Gromacs with GPU version and Plumed
2020...@sanxiau.edu.cn
My name is Xianyu Song and I am from the Chongqing Three Gorges University located in China. we are very interested in the plumed software for calculating free energy surfaces. Recently, we installed the Gromacs with GPU version which is equipped with plumed. However, the conducted Gromacs did not adopt computation with GPU. We will appreciate you very much if you can give us the corsponding suggestions on the Gromacs installation with GPU and plug-in plumed. The following is the installation steps:
Installation steps:
1. plumed installation
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/mkl/bin/mklvars.sh intel64
./configure --prefix=/opt/soft/plumed272 CC=mpiicc CXX=mpiicpc CXXFLAGS=-O3 --enable-mpi --disable-xdrfile LDFLAGS=-L/opt/intel/mkl/lib/intel64 CPPFLAGS=-I/opt/intel/mkl/include
make -j 8
make install
2. Gromacs installation
export CMAKE_PREFIX_PATH=/opt/gmxfftw338
/opt/cmake/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/opt/soft/gmxgpu20206-plumed -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=OFF -DGMX_GPU=ON -DGMX_SIMD=AVX_256
3. usage
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/mkl/bin/mklvars.sh intel64
export LD_LIBRARY_PATH=/opt/gmxfftw338/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/soft/plumed272/lib:$LD_LIBRARY_PATH
source /opt/soft/gmxgpu20206-plumed/bin/GMXRC.bash
gmx_mpi grompp -f npt1.mdp -c nvt_system.gro -p top.top -o npt_plumed -maxwarn 300
gmx_mpi mdrun -ntomp 32 -plumed plumed.dat -v -deffnm npt_plumed (cpu, md runs nomally)
gmx_mpi mdrun -ntomp 32 -plumed plumed.dat -v -deffnm npt_plumed -nb gpu (or -bonded gpu) (gpu, error)
Fatal error:
Cannot run short-ranged nonbonded interactions on a GPU because there is none detected.
We are looking forward to your reply. Thanks a lot.
Best wishes.
Xianyu Song
https://www.researchgate.net/profile/Xianyu_Song
https://scholar.google.com.hk/citations?user=gbYuppEAAAAJ&hl=zh-CN
