Minimum description of the job script

Example of the job script

#!/bin/sh
#SBATCH -J  CO
#SBATCH -p  cmdinteractive
#SBATCH -N  1
#SBATCH -n  4

# Load the modules

module load intel_compiler/2020.4.304
module load intel_mpi/2020.4.304
module load intel_mkl/2020.4.304

# Set the executable of the STATE code

ln -fs ${HOME}/STATE/src/state/src/STATE

# Set the pseudopotential data

ln -fs ../gncpp/pot.C_pbe1
ln -fs ../gncpp/pot.O_pbe1

# Set the input/output files

INPUT_FILE=nfinp_scf
OUTPUT_FILE=nfout_scf

# Run!

ulimit -s unlimited

srun ./STATE < ${INPUT_FILE} > ${OUTPUT_FILE}

Header

#!/bin/sh
#SBATCH -J  CO
#SBATCH -p  cmdinteractive
#SBATCH -N  1
#SBATCH -n  4

1st line:

#!/bin/sh

Name of the shell used

2nd line:

#SBATCH -J  CO

Name of the job, which is shown when you use the squeue command

3rd line:

#SBATCH -p  cmdinteractive

Name of the partition (queue)

4th line:

#SBATCH -N  1

Number of nodes

5th line:

#SBATCH -n  4

Number of MPI processes

In the case OpenMPI (thread) parallelization needs to be activated, add the following (in this case, 2 thread parallelization will be performed):

#SBATCH -c  2

In this example, we use 4 cores with 1 node.

Note

Each node of ohtaka has 128 cores, and (number of MPI processes) times (number of OpenMPI processes) should be within the resource you request.

Body

#!/bin/sh
#SBATCH -J  CO
#SBATCH -p  cmdinteractive
#SBATCH -N  1
#SBATCH -n  4

# Load the modules

module load intel_compiler/2020.4.304
module load intel_mpi/2020.4.304
module load intel_mkl/2020.4.304

# Set the executable of the STATE code

ln -fs ${HOME}/state/src/STATE

# Set the pseudopotential data

ln -fs ../gncpp/pot.C_pbe1
ln -fs ../gncpp/pot.O_pbe1

# Set the input/output files

INPUT_FILE=nfinp_scf
OUTPUT_FILE=nfout_scf

# Run!

ulimit -s unlimited

srun ./STATE < ${INPUT_FILE} > ${OUTPUT_FILE}

Modules

# Load the modules

module load intel_compiler/2020.4.304
module load intel_mpi/2020.4.304
module load intel_mkl/2020.4.304

Please do not change them, unless you build STATE with different modules.

STATE executable

# Set the executable of the STATE code

ln -fs ${HOME}/STATE/src/state/src/STATE

Please do not change this line, unless you don’t change the name of the STATE executable

Pseudopotentials

# Set the pseudopotential data

ln -fs ../gncpp/pot.C_pbe1
ln -fs ../gncpp/pot.O_pbe1

Please choose all the pseudopotentials you need to use and write here (change C_pbe1 and O_pbe1, and add more lines if necessary)

Input/output files

# Set the input/output files

INPUT_FILE=nfinp_scf
OUTPUT_FILE=nfout_scf

Please change the input (nfinp_scf) and output (nfout_scf) file names as necessary.

You don’t have to change the following lines in the job script.

Minimum list of submission commands

Submission of a job

$ sbatch [job script]

Check the job status

$ squeue

Cancel the job

$ scancel [Job ID]

Use squeue to know your JOB ID

Available resources on ohtaka

Partition (queue)	Min. # of nodes	Max. # of nodes	Max. hours
cpdinteractive	1	8	24 hours
cmd1cpu	1	1	24 hours
cmd16cpu	2	16	24 hours

Warning

Max. number of nodes allocated for the CMD workshop is 16. If you used too may cores, other users in the course have to wait until their reqired number nodes are available. Please choose the number of cores with care. In the begininng, it is better to play within one node (128 cores) to get accustomed to use many cores/nodes.