# 給家貞
## jobscript

#!/bin/bash
#PBS -N gromacs_lignocellulose_normal
#PBS -q normal
#PBS -l select=32:ncpus=24:mpiprocs=24:ompthreads=1
#PBS -l walltime=2:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o output.txt

echo "start"
module load intel/19.0.0.117
export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/cmake/cmake320/bin:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/app/intel/xe2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64:/app/intel/xe2019/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64
## gcc
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$LD_LIBRARY_PATH

date
##gromacs
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithintelcc/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithintelcc/lib64:$LD_LIBRARY_PATH

module load intelmpi
which mpirun
mpirun --version
export OMP_NUM_THREADS=1
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/input/lignocellulose/32nodes/gromacs_final_result/run
time mpirun -np 768 --map-by numa mdrun_mpi -ntomp 1 -v -pin on -s lignocellulose-rf.tpr -nsteps 100000 -noconfout -nb cpu
date
echo "end"

## installation_guide
### cmake-3.20

## cmake-3.20
mkdir /usr/local/cmake
cd /usr/local/cmake/
wget https://github.com/Kitware/CMake/releases/download/v3.20.0-rc2/cmake-3.20.0-rc2.tar.gz
tar xvf cmake-3.20.0-rc2.tar.gz
cd cmake-3.20.0-rc2/
./bootstrap --prefix=/usr/local/cmake
gmake -j16
gmake install
cmake --version
export PATH=/home/nckuhpclab08/cmake/cmake320rc2/bin:$PATH

### gcc-7.3.0
[gcc](https://hackmd.io/DfCua1aBSju17nlYxgdjvA)
### intelmpi

module load intel/19.0.0.117
export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort

### mkl
只要勾mkl的部分

wget https://registrationcenter-download.intel.com/akdlm/irc_nas/17977/l_BaseKit_p_2021.3.0.3219_offline.sh
bash l_BaseKit_p_2021.3.0.3219_offline.sh
mkdir mkl
mv intel lib l_BaseKit_p_2021.3.0.3219_offline.sh mkl
cd /home/nckuhpclab08/mkl/intel/oneapi/mkl/2021.3.0/env
source vars.sh

### gromacs-2020.6
[gromacs-2020.6下載](https://manual.gromacs.org/documentation/2020.6/download.html)

tar xvf gromacs-2020.5.tar.gz
cd gromacs-2020.5/
mkdir build
cd build
cmake -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=$MKLROOT/lib/intel64/libmkl_rt.so -DMKL_INCLUDE_DIR=$MKLROOT/include -DGMX_SIMD=AVX2_256 -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=OFF -DGMX_GPU=OFF -DGMX_HWLOC=OFF -DCMAKE_INSTALL_PREFIX=/home/nckuhpclab08/gromacs_mkl -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_BUILD_TYPE=Release -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE ..
make -j $(nproc)
make install
export Pexport PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithintelcc/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithintelcc/lib64:$LD_LIBRARY_PATH

### input 網址
[gromacs_input](https://hpcadvisorycouncil-my.sharepoint.com/personal/pengzhiz_hpcadvisorycouncil_com/_layouts/15/onedrive.aspx?originalPath=aHR0cHM6Ly9ocGNhZHZpc29yeWNvdW5jaWwtbXkuc2hhcmVwb2ludC5jb20vOmY6L3AvcGVuZ3poaXovRW5RTXJPcC1ycHBNaUphazdiY3ZuVTBCMzJ6SmI2WTRKd0pqNWNkellXTWxJZz9ydGltZT1GRTZBaWE2UzJVZw&id=%2Fpersonal%2Fpengzhiz%5Fhpcadvisorycouncil%5Fcom%2FDocuments%2FCompetitions%2FAPAC%20HPC%2DAI%202021%2FGROMACS%2FInput%20files)