---
# System prepended metadata

title: 新加坡gromacs_lignocellulose_job_script
tags: [Gromacs]

---

# 新加坡gromacs_lignocellulose_job_script
###### tags: `Gromacs`
```=
module unload binutils/2.26 gmp/6.1.0 mpfr/3.1.4 mpc/1.0.3 isl/0.14 gcc/4.9.3 intelmpi gromacs/5.1.2/gcc493/impi
module load gromacs

#!/bin/bash
#PBS -N gromacs_lignocellulose_openmpi3.1.0_normal
#PBS -q normal
#PBS -l select=32:ncpus=24:mpiprocs=24:ompthreads=1:mem=96gb
#PBS -l walltime=00:10:00
#PBS -P 50000033
#PBS -j oe
#PBS -o test1.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi3.1.0/install/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi3.1.0/install/lib:$LD_LIBRARY_PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$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
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/lib64:$LD_LIBRARY_PATH
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/oneapi/mkl/2021.3.0/env
source vars.sh
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/32nodes/run

node=32
ncpu=24

rm -f hostfile1
for (( i=1; i<=$node; i=i+1 ))
do
        S[${i}]=`sed -n "$(($i*$ncpu))p" $PBS_NODEFILE`
        echo "${S[$i]} slots=$ncpu" >> hostfile1
done
time mpirun --hostfile /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/16nodes/run/hostfile1 -np 768 --bynode mdrun_mpi -v -s -ntomp 1 lignocellulose-rf.tpr -nsteps 100000 -noconfout
date
echo "end"



```

time mpirun -np 24 --map-by numa mdrun_mpi -v -s stmv.tpr -nsteps 100000 -noconfout
```=
#!/bin/bash
#PBS -N gromacs_lignocellulose_openmpi3.1.0_normal
#PBS -q normal
#PBS -l select=16:ncpus=24:mpiprocs=24:ompthreads=1:mem=96gb
#PBS -l walltime=00:10:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_openmpi3.1.0_16nodes_24_ncp_24mpi_2omp.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$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
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacs_openmpi3.1.0/install/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacs_openmpi3.1.0/install/lib64:$LD_LIBRARY_PATH
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/oneapi/mkl/2021.3.0/env
source vars.sh
export PATH=$PATH:/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi3.1.0/install/bin
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi3.1.0/install/lib
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/16nodes/run
time mpirun -np 384 --map-by numa mdrun_mpi -v -s -ntomp 1 lignocellulose-rf.tpr -nsteps 100000 -noconfout
date
echo "end"
```










```=

#!/bin/bash
#PBS -N gromacs_lignocellulose_test_normal
#PBS -q normal
#PBS -l select=8:ncpus=24:mpiprocs=24:ompthreads=2
#PBS -l walltime=24:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_gromac_8nodes_24_ncp_24mpi_2omp.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$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
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/hpcx/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat6.10-x86_64/sources/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/hpcx/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat6.10-x86_64/sources/openmpi/lib:$LD_LIBRARY_PATH
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/intel/oneapi/mkl/2021.3.0/env
source vars.sh
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/install/bin:$PATH
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/8odes/run
time mpirun -np 192 -N 24 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout
date
echo "end"
```

### gromacs_intelmpi
```=
#!/bin/bash
#PBS -N gromacs_lignocellulose_intelmpi_normal
#PBS -q normal
#PBS -l select=16:ncpus=24:mpiprocs=24:ompthreads=2
#PBS -l walltime=24:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_gromac_4nodes_24ncp_24mpi-2omp.txt

echo "start"
date
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:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$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
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacswithintelcc/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacswithintelcc/lib64:$LD_LIBRARY_PATH
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/input/lignocellulose/4nodes/run
time mpirun mdrun_mpi -v -s lignocellulose-rf.tpr -maxh 0.1 -resethway -nsteps 10000 -noconfout
date
echo "end"

```
### gromacs build with new open mpi
```=
#!/bin/bash
#PBS -N gromacs_lignocellulose_test_normal
#PBS -q normal
#PBS -l select=16:ncpus=24:mpiprocs=24:ompthreads=2
#PBS -l walltime=24:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_gromac_4nodes_16ppn_mormal.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/hpcx/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat6.10-x86_64/sources/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/hpcx/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat6.10-x86_64/sources/openmpi/lib:$LD_LIBRARY_PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$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
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/intel/oneapi/mkl/2021.3.0/env
source vars.sh
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/install/bin:$PATH
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/16nodes/run
time mpirun mdrun_mpi -v -s lignocellulose-rf.tpr -maxh 0.1 - resethway -nsteps 10000 -noconfout
date
echo "end"
```



### gromacs build with hpcx
```=
#!/bin/bash
#PBS -N gromacs_lignocellulose_test_normal
#PBS -q normal
#PBS -l select=16:ncpus=24:mpiprocs=24:ompthreads=2
#PBS -l walltime=24:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_gromac_4nodes_16ppn_mormal.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$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
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/hpcx/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat6.10-x86_64/modulefiles
module use $PWD
module load hpcx-ompi
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/intel/oneapi/mkl/2021.3.0/env
source vars.sh
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/install/bin:$PATH
which mpirun
mpirun --version
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/inputtest/input/lignocellulose/16nodes/run
time mpirun mdrun_mpi -np 384  -v -s -mca pml ucx -x UCX_NET_DEVICES=mlx5_0:1 lignocellulose-rf.tpr -nsteps 10000 -noconfout
date
echo "end"
```



### gromacs build with openmpi
medium 
normal
```=
#!/bin/bash
#PBS -N gromacs_lignocellulose_test_normal
#PBS -q normal
#PBS -l select=2:ncpus=16:mpiprocs=1:ompthreads=2
#PBS -l walltime=24:00:00
#PBS -P 50000033
#PBS -j oe
#PBS -o pbsout_gromac_2nodes_16ppn_mormal.txt

echo "start"
date
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/cmake/cmake320/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gcc/lib64:$LD_LIBRARY_PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi/openmpi401/bin:$PATH
export LD_LIBRARY_PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/openmpi/openmpi401/lib:$LD_LIBRARY_PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/gromacswithopenmpi/install/bin:$PATH
export PATH=/home/users/industry/ai-hpc/apacsc19/scratch/gromacs/ucx/ucx/bin:$PATH
cd /home/users/industry/ai-hpc/apacsc19/scratch/gromacs/mkl/intel/oneapi/mkl/2021.3.0/env
source vars.sh
which mpirun
mpirun --version
cd 

mpirun -n $NPROCS --hostfile $HOSTFILE --map-by ppr:$NUMBER_PROCESSES_PER_NUMA:numa:pe=$NUMBER_THREADS_PER_PROCESS -report-bindings $MPI_EXECUTABLE

time mpirun -np 128 mdrun_mpi -v -s lignocellulose-rf.tpr -nsteps 100000 -noconfout
date
echo "end"
```