课题组计算服务器任务提交脚本

VASP提交脚本

在任务目录新建提交脚本

vim job.pbs

粘贴以下内容：

#!/bin/bash
#===========================================================#
# Job submission script for VASP                            #
# Created by flmore on April 24, 2023                       #
# update url: https://flmore.github.io/2022/d81ba705.html   #
#===========================================================#
# 1. PBS job control

#PBS -S /bin/bash
#PBS -N vasp
#PBS -l nodes=1:ppn=24
#PBS -q batch
#PBS -l walltime=30:00:00
#PBS -m e
#PBS -M your-email@xxx.com # A reminder message will be sent to this mailbox when the task is over.

# 2. load  environment variable
source /opt/intel/oneapi/setvars.sh  > /dev/null
export PATH=/usr/local/bin:$PATH
export I_MPI_OFFLOAD_DEVICES=0
export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:ofi

# 3. run program
NP=`cat $PBS_NODEFILE | wc -l`
cd $PBS_O_WORKDIR

#VASP_EXEC=vasp_gam-5.4.4_avx2
#VASP_EXEC=vasp_gam-5.4.4_vtst_avx2
#VASP_EXEC=vasp_gam-6.3.2_avx2
VASP_EXEC=vasp_std-5.4.4_avx2
#VASP_EXEC=vasp_std-5.4.4_vtst_avx2
#VASP_EXEC=vasp_std-6.3.2_O3_avx512
#VASP_EXEC=vasp_std-6.3.2_avx2
#VASP_EXEC=vasp_std-6.3.2_avx512

SINGPATH=/opt/vasp/bin/vasp-sin-ed-combine-v0.0.2.sif
mpirun -np $NP singularity exec $SINGPATH $VASP_EXEC &> out.log

粘贴以下内容（以下内容仅作备份，无法在升级后的集群正常提交）

#!/bin/bash
#===========================================================#
# Job submission script for VASP                            #
# Created by flmore on October 14, 2022                     #
# update url: https://flmore.github.io/2022/d81ba705.html   #
#===========================================================#
# 1. PBS job control

#PBS -S /bin/bash
#PBS -N vasp
#PBS -l nodes=1:ppn=24
#PBS -q batch
#PBS -l walltime=30:00:00
#PBS -m e
#PBS -M your-email@xxx.com # A reminder message will be sent to this mailbox when the task is over.

# 2. load intel oneapi environment variable
source /opt/intel/oneapi/setvars.sh intel64 > /dev/null
export I_MPI_OFFLOAD_DEVICES=0
export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:ofi

# 3. run program
NP=`cat $PBS_NODEFILE | wc -l`
cd $PBS_O_WORKDIR

VASP=/opt/vasp/vasp.5.4.4/bin/vasp_std_intel-oneapi_gcc-11.2.0-avx2 # set vasp program path
#VASP=/opt/vasp/vasp.5.4.4/bin/vasp_gam_intel-oneapi_gcc-11.2.0-avx2
#VASP=/opt/vasp/vasp.5.4.4/bin/vasp_ncl_intel-oneapi_gcc-11.2.0-avx2
#VASP=/opt/vasp/vasp.5.4.4_vtst/bin/vasp_std_vtst_intel-oneapi_gcc-11.2.0-avx2 # for CI-NEB Calc.
#VASP=/opt/vasp/vasp.6.3.2/bin/vasp_std_intel-oneapi_gcc-11.2.0-avx2 # vasp.6.3.2 for MLFF.
#VASP=/opt/vasp/vasp.6.3.2/bin/vasp_gam_intel-oneapi_gcc-11.2.0-avx2
#VASP=/opt/vasp/vasp.6.3.2/bin/vasp_ncl_intel-oneapi_gcc-11.2.0-avx2


mpirun -np $NP $VASP &> out.log

GAUSSIAN提交脚本

在任务目录新建提交脚本

vim job.pbs

粘贴以下内容

#!/bin/bash
#===========================================================#
# this script is used to submit gaussian tasks              #
# created time: 2023.04.24                                  #
# edit by flmore                                            #
# update url: https://flmore.github.io/2022/d81ba705.html   #
# ref url: http://bbs.keinsci.com/thread-22162-1-1.html     #
#===========================================================#

# 1. PBS job control
#PBS -N Gaussian
#PBS -l nodes=1:ppn=24
#PBS -l walltime=30:00:00
#PBS -l mem=96000mb
#PBS -q batch
#PBS -j oe

# 2. load Gaussian16 env
source /opt/gaussian/gaussian-env.sh

# 3. run g16 program
# run on AMD CPU
export PGI_FASTMATH_CPU=sandybridge
cd $PBS_O_WORKDIR

for inf in *.gjf
do
    echo $inf
    g16 $inf
    wait
    formchk ${inf%.gjf}.chk
done &> out.log

# Delete Temporary Files to Reduce Hard Disk Usage
rm -rf /opt/gaussian/scratch/*

粘贴以下内容（以下内容仅作备份，无法在升级后的集群正常提交）

#!/bin/bash
#===========================================================#
# this script is used to submit gaussian tasks              #
# created time: 2021.11.24                                  #
# edit by flmore                                            #
# update url: https://flmore.github.io/2022/d81ba705.html   #
# ref url: http://bbs.keinsci.com/thread-22162-1-1.html     #
#===========================================================#

# 1. PBS job control
#PBS -N Gaussian
#PBS -l nodes=1:ppn=24
#PBS -l walltime=30:00:00
#PBS -l mem=96000mb
#PBS -q batch
#PBS -j oe

# 2. load Gaussian16 env
export g16root=/opt/gaussian
export GAUSS_SCRDIR=~/.g16/scratch
source /opt/gaussian/g16/bsd/g16.profile

# 3. run g16 program
# run on AMD CPU
export PGI_FASTMATH_CPU=sandybridge
cd $PBS_O_WORKDIR

for inf in *.gjf
do
    echo $inf
    g16 $inf
    wait
    formchk ${inf%.gjf}.chk
done &> out.log

# Delete Temporary Files to Reduce Hard Disk Usage
rm -rf $HOME/.g16/scratch/*