Change to new wf format and required modifications

.travis.yml

@@ -7,4 +7,4 @@ install:
 - git clone https://github.com/systemslab/popper /tmp/popper
 - export PYTHONUNBUFFERED=1
 - pip install /tmp/popper/cli
-script: popper run
+script: popper run -f workflows/containerized/wf.yml

workflows/containerized/conf_host.yml

@@ -0,0 +1,7 @@
+engine:
+  name: docker
+  options:
+    privileged: True
+
+resource_manager:
+  name: host

workflows/containerized/conf_slurm.yml

@@ -0,0 +1,7 @@
+engine:
+  name: docker
+  options:
+    privileged: True
+
+resource_manager:
+  name: slurm

workflows/containerized/scripts/build.sh

@@ -1,6 +1,8 @@
 #!/bin/bash
 set -e
 
+export GITHUB_WORKSPACE=$(pwd)
+
 if [ ! -d "./submodules/pEVSL" ]; then
   echo "Expecting ./submodules/pEVSL/ folder"
   exit 1

workflows/containerized/scripts/run.sh

@@ -11,6 +11,7 @@ set -e
 #SBATCH --time=2:00:00
 #SBATCH -A TG-EAR170019
 
+export GITHUB_WORKSPACE=$(pwd)
 
 if [ -z "$MPI_NUM_PROCESSES" ]; then
   echo "No MPI_NUM_ROCESSES variable defined"

workflows/containerized/scripts/test.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+set -e
+
+cd ./submodules/pEVSL/TESTS/Lap/
+mpirun --allow-run-as-root -np 1 ./LapPLanN.ex -n 400 ./LapPLanN.ex -nx 20 -ny 20 -nz 20 -nslices 5 -a 0.6 -b 1.2

workflows/containerized/scripts/validate.sh

@@ -1,5 +1,8 @@
 #!/usr/bin/env bash
 set -e
+
+export GITHUB_WORKSPACE=$(pwd)
+
 cat $GITHUB_WORKSPACE/workflows/containerized/normalmodes.log | grep "relative err. " > temp.log
 
 while read p; do

workflows/containerized/wf.yml

@@ -0,0 +1,28 @@
+version: 1
+steps:
+- id: build
+  uses: ./workflows/containerized/actions/normalmodes
+  runs: ./workflows/containerized/scripts/build.sh
+  env:
+    PEVSL_MAKEFILE_IN: ./workflows/containerized/makeconf/pEVSL_mkl.in
+    NORMALMODES_MAKEFILE_IN: ./workflows/containerized/makeconf/NormalModes_mkl.in
+    NUM_BUILD_JOBS: 1
+
+- id: test
+  uses: ./workflows/containerized/actions/normalmodes
+  runs: ./workflows/containerized/scripts/test.sh
+
+- id: run
+  uses: ./workflows/containerized/actions/normalmodes
+  runs: ./workflows/containerized/scripts/run.sh
+  env:
+    MPI_NUM_PROCESSES: 1
+    INPUT_DIR: submodules/NormalModes/demos/
+
+- id: validate
+  uses: popperized/bin/sh@master
+  runs: ./workflows/containerized/scripts/validate.sh
+
+- id: generate vtk
+  uses: docker://popperized/octave:4.4
+  args: ./workflows/containerized/scripts/visualCmain.m