Application management

application: v2

# The name of the application in UCloud
name: native-gromacs  

# The version of the application in UCloud. Should generally match the version
# specified in the software section.
version: 2021.5       

software:
  type: Native

features:
  multiNode: true # NOTE: Without this, you will not be able to select multiple nodes

parameters:
  # The most important parameter is the Workflow parameter added below. But for
  # now, we will add an input directory parameter called "dir" which will be 
  # consumed by the workflow below.

  dir:
    type: Directory
    title: "Input directory"
    optional: false
    description: "This is an input directory used by the workflow"

  wf:
    type: Workflow
    optional: false
    title: "Workflow"
    description: |
      Change this workflow to customize what the batch script should do.

    # This is a Jinja2 template presented to the end-user and can be changed 
    # by them. Remember, that these files are service-provider agnostic and 
    # should not contain information specific to any service-provider. The 
    # service-provider is capable of configuring what happens at various 
    # points. For example the {- systemLoad -} and {- applicationLoad -} 
    # commands below are configured by the service-provider to actually load 
    # the software onto the machine.

    job: |
      {#
          
      This script is submitted to Slurm via the sbatch command.
          
      The following sbatch directives are automatically applied based on job parameters:
          
      --account=...           --partition=...           --qos=...
      --constraint=...        --output=...              --error=...
      --time=...              --cpus-per-task=...-      --gpus-per-task=...
      --mem=...               --nodes=...               --job-name=...
      --chdir=...

      Directives can be overwritten via the following method: 
      {{ sbatch("chdir", "/tmp/new/directory") }}
            
      #}
      
      {# Sbatch directives start - Change as required #}
        {{ sbatch("cpus-per-task", 4) }}
        {{ sbatch("ntasks-per-node", ucloud.machine.cpu / 4) }}
        {{ sbatch("ntasks", (ucloud.machine.nodes * ucloud.machine.cpu) / 4) }}
      {# Sbatch directives end #}
      
      {# Preambles start - Avoid touching these unless required. #}
        {- systemLoad -}
        {- applicationLoad -}
      {# Preambles end #}
    
      {# ==================================================================== #}
      {# Start the job - change as required                                                                              #}
      {# ==================================================================== #}
    
      {# NOTE: the data input parameter is bound to the Jinja2 variable of the same name. #} 
      {# This value is automatically escaped. #}

      cd {{ dir }}
      CMD=${CMD:=gmx_mpi}
      
      set -x
      set -e

      {# NOTE: srun() will expand to the correct invocation (configurable by #}
      {# service-provider) of srun in a given context #}
      {{ srun() }} $CMD pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce
      {{ srun() }} $CMD editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c \
          -d 1.0 -bt cubic
      {{ srun() }} $CMD solvate -cp 1AKI_newbox.gro -cs spc216.gro \
          -o 1AKI_solv.gro -p topol.top
      {{ srun() }} $CMD grompp -f ions.mdp -c 1AKI_solv.gro  -p topol.top -o ions.tpr
      {{ srun() }} $CMD genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top \
          -pname NA -nname CL -neutral
      {{ srun() }} $CMD grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top \
          -o em.tpr
      {{ srun() }} $CMD mdrun -v -deffnm em -nt 32
      {{ srun() }} $CMD grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top \
          -o nvt.tpr
      {{ srun() }} $CMD mdrun -v -deffnm nvt -nt 32
      {{ srun() }} $CMD grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt \
          -p topol.top -o npt.tpr
      {{ srun() }} $CMD mdrun -v -deffnm npt
      {{ srun() }} $CMD grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top \
          -o md_0_1.tpr
      {{ srun() }} $CMD mdrun -v -deffnm md_0_1
      {{ srun() }} $CMD trjconv -s md_0_1.tpr -f md_0_1.xtc \
          -o md_0_1_noPBC.xtc -pbc mol -center
      {{ srun() }} $CMD rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns
      {{ srun() }} $CMD rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_xtal.xvg -tu ns

      {# ==================================================================== #}
      {# End of job                                                                                                      #}
      {# ==================================================================== #}
      
      {# Postambles start - Avoid touching these unless required. #}
        {- applicationUnload -}
        {- systemUnload -}
      {# Postambles end #}

    # This is a README visible to the user before they launch the application.
    readme: |
      This is an example workflow using GROMACS.

      ### Some GROMACS Basics

      Rerum ut eos earum neque. Velit molestias illum consectetur blanditiis 
      quis veritatis officiis cupiditate. Ut quis in consequuntur 
      necessitatibus unde.
      
      ```
      gmx help (module)
      ```

      Commodi nisi non earum cupiditate. Sint ut repudiandae sed provident vel 
      magnam tempora delectus. Consequatur vero sed perspiciatis ut nihil ut. 
      Eligendi quam nulla similique reprehenderit eveniet qui. In nisi dolorum
      iure fuga ipsam velit nihil repellat.

      ```
      gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
      ```

# Keep this empty for now. Will become optional later.
invocation: ""

application: v2 # Required to signify version used for the application definition

name: example
version: v1.32

parameters:
  count:
    type: Integer
    title: "An optional counter"
    description: >
      This is an optional counter which will be bound to the environment variable
      called `COUNT`.
  a_flag:
    type: Boolean
    title: "An optional flag"
    description: >
      This is an optional flag. If turned on, it will produce `--flag` if it is
      not turned on (the default) then it will not produce any arguments.
  input:
    type: File
    optional: false
    title: "Example input file"
    description: >
      This is an example input file. It was made mandatory by setting
      `optional: false`
  output:
    type: Directory
    optional: false
    title: "Output directory"
    description: >
      This is a directory used for output.

software:
  type: Native

environment:
  COUNT: "{{ count }}"

invocation: |
  example-exe \
    --input {{ input }} \
    {{ output | option("--out") }} \
    {{ a_flag | flag("--flag") }}

application: v2

name: minimal
version: v1.32

software:
  type: Native

invocation: |
  echo "Hello World!"