Merge branch 'DataExplorerContainer' into 'master'

Simplified Data Explorer container

See merge request ogs/ogs!3751

Applications/ApplicationsLib/CMakeLists.txt

@@ -7,17 +7,25 @@ ogs_add_library(ApplicationsLib ${LIB_SOURCES})
 
 target_link_libraries(
     ApplicationsLib
-    PUBLIC BaseLib GeoLib NumLib Processes
+    PUBLIC BaseLib GeoLib NumLib
     PRIVATE CMakeInfoLib
             MathLib
             MeshLib
             MeshGeoToolsLib
-            ParameterLib
-            ProcessLib
             $<$<BOOL:${OGS_USE_PYTHON}>:pybind11::pybind11>
             $<$<BOOL:${OGS_USE_PETSC}>:petsc>
 )
 
+if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
+    target_link_libraries(
+        ApplicationsLib
+        PUBLIC Processes
+        PRIVATE ParameterLib ProcessLib
+    )
+elseif(OGS_BUILD_GUI)
+    target_link_libraries(ApplicationsLib PRIVATE nlohmann_json)
+endif()
+
 if(OGS_USE_LIS)
     target_include_directories(ApplicationsLib PUBLIC ${LIS_INCLUDE_DIR})
 endif()

scripts/ci/jobs/container.yml

@@ -7,7 +7,7 @@ container:
     - if: '$CI_COMMIT_BRANCH == "master"'
     - if: $CI_COMMIT_TAG
     - changes:
-      - scripts/ci/jobs/container.yml
+        - scripts/ci/jobs/container.yml
     - if: $CI_COMMIT_BRANCH =~ /^v[0-9]\.[0-9]\.[0-9]/
     - when: manual
       allow_failure: true
@@ -28,16 +28,16 @@ container:
       --cvode --ccache
       --cmake_args ' -DOGS_CPU_ARCHITECTURE=sandybridge -DOGS_BUILD_TESTING=OFF'
       --base_image 'centos:8' --ompi 4.0.5 --mpi_benchmarks
+    - |
+      for sif in _out/images/*.sif; do
+        singularity exec $sif ogs --version
+      done
     - >
       poetry run ogscm compiler.py ogs.py -B -C -R --ogs ../..
       --build_args ' --progress=plain'
       --cvode --ccache
-      --cmake_args ' -DOGS_CPU_ARCHITECTURE=sandybridge -DOGS_BUILD_TESTING=OFF'
+      --cmake_args ' -DOGS_CPU_ARCHITECTURE=sandybridge -DOGS_BUILD_CLI=OFF -DOGS_BUILD_UTILS=OFF -DOGS_BUILD_TESTING=OFF'
       --gui
-    - |
-      for sif in _out/images/*.sif; do
-        singularity exec $sif ogs --version
-      done
   artifacts:
     name: container
     paths:

web/content/docs/userguide/basics/container.md

@@ -39,16 +39,16 @@ Simply download an image from the [latest master-branch build](https://gitlab.op
 
 ```bash
 # Linux only:
-singularity exec --app ogs ogs-6.2.2-serial.sif ogs some/path/project.prj
+singularity exec ogs-6.x.x-serial.sif ogs some/path/project.prj
 ```
 
 This starts the container, mounts your home directory inside the container, passes the current working directory and runs the ogs executable (in your home directory which is mounted inside the container) with the passed project file. Everything works as expected and is transparent to the user. When ogs finishes the container stops and returns to the host system.
 
-The `--app ogs` selects a predefined execution environment in the container (i.e. setting the `PATH` to `/scif/apps/ogs/bin` in which all the executables are located). You could also (and **on macOS you have to**) run without the `--app`-parameter but then you had to specify the full executable path in the container:
+You can also specify the full executable path in the container:
 
 ```bash
 # Works on macOS too:
-singularity exec ogs-6.2.2-serial.sif /scif/apps/ogs/bin/ogs ...
+singularity exec ogs-6.x.x-serial.sif /usr/local/ogs/bin/ogs ...
 ```
 
