flmore's blog
0%

宋老师课题组队列系统任务提交脚本

Posted on Edited on In
本文记录了宋老师课题组服务器集群的任务提交脚本，方便大家取用和更新。

VASP提交脚本

在任务目录新建提交脚本

1
vim job.pbs

粘贴以下内容：

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
#!/bin/bash
#===========================================================#
# Job submission script for VASP                            #
# Created by flmore on February 12, 2023                    #
# update url: https://flmore.github.io/2023/33c11a8e.html   #
#===========================================================#
# 1. PBS job control

#PBS -S /bin/bash
#PBS -N vasp
#PBS -l nodes=1:ppn=24 # We can also manually set the specified node to calculate.
#PBS -q batch
#PBS -l walltime=30:00:00
#PBS -m e
#PBS -M your-email-name@example.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
#export MKL_DEBUG_CPU_TYPE=5
#export MKL_CBWR=AVX2
#export I_MPI_PIN_DOMAIN=numa

# 3. Select the appropriate vasp version (need test for diff calc!)
#VASP_EXEC=vasp_gam-5.4.4_O3_avx512
#VASP_EXEC=vasp_gam-5.4.4_avx2
#VASP_EXEC=vasp_gam-5.4.4_avx512
#VASP_EXEC=vasp_gam-5.4.4_vtst_O3_avx512
#VASP_EXEC=vasp_gam-5.4.4_vtst_avx2
#VASP_EXEC=vasp_gam-5.4.4_vtst_avx512
#VASP_EXEC=vasp_gam-6.3.2_O3_avx512
#VASP_EXEC=vasp_gam-6.3.2_avx2
#VASP_EXEC=vasp_gam-6.3.2_avx512
#VASP_EXEC=vasp_ncl-5.4.4_O3_avx512
#VASP_EXEC=vasp_ncl-5.4.4_avx2
#VASP_EXEC=vasp_ncl-5.4.4_avx512
#VASP_EXEC=vasp_ncl-5.4.4_vtst_O3_avx512
#VASP_EXEC=vasp_ncl-5.4.4_vtst_avx2
#VASP_EXEC=vasp_ncl-5.4.4_vtst_avx512
#VASP_EXEC=vasp_ncl-6.3.2_O3_avx512
#VASP_EXEC=vasp_ncl-6.3.2_avx2
#VASP_EXEC=vasp_ncl-6.3.2_avx512
#VASP_EXEC=vasp_std-5.4.4_O3_avx512
VASP_EXEC=vasp_std-5.4.4_avx2
#VASP_EXEC=vasp_std-5.4.4_avx512
#VASP_EXEC=vasp_std-5.4.4_vtst_O3_avx512
#VASP_EXEC=vasp_std-5.4.4_vtst_avx2
#VASP_EXEC=vasp_std-5.4.4_vtst_avx512
#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

# 4. run program
NP=`cat $PBS_NODEFILE | wc -l`
cd $PBS_O_WORKDIR
#SINGPATH=/opt/sin-vasp.6.3.2-avx2.sif
SINGPATH=/opt/vasp/vasp-sin-ed-combine-v0.0.2.sif
mpirun -np $NP singularity exec $SINGPATH $VASP_EXEC &> out.log

CP2K提交脚本

提交方式

在任务目录新建提交脚本

1
vim job.pbs

粘贴以下内容：

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
#!/bin/bash
#===========================================================#
# Job submission script for CP2K                            #
# Created by flmore on February 12, 2022                     #
# update url: https://flmore.github.io/2023/33c11a8e.html   #
#===========================================================#
# 1. PBS job control

#PBS -S /bin/bash
#PBS -N cp2k
#PBS -l nodes=1:ppn=24
#PBS -q batch
#PBS -l walltime=30:00:00
#PBS -m e
#PBS -M your-email-name@example.com # A reminder message will be sent to this mailbox when the task is over.

# 2. load  environment variable
export MPI_HOME=/opt/mpich/mpich-3.4.3
export PATH=$MPI_HOME/bin:$PATH
export PATH=$PATH:$MPI_HOME/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI_HOME/lib
export MANPATN=$MANPATH:$MPI_HOME/man

export PATH=/usr/local/bin:$PATH

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


#SINGPATH=/opt/cp2k/cp2k_v2022.1_psmp_avx2.sif # run for mn1,cn[01-15]
SINGPATH=/opt/cp2k/cp2k_v2022.1_psmp_avx512.sif # run for cn[16-20]
#SINGPATH=/opt/cp2k/cp2k_v2022.1_psmp_avx2_plumed-add-opes.sif # run for mn1,cn[01-15]
#SINGPATH=/opt/cp2k/cp2k_v2022.1_psmp_avx512_plumed-add-opes.sif # run for cn[16-20]
#singularity exec -B ${PWD}:/mnt -H /mnt ${SINGPATH} mpirun -np 24 cp2k.psmp inp | tee ${2:-out.log}
mpirun -np $NP singularity exec -B ${PWD}:/mnt -H /mnt ${SINGPATH} cp2k.psmp inp | tee ${2:-out.log}

版本说明

每个版本的文件名包含了cp2k的版本信息、适用于在支持哪种指令集的CPU上运行和额外添加的功能。

如cp2k_v2022.1_psmp_avx512_plumed-add-opes.sif 含义为：

  • cp2k编译的版本是2022.1，psmp版；
  • 仅能在支持avx512指令集的CPU上运行；
  • 开启了 plumed 中的 opes模块。

Gaussian 提交脚本

待更新

Gromacs 提交脚本

待更新