velph.toml-[scheduler] section

velph.toml-[scheduler] section#

The generate commands, such as velph relax generate and velph phelel generate, write a job script _job.sh in the directory of each calculation. The job script is made from [scheduler] and [vasp.<input set>.scheduler] of velph.toml. This page gives all the rules by which it is made, so that the page can also be given to a large language model (LLM) to write scheduler_template (see Writing scheduler_template with an LLM).

How _job.sh is written#

For each calculation, a generate command writes _job.sh in the following steps.

  1. The settings of the calculation are the keys of [scheduler] and those of [vasp.<input set>.scheduler] of its input set. A key in [vasp.<input set>.scheduler] replaces the same key of [scheduler].

  2. The name of the calculation is appended to the value of job_name:

    Calculations

    job_name

    velph relax generate

    {job_name}-iter1, {job_name}-iter2, …

    Supercells of velph phelel generate, velph phonopy generate and velph phono3py generate

    {job_name}-000, {job_name}-001, …

    The other generate commands

    {job_name}

  3. Each key in braces in scheduler_template, such as {job_name}, is replaced by the value of the key. This is done by the format method of Python strings (see format string syntax).

  4. The result is written as _job.sh.

When velph.toml has no [scheduler], _job.sh is not written, also when [vasp.<input set>.scheduler] is given.

For example, velph relax generate with

[scheduler]
scheduler_template = '''#!/bin/bash
# key-{key}
# jobname: {job_name}
{myargument}
'''
key = "value"
job_name = "mycalc"
myargument = "sleep 10"

writes the following relax/iter1/_job.sh:

#!/bin/bash
# key-value
# jobname: mycalc-iter1
sleep 10

velph scheduler shows _job.sh of each input set without writing any file (see velph scheduler).

Keys#

  • scheduler_template : the template of _job.sh, a string. It is required.

  • job_name : the name of the job. The name of the calculation is appended to it.

  • Any other key can be given, with any name. Its value is a string, an integer, a float or a boolean. A key that scheduler_template does not have in braces is not used.

Note

scheduler_name of velph 0.14, which chose a job script of SGE or Slurm written in velph, is removed. A velph.toml of velph 0.15 or a template with scheduler_name is an error. In a velph.toml of velph 0.14, velph convert and the subcommands replace it by the scheduler_template that gives the same job script. See Job scripts of scheduler_name for this scheduler_template.

Writing scheduler_template#

Write scheduler_template as a multi-line literal string of TOML, between ''' and '''. The text between them is used as it is, except that the line break right after the first ''' is removed. Between """ and """, a backslash starts an escape sequence, and a backslash at the end of a line joins the line with the next one. For example, mpirun \ and vasp_std on two lines become mpirun vasp_std on one line.

To write { or } in _job.sh, write {{ or }} in scheduler_template. Job scripts often have braces, for example:

In the job script

In scheduler_template

${SLURM_NTASKS}

${{SLURM_NTASKS}}

awk '{print $1}'

awk '{{print $1}}'

f() { echo done; }

f() {{ echo done; }}

$SLURM_NTASKS without braces needs no change.

Errors#

A generate command stops with one of the following errors before it writes any file. velph scheduler shows these errors for each input set.

  • "<key>" used in the job script template is not given in [scheduler] or [vasp.<input set>.scheduler]. : scheduler_template has {<key>}, but the settings do not have <key>. When <key> is not meant as a key, for example print $1 of awk '{print $1}', write {{ and }} in place of its braces.

  • The job script template cannot be read: ... : scheduler_template has a single { or }, or {} or {0}. To write { or } in _job.sh, write {{ or }}.

  • "scheduler_template" has to be given in [scheduler] or [vasp.<input set>.scheduler]. : the settings of the calculation do not have scheduler_template.

The following errors are given when velph.toml is read:

  • "scheduler_name" is removed. and "custom_template" is removed. : these keys of earlier versions of velph cannot be given.

