Saving LAMMPS Results

This example LAMMPS CPU workflow uses StageoutScript to save results to a persistent volume. If you wanted to, for example, modify the workflow template to save your results to AWS S3 instead of the persistent volume, you could copy and edit the preinstalled application as described in the workflow catalog documentation. Then you could make a small change to the workflow template like so:

version: v1
volumes:
  scratch:
    reference: {{ .ScratchVolume }}
    ingress:
      - destination:
          uri: file://stagein.sh
        source:
          uri: {{ .ExperimentUrl }}/{{ .StageinScript }}
{{- if .StageoutScript }}
      - destination:
          uri: file://stageout.sh
        source:
          uri: {{ .ExperimentUrl }}/{{ .StageoutScript }}
    egress:
      - source:
          uri: file://{{ .RunName }}.tar.gz
        destination:
          uri: s3://{{.OutputPath}}/{{ .RunName }}.tar.gz
          secret: {{ .S3Secret }}
{{- end }}
...snip...
{{- if .StageoutScript }}
  stageout:
    command:
      - /bin/sh
      - stageout.sh
      - {{.RunName}}
    cwd: /scratch
    image:
      uri: docker://alpine:latest
    mounts:
      scratch:
        location: /scratch
    name: stageout
    requires:
    - run-lammps
    resource:
      cpu:
        cores: 1
      memory:
        size: 512MIB
{{- end }}

Note that we added an egress section which requires us to add a S3Secret parameter and we removed a persistent data volume.

Then you would provide a different stageout script like so to create the tar archive used in egress:

#! /bin/sh
set -ex

run="${1}"

if [ -d  "${run}" ] ; then
    tar -czf "${run}.tar.gz" "${run}"
else
    echo "did not save results to persistent store"
fi