Intel Compilers
Intel Compilers Edition Update Version Mapping
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Just took a snapshot of Intel 2018 to 2020
Compiling Gromacs-2019.3 with Intel MKL and CUDA
Prerequisites
GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3
Intel Compilers and Prerequisites
% source /usr/local/intel/2018u3/bin/compilervars.sh intel64
% source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64
% source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64
% source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
% MKLROOT=/usr/local/intel/2018u3/mklCreate a setup file
% touch gromacs_gpgpu.shPut the following into the gromacs_cpu.sh
CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl_cuda10.1 -DREGRESSIONTEST_DOWNLOAD=ON
-DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip"
-DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip -I/usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mpi/intel64/include/"
-DGMX_GPU=on
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-10.1
-DCMAKE_BUILD_TYPE=Release
-DCUDA_HOST_COMPILER:FILEPATH=/usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/bin/intel64/icpc% ./gromacs_gpgpu.sh% make% make installTesting and Verification
$ source /your/installation/prefix/here/bin/GMXRC
./gmxtest.pl all -np 2Compiling Gromacs-2019.3 with Intel 2018 and MKL
Prerequisites
GCC-6.5 Compilers and associates libraries
m4-1.4.18
mpfr-3.1.4
cmake-3.15.1
gmp-6.1.0
mpc-1.0.3
Intel Compilers and Prerequisites
source /usr/local/intel/2018u3/bin/compilervars.sh intel64 source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64 source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64 source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64 MKLROOT=/usr/local/intel/2018u3/mkl
Create a setup file
touch gromacs_cpu.sh
Put the following into the gromacs_cpu.sh
CC=mpicc CXX=mpicxx cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_FFT_LIBRARY=mkl -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2019.3_intel18_mkl -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_C_FLAGS:STRING="-cc=icc -O3 -xHost -ip" -DCMAKE_CXX_FLAGS:STRING="-cxx=icpc -O3 -xHost -ip" -DGMX_GPU=off -DCMAKE_BUILD_TYPE=Release
./gromacs_cpu.sh
make
make install
Testing and Verification
$ source /your/installation/prefix/here/bin/GMXRC ./gmxtest.pl all -np 2
The Linux Cluster 