Provide compilation option for existing dumux installation (#702)

Author: Fujikawas

changelog-entries/702.md

@@ -0,0 +1 @@
+- Changed the run script of solvers with DuMux to compile the case before running, also accept given path to DuMux and adpater.

free-flow-over-porous-media/README.md

@@ -27,15 +27,13 @@ preCICE configuration (image generated using the [precice-config-visualizer](htt
 
 ## Available solvers
 
-Both the participants are computed using the simulation code [DuMu<sup>x</sup>](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/).
+Both the participants are computed using the simulation code [DuMux](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/).
 
 ## Solver setup
 
 To solve the flows with the DuMux framework, the necessary DUNE modules need to be downloaded and set up. This is done by running `sh setup-dumux.sh` in the tutorial folder.
 
-Note that if an existing installation of DUNE modules is detected in a default location, this may lead to problems in running the `setup-dumux.sh` script. The script suppresses the environment variable `DUNE_CONTROL_PATH`.
-
-To only recompile the participants, run `sh compile-dumux-cases.sh` in the tutorial folder.
+If an existing path, containing compiled DUNE modules, DuMux and DuMux-adapter, is to be used for compiling the solvers, the path can be specified by setting the arguments while running the script `run.sh` with `-l <path-to-DUNE-common>` in each solver folder. The environment variable `DUNE_CONTROL_PATH` is suppressed by the script. The `run.sh` scripts in the DuMux solver folders will first compile the solver if not already compiled, and then run the simulation.
 