 Running a benchmark:
@@ -57,29 +57,29 @@ Running a benchmark:
 # Create output directories
 mkdir -p _out _out_mpi
 # Run serial benchmark
-singularity exec --app ogs ogs-6.2.2-serial.sif ogs -o _out [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
+singularity exec ogs-6.x.x-serial.sif ogs -o _out [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
 # Run serial benchmark with output validation (via vtkdiff)
-singularity exec --app ogs ogs-6.2.2-serial.sif ogs -o _out -r [ogs-sources]/Tests/Data/Mechanics/Linear [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
+singularity exec ogs-6.x.x-serial.sif ogs -o _out -r [ogs-sources]/Tests/Data/Mechanics/Linear [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
 # Run parallel benchmark with MPI
-mpirun -np 4 singularity exec --app ogs ogs-6.2.2-openmpi-2.1.2.sif ogs -o _out_mpi [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
+mpirun -np 4 singularity ogs ogs-6.x.x-openmpi-2.1.2.sif ogs -o _out_mpi [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
 ```
 
 You can run other contained executables as well, e.g. `vtkdiff`:
 
 ```bash
-singularity exec --app ogs ogs-6.2.2-serial.sif vtkdiff --help
+singularity exec ogs-6.x.x-serial.sif vtkdiff --help
 ```
 
 You can interactively explore the container with `singularity shell` (you can see that you are **in** the container because of the `Singularity [container image file]:...>` prefix of the shell):
 
 ```bash
 # Shell into container
-singularity shell ogs-6.2.2-serial.sif
+singularity shell ogs-6.x.x-serial.sif
 # List files in the container
-Singularity ogs-6.2.2-serial.sif:...> ls /scif/apps/ogs/bin
+Singularity ogs-6.x.x-serial.sif:...> ls /scif/apps/ogs/bin
 ... ogs tetgen vtkdiff
 # Exit the container and get back to your hosts shell
-Singularity ogs-6.2.2-serial.sif:...> exit
+Singularity ogs-6.x.x-serial.sif:...> exit
 ```
 
 ### Custom Python environment for the container
@@ -100,13 +100,13 @@ exit
 # Now outside the container
 # The virtualenv-directory .venv still persists
 # If you want to run something in the container with exec, source the venv before:
-singularity exec --app ogs my-container.sif bash -c 'source .venv/bin/activate && ogs ...'
+singularity exec my-container.sif bash -c 'source .venv/bin/activate && ogs ...'
 ```
 
 ### Run the DataExplorer inside a Container
 
 * Get a Singularity container with the DataExplorer (has `-gui` in its name)
-* `singularity exec --app ogs ogs-xxx-gui-xxx.sif DataExplorer`
+* `singularity exec ogs-xxx-gui-xxx.sif DataExplorer`
 
 You may use this container on e.g. `envinf1` with X11 forwarding (`ssh -XY envinf1`).
 
@@ -124,15 +124,15 @@ Although Singularity is the preferred container runtime you can use [Docker](htt
 
 * Get the container: `docker pull registry.opengeosys.org/ogs/ogs/ogs-serial`
 * Start interactive container session: `docker run --rm -it registry.opengeosys.org/ogs/ogs/ogs-serial`
-* Run ogs: `/scif/apps/ogs/bin/ogs --version`
+* Run ogs: `/usr/local/ogs/bin/ogs --version`
 * Exit the container: `exit`
 
 You will notice that the interactive session in your container is isolated from your host, i.e. you do not have access to files on your host. You need to explicitly [mount](https://docs.docker.com/storage/bind-mounts/) them on `docker run`:
 
 ```bash
 mkdir ~/ogs_out
-docker run --rm -it -v $HOME/code/ogs6/ogs/Tests/Data:/tmp/data:ro -v $HOME/ogs_out:/tmp/out registry.opengeosys.org/ogs/ogs/ogs-seria
-/scif/apps/ogs/bin/ogs -o /tmp/out /tmp/data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e4.prj
+docker run --rm -it -v $HOME/code/ogs6/ogs/Tests/Data:/tmp/data:ro -v $HOME/ogs_out:/tmp/out registry.opengeosys.org/ogs/ogs/ogs-serial
+/usr/local/ogs/bin/ogs -o /tmp/out /tmp/data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e4.prj
 exit
 ls ~/ogs_out
 # [shows ogs generated output files]