Seissol first example to workflow

.gitignore

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 *.sw?
 
+.idea

.gitmodules

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-[submodule "seissol"]
-	path = seissol
+[submodule "submodules/seissol"]
+	path = submodules/seissol
 	url = https://github.com/ivotron/seissol

.travis.yml

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+---
+dist: xenial
+language: python
+python: 3.7
+services: docker
+install:
+- git clone https://github.com/systemslab/popper /tmp/popper
+- export PYTHONUNBUFFERED=1
+- pip install /tmp/popper/cli
+script: popper run

workflows/tpv33/README.md

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+# SeisSol TPV33 Benchmark
+
+This example workflow follows the [_A First Example_][tutorial] 
+tutorial from SeisSol's official documentation, which corresponds to 
+the [SCEC TPV33 benchmark][scec].
+
+## Workflow
+
+The workflow defined in [`main.workflow`](./main.workflow)) consists 
+of four actions:
+
+  * **`remove previous builds`**. Deletes any previously-compiled 
+    binaries to avoid any confusion while running the workflow.
+
+  * **`build`**: Compiles SeisSol and generates the executable. The 
+    build environment is defined in the accompanying 
+    [`actions/seissol`](./actions/seissol) action folder, specifically 
+    in the [`Dockerfile`](./actions/seissol/Dockerfile).
+
+  * **`download data and parameters`**: Downloads the data and 
+    parameter files required to execute the benchmark. These are saved 
+    in an `execution/` folder.
+
+  * **`execute`**: Runs the benchmark with the specified parameters:
+      * `OMP_NUM_THREADS`. Number of OpenMP threads to use.
+      * `MPI_NUM_PROCESSES`. Number of MPI processes to use.
+      * `SEISSOL_END_TIME`. Abort condition for the simulation (real 
+        number).
+
+[tutorial]: https://seissol.readthedocs.io/en/latest/a-first-example.html#a-first-example
+[scec]: http://scecdata.usc.edu/cvws/tpv33docs.html

workflows/tpv33/actions/seissol/Dockerfile

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+FROM ubuntu:disco
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt update && \
+    apt install -y \
+      curl git \
+      build-essential gfortran cmake \
+      libeigen3-dev \
+      libopenmpi-dev \
+      libhdf5-dev libhdf5-mpi-dev \
+      libparmetis-dev \
+      virtualenv && \
+    virtualenv -p python3 /scons && \
+    bash -c 'source /scons/bin/activate && pip install numpy>=1.12.0 lxml scons' && \
+    rm -rf /var/lib/apt/lists/*
+
+# install libxsmm
+RUN curl -LO https://github.com/hfp/libxsmm/archive/master.tar.gz && \
+    tar xvfz master.tar.gz && \
+    cd libxsmm-master && \
+    make generator && \
+    cp bin/libxsmm_gemm_generator /usr/bin && \
+    cd / && \
+    rm -rf libxsmm-master /var/lib/apt/lists/*
+
+ADD entrypoint.sh /
+
+ENTRYPOINT ["/entrypoint.sh"]

workflows/tpv33/actions/seissol/entrypoint.sh

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+#!/bin/bash
+set -e
+
+source /scons/bin/activate
+
+if [ -z "$SEISSOL_SRC_DIR" ]; then
+  echo "Expecting SEISSOL_SRC_DIR variable"
+  exit 1
+fi
+
+cd $SEISSOL_SRC_DIR
+
+scons "$@"