 ## Running the simulation
 
@@ -55,6 +53,12 @@ cd porous-media-dumux
 ./run.sh
 ```
 
+This assumes a DuMux and DUNE modules installation in the case folder. You can specify the path to an existing DUNE installation with with `-l`:
+
+```bash
+./run.sh -l <path-to-DUNE-common>
+```
+
 Participants can be executed only in serial. Parallel execution is not supported. The case takes approximately two minutes to finish.
 
 ## Post-processing

free-flow-over-porous-media/compile-dumux-cases.sh

@@ -4,6 +4,43 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+
+usage() { echo "Usage: cmd [-l <path-to-DUNE-common>]" 1>&2; exit 1; }
+
+DUNE_COMMON_PATH_SET=
+DUNE_COMMON_PATH_ARG=
+
+while getopts ":l:" opt; do
+  case ${opt} in
+  l)
+    DUNE_COMMON_PATH_SET=1
+    DUNE_COMMON_PATH_ARG="$OPTARG"
+    ;;
+  *)
+    usage
+    ;;
+  esac
+done
+
+if [ ! -d "build-cmake" ]; then
+  echo "Solver not built. Building now..."
+  CASE_DIR=$(pwd)/..
+
+  if [ -z "$DUNE_COMMON_PATH_SET" ]; then
+    ../dune-common/bin/dunecontrol --opts=../dumux/cmake.opts --only=free_flow_dumux all
+  else
+    export DUNE_CONTROL_PATH=$DUNE_COMMON_PATH_ARG:$CASE_DIR
+    "$DUNE_COMMON_PATH_ARG"/dune-common/bin/dunecontrol --opts="$DUNE_COMMON_PATH_ARG"/dumux/cmake.opts --only=free_flow_dumux all
+  fi
+else
+  echo "build-cmake folder found."
+  cd build-cmake
+  make free_flow_dumux
+  cd ..
+fi
+# Move free_flow_dumux executable to the participant folder level
+mv build-cmake/solver-dumux/free_flow_dumux .
+
 ./free_flow_dumux params.input
 
 close_log

free-flow-over-porous-media/free-flow-dumux/run.sh

@@ -4,6 +4,43 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
+
+usage() { echo "Usage: cmd [-l <path-to-DUNE-common>]" 1>&2; exit 1; }
+
+DUNE_COMMON_PATH_SET=
+DUNE_COMMON_PATH_ARG=
+
+while getopts ":l:" opt; do
+  case ${opt} in
+  l)
+    DUNE_COMMON_PATH_SET=1
+    DUNE_COMMON_PATH_ARG="$OPTARG"
+    ;;
+  *)
+    usage
+    ;;
+  esac
+done
+
+if [ ! -d "build-cmake" ]; then
+  echo "Solver not built. Building now..."
+  CASE_DIR=$(pwd)/..
+
+  if [ -z "$DUNE_COMMON_PATH_SET" ]; then
+    ../dune-common/bin/dunecontrol --opts=../dumux/cmake.opts --only=porous_media_dumux all
+  else
+    export DUNE_CONTROL_PATH=$DUNE_COMMON_PATH_ARG:$CASE_DIR
+    "$DUNE_COMMON_PATH_ARG"/dune-common/bin/dunecontrol --opts="$DUNE_COMMON_PATH_ARG"/dumux/cmake.opts --only=porous_media_dumux all
+  fi
+else
+  echo "build-cmake folder found."
+  cd build-cmake
+  make porous_media_dumux
+  cd ..
+fi
+# Move porous_media_dumux executable to the participant folder level
+mv build-cmake/solver-dumux/porous_media_dumux .
+
 ./porous_media_dumux params.input
 
 close_log

free-flow-over-porous-media/porous-media-dumux/run.sh

@@ -31,5 +31,6 @@ DUNE_CONTROL_PATH=. python3 dumux/bin/installexternal.py spgrid
 # Re-build environment
 DUNE_CONTROL_PATH=. ./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all
 
-# Compile and move macro-dumux and micro-dumux executables to the participant folder level
-./compile-dumux-cases.sh
+# Move solver executables to the participant folder level
+mv free-flow-dumux/build-cmake/solver-dumux/free_flow_dumux free-flow-dumux/
+mv porous-media-dumux/build-cmake/solver-dumux/porous_media_dumux porous-media-dumux/

free-flow-over-porous-media/setup-dumux.sh

@@ -27,15 +27,15 @@ preCICE configuration (image generated using the [precice-config-visualizer](htt
 
 ## Available solvers and dependencies
 
-* Both the macro and micro simulations can be solved using the finite element library [Nutils](https://nutils.org/install.html) v7 or the simulation framework [DuMu<sup>x</sup>](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/).
+* Both the macro and micro simulations can be solved using the finite element library [Nutils](https://nutils.org/install.html) v7 or the simulation framework [DuMux](https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/).
 * While using Nutils, the macro simulation is written in Python, so it requires the [Python bindings of preCICE](https://precice.org/installation-bindings-python.html).
 * The [Micro Manager](https://precice.org/tooling-micro-manager-installation.html) controls all micro-simulations and facilitates coupling via preCICE. Use the [develop](https://github.com/precice/micro-manager/tree/develop) branch of the Micro Manager.
 
-### DuMu<sup>x</sup> setup
+### DuMux setup
 
-To solve either the macro or micro simulations with the DuMu<sup>x</sup> framework, the necessary DUNE modules need to be downloaded and set up. This is done by running `sh setup-dumux.sh` in the tutorial folder.
+To solve either the macro or micro simulations with the DuMux framework, the necessary DUNE modules need to be downloaded and set up. This is done by running `sh setup-dumux.sh` in the tutorial folder.
 
-Note that if an existing installation of DUNE modules is detected in a default location, this may lead to problems in running the `setup-dumux.sh` script. The environment variable `DUNE_CONTROL_PATH` is suppressed by the script.
+If an existing path, containing compiled DUNE modules, DuMux and DuMux-adapter, is to be used for compiling the solvers, the path can be specified by setting the arguments while running the script `run.sh` with `-l <path-to-DUNE-common>` in each solver folder. The environment variable `DUNE_CONTROL_PATH` is suppressed by the script. The `run.sh` scripts in the DuMux solver folders will first compile the solver if not already compiled, and then run the simulation.
 
 ## Running the simulation
 
@@ -55,7 +55,18 @@ cd micro-nutils
 ./run.sh -s
 ```
 
