8?q?=E6=96=B0=E5=BB=BA=202021.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- templates/gromacs/2021.3/.keep | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 templates/gromacs/2021.3/.keep diff --git a/templates/gromacs/2021.3/.keep b/templates/gromacs/2021.3/.keep new file mode 100644 index 0000000..e69de29 -- Gitee From 0d08c0a8132e5bd6b2680d2aa2faf11aebd21f15 Mon Sep 17 00:00:00 2001 From: chunlin Date: Mon, 3 Apr 2023 08:59:39 +0000 Subject: [PATCH 2/2] add templates/gromacs/2021.3/data.gromacs.arm.gpu.config. Signed-off-by: chunlin --- .../2021.3/data.gromacs.arm.gpu.config | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 templates/gromacs/2021.3/data.gromacs.arm.gpu.config diff --git a/templates/gromacs/2021.3/data.gromacs.arm.gpu.config b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config new file mode 100644 index 0000000..92c20f2 --- /dev/null +++ b/templates/gromacs/2021.3/data.gromacs.arm.gpu.config @@ -0,0 +1,86 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +gromacs/2021.3 http://ftp.gromacs.org/pub/gromacs/gromacs-2021.3.tar.gz + +[DEPENDENCY] +set -e +set -x +module use ./software/modulefiles +module purge +./jarvis -install kgcc/9.3.1 com +./jarvis -install openblas/0.3.18 gcc +module load kgcc9/9.3.1 +./jarvis -install hmpi/1.1.1 gcc +module load hmpi1/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort +./jarvis -install fftw/3.3.8 gcc+mpi +tar -xvf ${JARVIS_DOWNLOAD}/gromacs-2021.3.tar.gz + +[ENV] +module use ./software/modulefiles +module purge +module load kgcc9/9.3.1 +export PATH=/usr/local/cuda/bin:$PATH +module load hmpi1/1.1.1 +module load ./software/moduledeps/kgcc9-hmpi1/fftw/3.3.8 +module load ./software/moduledeps/gcc7/openblas/0.3.18 +export CC=mpicc CXX=mpicxx FC=mpifort +export GMX_FORCE_UPDATE_DEFAULT_GPU=true +export GMX_GPU_PME_PP_COMMS=true +export GMX_GPU_DD_COMMS=true + +[APP] +app_name = gromacs +build_dir = $JARVIS_ROOT/gromacs-2021.3 +binary_dir = $JARVIS_ROOT/gromacs/bin +case_dir = $JARVIS_ROOT/workloads/gromacs/ADH/adh_dodec + +[BUILD] +sed -i '216s/return fftw_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp +sed -i '218s/return fftwf_version;/return 0;/g' src/gromacs/utility/binaryinformation.cpp +sed -i '498s/int fftwflags = FFTW_DESTROY_INPUT;/int fftwflags = 0;/g' src/gromacs/fft/fft5d.cpp +rm -rf build +mkdir build +cd build +openblas_path=$JARVIS_LIBS/gcc7/openblas/0.3.18 +fftw_path=$JARVIS_LIBS/kgcc9/hmpi1/fftw/3.3.8 +FLAGS="-mcpu=tsv110 -O3"; CFLAGS=$FLAGS CXXFLAGS="-mcpu=tsv110 -lgfortran -O3" CC=mpicc CXX=mpicxx FC=mpifort \ +cmake \ +-DCMAKE_INSTALL_PREFIX=$JARVIS_ROOT/gromacs \ +-DBUILD_SHARED_LIBS=on \ +-DBUILD_TESTING=on \ +-DREGRESSIONTEST_DOWNLOAD=off \ +-DGMX_BUILD_OWN_FFTW=off \ +-DGMX_SIMD=ARM_NEON_ASIMD \ +-DGMX_DOUBLE=off \ +-DGMX_EXTERNAL_BLAS=on \ +-DGMX_EXTERNAL_LAPACK=on \ +-DGMX_FFT_LIBRARY=fftw3 \ +-DGMX_BLAS_USER=$openblas_path/lib/libopenblas.a \ +-DGMX_LAPACK_USER=$openblas_path/lib/libopenblas.a \ +-DFFTWF_LIBRARY=$fftw_path/lib/libfftw3f.so \ +-DFFTWF_INCLUDE_DIR=$fftw_path/include \ +-DGMX_GPU=CUDA \ +-DGMX_MPI=off \ +-DGMX_OPENMP=on \ +-DGMX_X11=off \ +-DHWLOC_LIBRARIES=/usr/lib64 \ +-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \ +../ + +make -j40 V=1 +make install + +[CLEAN] +./clean_build + +[RUN] +run = CUDA_VISIBLE_DEVICES=2,3 +#run = CUDA_VISIBLE_DEVICES=2,3 && nsys profile --stats=true +#binary = gmx grompp -f pme_verlet.mdp +#binary = gmx mdrun -s ./topol.tpr -ntomp 10 -nb gpu -bonded gpu -pme gpu -nstlist 400 -v -nsteps 100000 -resetstep 90000 -noconfout +binary = gmx mdrun -s ./topol.tpr -ntmpi 2 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -v -nsteps 100000 -resetstep 90000 -noconfout +#binary = gmx mdrun -s ./topol.tpr -ntmpi 4 -ntomp 10 -nb gpu -bonded gpu -pme gpu -npme 1 -nstlist 400 -v -nsteps 100000 -resetstep 90000 -noconfout +nodes = 1 -- Gitee