.. _instruction_ohtaka:

:orphan:

Minimum description of the job script
=====================================

Example of the job script

.. code:: bash

  #!/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
------

.. code:: bash

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

* 1st line:

.. code:: bash

  #!/bin/sh

Name of the shell used

* 2nd line:

.. code:: bash

  #SBATCH -J  CO

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

* 3rd line:

.. code:: bash

  #SBATCH -p  cmdinteractive

Name of the partition (queue)

* 4th line:

.. code:: bash

  #SBATCH -N  1

Number of nodes 

* 5th line:

.. code:: bash

  #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):

.. code:: bash

  #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
----

.. code:: bash

  #!/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

.. code::

  # 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

.. code::

  # 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

.. code::

  # 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

.. code::

  # 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

.. code::

  $ sbatch [job script]

* Check the job status

.. code::

  $ squeue

* Cancel the job

.. code::

  $ 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.