-If you want to use DuMu<sup>x</sup>, use `cd macro-dumux` instead of `cd macro-nutils` and/or `cd micro-dumux` instead of `cd micro-nutils`.
+If you want to use DuMux, use `cd macro-dumux` instead of `cd macro-nutils` and/or `cd micro-dumux` instead of `cd micro-nutils`. For example, to run the macro simulation with DuMux in serial (default), run:
+
+```bash
+cd macro-dumux
+./run.sh -s
+```
+
+This assumes a DuMux and DUNE modules installation in the case folder. You can specify the path to an existing DUNE installation with with `-l`:
+
+```bash
+./run.sh -s -l <path-to-DUNE-common>
+```
 
 ## Running the simulation in parallel
 
@@ -74,7 +85,7 @@ Running `micro-dumux` is much faster. A serial simulation takes approximately 2
 
 ## Post-processing
 
-Here are the results from Nutils-Nutils and DuMu<sup>x</sup>-DuMu<sup>x</sup> combination:
+Here are the results from Nutils-Nutils and DuMux-DuMux combination:
 
 <img class="img-responsive" src="images/tutorials-two-scale-heat-conduction-results.png" alt="Macro and micro data of macro-nutils - micro-nutils simulation" width=50% height=30%/>
 
@@ -88,4 +99,4 @@ The participant `macro-nutils` outputs `macro-*.vtk` files which can be viewed i
 
 The micro simulations themselves have a circular micro structure which is resolved in every time step. To output VTK files for each micro simulation, uncomment the `output()` function in the file `micro-nutils/micro.py`. The figure above shows the changing phase field used to represent the circular micro structure and the diffuse interface width.
 
-Similar to the output data files from simulation with Nutils, the `VTU` files from macro and micro solvers, that are written in DuMu<sup>x</sup>, could also be rendered and inspected with ParaView with the mentioned method.
+Similar to the output data files from simulation with Nutils, the `VTU` files from macro and micro solvers, that are written in DuMux, could also be rendered and inspected with ParaView with the mentioned method.

two-scale-heat-conduction/README.md

@@ -4,26 +4,63 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
-usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
+usage() { echo "Usage: cmd [-s] [-p n] [-l <path-to-DUNE-common>]" 1>&2; exit 1; }
 
-# Check if no input argument was provided
-if [ -z "$*" ] ; then
-  echo "No input argument provided. Macro solver is launched in serial"
-  ./macro_dumux params.input
-fi
+SERIAL_RUN=
+PARALLEL_RUN=
+RANK_COUNT=
+DUNE_COMMON_PATH_SET=
+DUNE_COMMON_PATH_ARG=
 
-while getopts ":sp" opt; do
+while getopts ":sp:l:" opt; do
   case ${opt} in
   s)
-    ./macro_dumux params.input
+    SERIAL_RUN=1
     ;;
   p)
-    mpiexec -n "$2" macro_dumux params.input
+    RANK_COUNT="$OPTARG"
+    PARALLEL_RUN=1
+    ;;
+  l)
+    DUNE_COMMON_PATH_SET=1
+    DUNE_COMMON_PATH_ARG="$OPTARG"
     ;;
   *)
     usage
     ;;
   esac
 done
 