workflows/tpv33/main.workflow

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+workflow "tpv33" {
+  on = "push"
+  resolves = "execute"
+}
+
+action "remove previous builds" {
+  uses = "actions/bin/sh@master"
+  args = ["rm -f submodules/seissol/build/SeisSol_*"]
+}
+
+action "build" {
+  needs = "remove previous builds"
+  uses = "./workflows/tpv33/actions/seissol"
+  args = [
+   "compileMode=release",
+   "order=2",
+   "parallelization=hybrid",
+   "hdf5=yes",
+   "metis=yes",
+   "commThread=no",
+   "compiler=gcc",
+   "-j8",
+  ]
+  env = {
+    SEISSOL_SRC_DIR = "submodules/seissol"
+  }
+}
+
+action "download data and parameters"{
+  needs = "build"
+  uses = "./workflows/tpv33/actions/seissol"
+  runs = ["sh", "-c", "workflows/tpv33/scripts/download.sh"]
+  env = {
+    SEISSOL_SRC_DIR = "submodules/seissol"
+  }
+}
+
+action "execute"{
+  needs = "download data and parameters"
+  uses = "./workflows/tpv33/actions/seissol"
+  runs = ["sh", "-c","workflows/tpv33/scripts/execute.sh"]
+  env = {
+    SEISSOL_SRC_DIR = "submodules/seissol"
+    OMP_NUM_THREADS = 1
+    MPI_NUM_PROCESSES = 1
+    SEISSOL_END_TIME = 0.00001
+  }
+}

workflows/tpv33/scripts/download.sh

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+#!/usr/bin/env bash
+set -e
+
+if [ -z "$SEISSOL_SRC_DIR" ]; then
+  echo "Expecting SEISSOL_SRC_DIR variable"
+  exit 1
+fi
+
+mkdir -p "$GITHUB_WORKSPACE/workflows/tpv33/execution"
+
+cd "$GITHUB_WORKSPACE/workflows/tpv33/execution"
+
+curl -LO https://syncandshare.lrz.de/dl/fiEi52Xiwwqkf2sNpTrCHjhw/tpv33_gmsh.xdmf
+curl -LO https://syncandshare.lrz.de/dl/fi72mQiszp6vSs7qN8tdZJf9/tpv33_gmsh
+curl -LO https://github.com/SeisSol/Examples/archive/master.tar.gz
+
+tar xzf master.tar.gz
+cp Examples-master/tpv33/* .
+rm -rf Examples-master master.tar.gz
+
+echo "$GITHUB_WORKSPACE/$SEISSOL_SRC_DIR/Maple/" > DGPATH

workflows/tpv33/scripts/execute.sh

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+#!/usr/bin/env bash
+set -e
+
+if [ -z "$SEISSOL_SRC_DIR" ]; then
+  echo "Expecting SEISSOL_SRC_DIR variable"
+  exit 1
+fi
+if [ -z "$OMP_NUM_THREADS" ]; then
+  echo "No OMP_NUM_THREADS variable defined"
+  exit 1
+fi
+if [ -z "$MPI_NUM_PROCESSES" ]; then
+  echo "No MPI_NUM_ROCESSES variable defined"
+  exit
+fi
+if [ -z "$SEISSOL_END_TIME" ]; then
+  echo "No SEISSOL_END_TIME variable defined"
+  exit 1
+fi
+
+EXECUTION_DIR="$PWD/workflows/tpv33/execution/"
+
+# TODO: we assume that there's only one binary in the build/ folder. Instead, we 
+# can look for a SEISSOL_BIN variable and use that if defined; otherwise we can 
+# try to copy whatever binary is there but throw an error if there's more than 
+# one available
+SEISSOL_BIN="$(ls $GITHUB_WORKSPACE/$SEISSOL_SRC_DIR/build/SeisSol_*)"
+
+cp "$SEISSOL_BIN" "$EXECUTION_DIR"
+
+mkdir -p "$EXECUTION_DIR/output"
+
+# run
+cd "$EXECUTION_DIR"
+
+sed -i "s#EndTime = .*#EndTime = $SEISSOL_END_TIME#" parameters_tpv33_master.par
+
+mpirun \
+  --allow-run-as-root \
+  --oversubscribe \
+  -np "$MPI_NUM_PROCESSES" \
+  "$SEISSOL_BIN" \
+  parameters_tpv33_master.par