Code Examples

Different Ways to Style & Author Code

Inline Code

⚠️ Not documented yet.

Code Block

Syntax

Correct

```syntax
ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBN+Mh3U/3We4VYtV1QmWUFIzFLTUeegl1Ao5/QGtCRGAZn8bxX9KlCrrWISIjSYAwCajIEGSPEZwPNMBoK8XD8Q= ylo@klar
```


ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBN+Mh3U/3We4VYtV1QmWUFIzFLTUeegl1Ao5/QGtCRGAZn8bxX9KlCrrWISIjSYAwCajIEGSPEZwPNMBoK8XD8Q= ylo@klar

Command Line

Preferred

```cmd-line
module load kitten
```


module load kitten
Pros & Cons
  • Pro: Easy to write, maintain, and teach.
  • Pro: Follows the WHATWG standard example.
  • Pro: Can have syntax highlighting.
  • Con: Can not add internal markup (e.g. <code>something <strong>bold</strong></code>).

Avoided

<pre class="cmd-line"><code>module <strong>load <em>kitten</em></strong></code></pre>


module load kitten

Pros & Cons
  • Pro: Follows the WHATWG standard example.
  • Hmm: Can
    • either use internal markup (e.g. <code>something <strong>bold</strong></code>) (current setup)
    • or syntax highlighting (if developer changes configuration).
  • Con: Not easy to write, maintain, and teach.

Deprecated

<pre class="cmd-line">module <strong>load <em>kitten</em></strong></pre>


module load kitten

Pros & Cons
  • Pro: Can add internal markup (e.g. <code>something <strong>bold</strong></code>).
  • Con: Does not follow the WHATWG standard example.
  • Con: Can not have syntax highlighting (without caveats and overhead).

Job Script

Preferred

```job-script
#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module load gromacs/2022.1

ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
```


#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module load gromacs/2022.1

ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log
Pros & Cons
  • Pro: Easy to write, maintain, and teach.
  • Pro: Follows the WHATWG standard example.
  • Pro: Can have syntax highlighting.
  • Con: Can not add internal markup (e.g. <code>something <strong>bold</strong></code>).

Avoided

<pre class="job-script">
<code>#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module <strong>load <em>gromacs/2022.1</em></strong>

ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log</code></pre>


#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module load gromacs/2022.1
 
ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log

Pros & Cons
  • Pro: Follows the WHATWG standard example.
  • Hmm: Can
    • either use internal markup (e.g. <code>something <strong>bold</strong></code>) (current setup)
    • or syntax highlighting (if developer changes configuration).
  • Con: Not easy to write, maintain, and teach.

Deprecated

<pre class="job-script">#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module <strong>load <em>gromacs/2022.1</em></strong>

ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log</pre>


#!/bin/bash
#SBATCH -J myjob              # job name
#SBATCH -e myjob.%j.err       # error file name
#SBATCH -o myjob.%j.out       # output file name
#SBATCH -N 2                  # request 2 nodes
#SBATCH -n 96                 # request 2x48=96 MPI tasks
#SBATCH -p skx-normal         # designate queue
#SBATCH -t 24:00:00           # designate max run time
#SBATCH -A myproject          # charge job to myproject
module load gromacs/2022.1
 
ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log

Pros & Cons
  • Pro: Can add internal markup (e.g. <code>something <strong>bold</strong></code>).
  • Con: Does not follow the WHATWG standard example.
  • Con: Can not have syntax highlighting (without caveats and overhead).

Syntax Highlighting Reference

Syntax
Python-Markdown fenced_code_blocks
Python-Markdown code_hilite or PyMdown Extensions: Highlight (which extension is used is unclear)
Languages
Highlight.js: Supported Languages
Themes
Highlight.js: Demo

Examples

plaintext 

    #!/bin/bash
    #SBATCH -J myjob              # job name
    #SBATCH -e myjob.%j.err       # error file name
    #SBATCH -o myjob.%j.out       # output file name
    #SBATCH -N 2                  # request 2 nodes
    #SBATCH -n 96                 # request 2x48=96 MPI tasks
    #SBATCH -p skx-normal         # designate queue
    #SBATCH -t 24:00:00           # designate max run time
    #SBATCH -A myproject          # charge job to myproject
    module load gromacs/2022.1

    ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log

bash 

    #!/bin/bash
    #SBATCH -J myjob              # job name
    #SBATCH -e myjob.%j.err       # error file name
    #SBATCH -o myjob.%j.out       # output file name
    #SBATCH -N 2                  # request 2 nodes
    #SBATCH -n 96                 # request 2x48=96 MPI tasks
    #SBATCH -p skx-normal         # designate queue
    #SBATCH -t 24:00:00           # designate max run time
    #SBATCH -A myproject          # charge job to myproject
    module load gromacs/2022.1

    ibrun gmx_mpi mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log

json 

{
    "email": "user@gmail.com",
    "pw": "pass12345"
}

python 

import sys
!{sys.executable} -m pip install click

import click