+if [ ! -d "build-cmake" ]; then
+  echo "Solver not built. Building now..."
+  CASE_DIR=$(pwd)/..
+
+  if [ -z "$DUNE_COMMON_PATH_SET" ]; then
+    ../dune-common/bin/dunecontrol --opts=../dumux/cmake.opts --only=macro_dumux all
+  else
+    export DUNE_CONTROL_PATH=$DUNE_COMMON_PATH_ARG:$CASE_DIR
+    "$DUNE_COMMON_PATH_ARG"/dune-common/bin/dunecontrol --opts="$DUNE_COMMON_PATH_ARG"/dumux/cmake.opts --only=macro_dumux all
+  fi
+else
+  echo "build-cmake folder found."
+  cd build-cmake
+  make macro_dumux
+  cd ..
+fi
+# Move macro-dumux executable to the participant folder level
+mv ./build-cmake/appl/macro_dumux .
+
+if [ -n "$SERIAL_RUN" ] && [ -n "$PARALLEL_RUN" ]; then
+  echo "Cannot run both serial and parallel. Choose one option."
+  usage
+elif [ -z "$SERIAL_RUN" ] && [ -z "$PARALLEL_RUN" ]; then
+  echo "No run option provided. The macro solver is launched in serial."
+fi
+
+if [ -n "$PARALLEL_RUN" ]; then
+  mpiexec -n "$RANK_COUNT" macro_dumux params.input
+else
+  ./macro_dumux params.input
+fi
+
 close_log

two-scale-heat-conduction/compile-dumux-cases.sh

@@ -4,26 +4,63 @@ set -e -u
 . ../../tools/log.sh
 exec > >(tee --append "$LOGFILE") 2>&1
 
-usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
+usage() { echo "Usage: cmd [-s] [-p n] [-l <path-to-DUNE-common>]" 1>&2; exit 1; }
 
-# Check if no input argument was provided
-if [ -z "$*" ] ; then
-  echo "No input argument provided. Micro Manager is launched in serial"
-  micro-manager-precice micro-manager-config.json
-fi
+SERIAL_RUN=
+PARALLEL_RUN=
+RANK_COUNT=
+DUNE_COMMON_PATH_SET=
+DUNE_COMMON_PATH_ARG=
 
-while getopts ":sp" opt; do
+while getopts ":sp:l:" opt; do
   case ${opt} in
   s)
-    micro-manager-precice micro-manager-config.json
+    SERIAL_RUN=1
     ;;
   p)
-    mpiexec -n "$2" micro-manager-precice micro-manager-config.json
+    RANK_COUNT="$OPTARG"
+    PARALLEL_RUN=1
+    ;;
+  l)
+    DUNE_COMMON_PATH_SET=1
+    DUNE_COMMON_PATH_ARG="$OPTARG"
     ;;
   *)
     usage
     ;;
   esac
 done
 
+if [ ! -d "build-cmake" ]; then
+  echo "Solver not built. Building now..."
+  CASE_DIR=$(pwd)/..
+
+  if [ -z "$DUNE_COMMON_PATH_SET" ]; then
+      ../dune-common/bin/dunecontrol --opts=../dumux/cmake.opts --only=micro_sim all
+  else
+    export DUNE_CONTROL_PATH=$DUNE_COMMON_PATH_ARG:$CASE_DIR
+    "$DUNE_COMMON_PATH_ARG"/dune-common/bin/dunecontrol --opts="$DUNE_COMMON_PATH_ARG"/dumux/cmake.opts --only=micro_sim all
+  fi
+else
+  echo "build-cmake folder found."
+  cd build-cmake
+  make micro_sim
+  cd ..
+fi
+# Move micro_sim executable to the participant folder level
+mv ./build-cmake/appl/micro_sim*.so .
+
+if [ -n "$SERIAL_RUN" ] && [ -n "$PARALLEL_RUN" ]; then
+  echo "Cannot run both serial and parallel. Choose one option."
+  usage
+elif [ -z "$SERIAL_RUN" ] && [ -z "$PARALLEL_RUN" ]; then
+  echo "No run option provided. The macro solver is launched in serial."
+fi
+
+if [ -n "$PARALLEL_RUN" ]; then
+  mpiexec -n "$RANK_COUNT" micro-manager-precice micro-manager-config.json
+else
+  micro-manager-precice micro-manager-config.json
+fi
+
 close_log