# gromacs_lignocellulose_job_script_PBS
###### tags: `Gromacs`

#!/bin/bash
#PBS -N gromacs_lignocellulose
#PBS -q ct400
#PBS -l select=8:ncpus=25:mpiprocs=25
#PBS -l walltime=3:00:00
#PBS -P ACD110038
#PBS -j oe
#PBS -o pbsout_gromac_8nodes_25ppn.txt

export PATH=/home/nckuhpclab03/cmake/cmake/bin:$PATH
module load gcc/9.3.0
module load mpi/openmpi-4.0.5/gcc930
module load intel/2018_u1
module show intel/2018_u1
export PATH=/home/nckuhpclab03/gromacs/gromacs-2020.2/gromacs/bin:$PATH
export MKLROOT=/pkg/intel/2018_u1/compilers_and_libraries_2018.1.163/linux/mkl
cd /home/nckuhpclab03/lignocellulose/run
mpirun -np 200 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout

mpirun -np 25 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout

ct400_8nodes_32ppn_mpiprocs=1:ompthreads=2

#!/bin/bash
#PBS -N gromacs_lignocellulose
#PBS -q ct400
#PBS -l select=8:ncpus=32:mpiprocs=1:ompthreads=2
#PBS -l walltime=03:00:00
#PBS -P ACD110038
#PBS -j oe
#PBS -o pbsout_gromac_8nodes_32ppn.txt

export PATH=/home/nckuhpclab03/cmake/cmake/bin:$PATH
module load gcc/9.3.0
module load mpi/openmpi-4.0.5/gcc930
module load intel/2018_u1
module show intel/2018_u1
export PATH=/home/nckuhpclab03/gromacs/gromacs-2020.2/gromacs/bin:$PATH
export MKLROOT=/pkg/intel/2018_u1/compilers_and_libraries_2018.1.163/linux/mkl
cd /home/nckuhpclab03/lignocellulose/ct400/run
mpirun -np 256 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout

ct800_16nodes_32ppn_mpiprocs=1:ompthreads=2

#!/bin/bash
#PBS -N gromacs_lignocellulose
#PBS -q ct800
#PBS -l select=16:ncpus=32:mpiprocs=1:ompthreads=2
#PBS -l walltime=03:00:00
#PBS -P ACD110038
#PBS -j oe
#PBS -o pbsout_gromac_16nodes_32ppn.txt

export PATH=/home/nckuhpclab03/cmake/cmake/bin:$PATH
module load gcc/9.3.0
module load mpi/openmpi-4.0.5/gcc930
module load intel/2018_u1
module show intel/2018_u1
export PATH=/home/nckuhpclab03/gromacs/gromacs-2020.2/gromacs/bin:$PATH
export MKLROOT=/pkg/intel/2018_u1/compilers_and_libraries_2018.1.163/linux/mkl
cd /home/nckuhpclab03/lignocellulose/ct800/run
mpirun -np 512 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout

ct160_4nodes_32ppn_mpiprocs=1:ompthreads=2

#!/bin/bash
#PBS -N gromacs_lignocellulose
#PBS -q ct160
#PBS -l select=4:ncpus=32:mpiprocs=1:ompthreads=2
#PBS -l walltime=09:00:00
#PBS -P ACD110038
#PBS -j oe
#PBS -o pbsout_gromac_4nodes_32ppn.txt

export PATH=/home/nckuhpclab03/cmake/cmake/bin:$PATH
module load gcc/9.3.0
module load mpi/openmpi-4.0.5/gcc930
module load intel/2018_u1
module show intel/2018_u1
export PATH=/home/nckuhpclab03/gromacs/gromacs-2020.2/gromacs/bin:$PATH
export MKLROOT=/pkg/intel/2018_u1/compilers_and_libraries_2018.1.163/linux/mkl
cd /home/nckuhpclab03/lignocellulose/ct160/run
mpirun -np 128 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout