diff --git a/changelog-entries/702.md b/changelog-entries/702.md new file mode 100644 index 000000000..a516e714c --- /dev/null +++ b/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. \ No newline at end of file diff --git a/free-flow-over-porous-media/README.md b/free-flow-over-porous-media/README.md index cb1de8b47..ca5246ae2 100644 --- a/free-flow-over-porous-media/README.md +++ b/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 [DuMux](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 ` 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 +``` + Participants can be executed only in serial. Parallel execution is not supported. The case takes approximately two minutes to finish. ## Post-processing diff --git a/free-flow-over-porous-media/compile-dumux-cases.sh b/free-flow-over-porous-media/compile-dumux-cases.sh deleted file mode 100755 index c964ef4e4..000000000 --- a/free-flow-over-porous-media/compile-dumux-cases.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env sh -set -e -u - -# To compile free-flow-dumux and porous-media-dumux from scratch or recompile them after changes -./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=free_flow_dumux all -./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=porous_media_dumux all - -# Alternatively, you can manually recompile free-flow-dumux and porous-media-dumux when the `build-cmake` folder is present by uncommenting the following lines: -# ( -# cd free-flow-dumux/build-cmake/solver-dumux -# make free_flow_dumux -# ) - -# ( -# cd porous-media-dumux/build-cmake/solver-dumux -# make porous_media_dumux -# ) - -# Move free-flow-dumux and porous-media-dumux 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/ diff --git a/free-flow-over-porous-media/free-flow-dumux/run.sh b/free-flow-over-porous-media/free-flow-dumux/run.sh index d151945b6..82752f6cd 100755 --- a/free-flow-over-porous-media/free-flow-dumux/run.sh +++ b/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 ]" 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 \ No newline at end of file diff --git a/free-flow-over-porous-media/porous-media-dumux/run.sh b/free-flow-over-porous-media/porous-media-dumux/run.sh index 1ccbdb99d..64199d604 100755 --- a/free-flow-over-porous-media/porous-media-dumux/run.sh +++ b/free-flow-over-porous-media/porous-media-dumux/run.sh @@ -4,6 +4,43 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 + +usage() { echo "Usage: cmd [-l ]" 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 \ No newline at end of file diff --git a/free-flow-over-porous-media/setup-dumux.sh b/free-flow-over-porous-media/setup-dumux.sh index 56fc29fc6..ef1b8a19d 100755 --- a/free-flow-over-porous-media/setup-dumux.sh +++ b/free-flow-over-porous-media/setup-dumux.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/ diff --git a/two-scale-heat-conduction/README.md b/two-scale-heat-conduction/README.md index 782fec807..38c1602bb 100644 --- a/two-scale-heat-conduction/README.md +++ b/two-scale-heat-conduction/README.md @@ -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 [DuMux](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. -### DuMux setup +### DuMux setup -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. +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 ` 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 DuMux, 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 +``` ## 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 DuMux-DuMux combination: +Here are the results from Nutils-Nutils and DuMux-DuMux combination: Macro and micro data of macro-nutils - micro-nutils simulation @@ -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 DuMux, 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. diff --git a/two-scale-heat-conduction/compile-dumux-cases.sh b/two-scale-heat-conduction/compile-dumux-cases.sh deleted file mode 100755 index 390b1c437..000000000 --- a/two-scale-heat-conduction/compile-dumux-cases.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env sh -set -e -u - -# To compile macro-dumux and micro-dumux from scratch or recompile them after changes -./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=macro_dumux all -./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts --only=micro_sim all - -# Alternatively, you can manually recompile macro-dumux and micro-dumux when the `build-cmake` folder is present by uncommenting the following lines: -# ( -# cd macro-dumux/build-cmake/appl -# make macro_dumux -# ) -# ( -# cd micro-dumux/build-cmake/appl -# make micro_sim -# ) - -# Move macro-dumux and micro-dumux executables to the participant folder level -mv macro-dumux/build-cmake/appl/macro_dumux macro-dumux/ -mv micro-dumux/build-cmake/appl/micro_sim.cpython-*.so micro-dumux/ diff --git a/two-scale-heat-conduction/macro-dumux/run.sh b/two-scale-heat-conduction/macro-dumux/run.sh index 5ec63c7d2..87df2d2b3 100755 --- a/two-scale-heat-conduction/macro-dumux/run.sh +++ b/two-scale-heat-conduction/macro-dumux/run.sh @@ -4,21 +4,26 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; } +usage() { echo "Usage: cmd [-s] [-p n] [-l ]" 1>&2; exit 1; } -# Check if no input argument was provided -if [ -z "$*" ] ; 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="$OPTARG" ;; *) usage @@ -26,4 +31,36 @@ while getopts ":sp" opt; do esac done +if [ ! -d "build-cmake" ]; then + echo "Solver not built. Building now..." + CASE_DIR=$(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 "$RANK_COUNT" macro_dumux params.input +else + ./macro_dumux params.input +fi + close_log diff --git a/two-scale-heat-conduction/micro-dumux/run.sh b/two-scale-heat-conduction/micro-dumux/run.sh index 1f0db55aa..ac4d117cd 100755 --- a/two-scale-heat-conduction/micro-dumux/run.sh +++ b/two-scale-heat-conduction/micro-dumux/run.sh @@ -4,21 +4,26 @@ set -e -u . ../../tools/log.sh exec > >(tee --append "$LOGFILE") 2>&1 -usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; } +usage() { echo "Usage: cmd [-s] [-p n] [-l ]" 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="$OPTARG" ;; *) usage @@ -26,4 +31,36 @@ while getopts ":sp" opt; do esac done +if [ ! -d "build-cmake" ]; then + echo "Solver not built. Building now..." + CASE_DIR=$(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 diff --git a/two-scale-heat-conduction/setup-dumux.sh b/two-scale-heat-conduction/setup-dumux.sh index bea25a74c..150d5f0ae 100755 --- a/two-scale-heat-conduction/setup-dumux.sh +++ b/two-scale-heat-conduction/setup-dumux.sh @@ -34,4 +34,5 @@ DUNE_CONTROL_PATH=. python3 dumux/bin/installexternal.py spgrid 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 +mv macro-dumux/build-cmake/appl/macro_dumux macro-dumux/ +mv micro-dumux/build-cmake/appl/micro_sim*.so micro-dumux/