  • "scheduler_template" has to be a string : scheduler_template is not a string.

  • "<key>" has a table as value. : the value of a key is a table, which cannot be used.

[scheduler] in a template of velph init#

velph init writes [scheduler] in velph.toml only when its template has [scheduler], and it writes the [scheduler] of the template as it is. velph init has no default [scheduler]. Without [scheduler] in the template, velph.toml has no [scheduler], and the generate commands write no _job.sh. To write job scripts, give [scheduler] with scheduler_template in the template, or add it to velph.toml.

Writing scheduler_template with an LLM#

A job script that works on your computer can be converted to scheduler_template by an LLM. Give the LLM the text of this page and the job script, for example with the following request:

Write scheduler_template of the [scheduler] section of velph.toml from the job
script below, following the rules of the attached page. Replace the job name by
{job_name}, write "{{" or "}}" for "{" or "}" of the job script, and write the
template as a multi-line literal string of TOML.

(the job script)

Read the scheduler_template that the LLM writes, and check _job.sh with velph scheduler (see velph scheduler).

Examples#

Slurm#

[scheduler]
scheduler_template = '''#!/bin/bash
#SBATCH --job-name={job_name}
#SBATCH --partition={partition}
#SBATCH --ntasks={ntasks}
#SBATCH --time={walltime}
#SBATCH --output=%x-%j.out

module load intel-oneapi
mpirun -np ${{SLURM_NTASKS}} /usr/local/vasp/bin/vasp_std
'''
job_name = "PbTe"
partition = "short"
ntasks = 48
walltime = "12:00:00"

...
[vasp.phelel.scheduler]
partition = "long"
ntasks = 192
walltime = "48:00:00"

...
[vasp.phono3py.scheduler]
ntasks = 96

velph nac generate writes the following nac/_job.sh. ${{SLURM_NTASKS}} is written as ${SLURM_NTASKS}, which the shell replaces when the job runs.

#!/bin/bash
#SBATCH --job-name=PbTe
#SBATCH --partition=short
#SBATCH --ntasks=48
#SBATCH --time=12:00:00
#SBATCH --output=%x-%j.out

module load intel-oneapi
mpirun -np ${SLURM_NTASKS} /usr/local/vasp/bin/vasp_std

velph phelel generate writes the following phelel/disp-001/_job.sh, where partition, ntasks and walltime are those of [vasp.phelel.scheduler]. [vasp.phono3py.scheduler] replaces only ntasks.

#!/bin/bash
#SBATCH --job-name=PbTe-001
#SBATCH --partition=long
#SBATCH --ntasks=192
#SBATCH --time=48:00:00
#SBATCH --output=%x-%j.out

module load intel-oneapi
mpirun -np ${SLURM_NTASKS} /usr/local/vasp/bin/vasp_std

PBS#

[scheduler]
scheduler_template = '''#!/bin/bash
#PBS -N {job_name}
#PBS -q {queue}
#PBS -l select={nodes}:ncpus={ncpus}:mpiprocs={ncpus}
#PBS -l walltime={walltime}

cd ${{PBS_O_WORKDIR}}
module load intel-oneapi
mpirun /usr/local/vasp/bin/vasp_std
'''
job_name = "PbTe"
queue = "default"
nodes = 1
ncpus = 48
walltime = "12:00:00"

cd ${{PBS_O_WORKDIR}} is written as cd ${PBS_O_WORKDIR} in _job.sh.

SGE#

[scheduler]
scheduler_template = '''#!/bin/bash
#$ -N {job_name}
#$ -cwd
#$ -pe {pe} {slots}
#$ -l h_rt={walltime}

module load intel-oneapi
mpirun -np ${{NSLOTS}} /usr/local/vasp/bin/vasp_std
'''
job_name = "PbTe"
pe = "mpi"
slots = 48
walltime = "12:00:00"

${{NSLOTS}} is written as ${NSLOTS} in _job.sh.