diff --git a/DEVELOP.md b/DEVELOP.md new file mode 100644 index 0000000..830dd6c --- /dev/null +++ b/DEVELOP.md @@ -0,0 +1,11 @@ +# Developer documentation + +## Generating the API +The API is generated automatically from Catalyst_jll.jl using Clang.Generators. +Go to the subfolder `deps` and execute +```shell +julia --project=. -e "using Pkg; Pkg.instantiate()" +julia --project=. generator.jl +``` + +## Releasing a new version \ No newline at end of file diff --git a/LICENSE b/LICENSE index 25731ad..70f756d 100644 --- a/LICENSE +++ b/LICENSE @@ -1,201 +1,21 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/Project.toml b/Project.toml index e011035..0e48aea 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ -name = "ParaviewCatalyst" +name = "ParaViewCatalyst" uuid = "0fa3a46a-29f8-4c04-a671-08df7e71e505" -authors = ["Jake Bolewski "] +authors = ["Jake Bolewski ", "Benedict Geihe "] version = "0.1.0" [deps] diff --git a/README.md b/README.md new file mode 100644 index 0000000..da4211e --- /dev/null +++ b/README.md @@ -0,0 +1,80 @@ +# ParaViewCatalyst.jl +ParaViewCatalyst.jl provides a Julia interface to Catalyst, used for in-situ +visualization of simulation data. +The Catalyst library for Julia is provided by Catalyst_jll.jl at +[JuliaBinaryWrappers](https://github.com/JuliaBinaryWrappers/Catalyst_jll.jl/blob/main/src/Catalyst_jll.jl) +and [Yggdrasil](https://github.com/JuliaPackaging/Yggdrasil/tree/master/C/Catalyst). + + +## Getting started + +### Prerequisites +Although the [Catalyst API](https://catalyst-in-situ.readthedocs.io) is not restricted to +ParaView, this package is geared towards the +[ParaView implementation](https://docs.paraview.org/en/latest/Catalyst) of the Catalyst API. +As such ParaView needs to be present on the machine you run your simulation on. In +particular, a version is required that ships the Catalyst implementation as a library. On +Linux you should look for `libcatalyst-paraview.so`. +Its path has to be set as an environment variable, e.g. by +```bash +export CATALYST_IMPLEMENTATION_PATHS= +``` +Alternatively, when using ParaViewCatalyst.jl from your own application, you can use the keyword argument `libpath` of the function `catalyst_initialize`. + +### Testing + +#### Catalyst implementation +Go to the `examples` folder and start julia using +```shell +julia --project=. +``` +In package mode do +```julia +(examples) pkg> dev .. +(examples) pkg> instantiate +``` +then +```julia +julia> include("test_init.jl") +``` +You should see some information about the Catalyst implementation. In particular, you +should see `implementation: "paraview"`. +More verbose output can be enabled by setting the +environment variable `CATALYST_DEBUG=1`. + +#### Paraview +Launch ParaView. From the main menu, select "Catalyst", then "Connect", and accept the +default port. Select "Catalyst" again and then "Pause Simulation". Now launch Julia as done +before, and execute +```julia +julia> include("test_execute.jl") +``` +In ParaView click on the symbol in front of "Input", then click on the symbol in front of +"Extract: input". You should now see a square. In the properties tab under "Coloring", +select "testdata". Now select "Catalyst" from the main menu and "Continue". The square +should change its color every two seconds. + +### Using the interface +To use ParaViewCatalyst.jl from your code, you only need `catalyst_initialize()`, +`catalyst_execute(node)`, and `catalyst_finalize()`. All information is passed +through Conduit nodes, which are required to adhere to the +[Blueprint](https://docs.paraview.org/en/latest/Catalyst/blueprints.html). + +A user-defined ParaView pipeline script can be passed to `catalyst_initialize` using the +keyword argument `catalyst_pipeline`. By default src/catalyst_pipeline.py is used. This +script activates live visualization. The data can also be viewed on a remote machine. In +this case `options.CatalystLiveURL` has to be adjusted to point to the remote machine. +Once a pipeline in ParaView has been set up, it can be exported as a script by selecting +"File" from the main menu and then "Save Catalyst State". + + +## Examples +ParaViewCatalyst.jl is used by [Trixi.jl](https://github.com/trixi-framework/Trixi.jl). + +## Authors +ParaViewCatalyst.jl was initiated by Jake Bolewski (@jakebolewski) at https://github.com/CliMA/ +and is now maintained at https://github.com/trixi-framework. + + +## License +ParaViewCatalyst.jl is licensed under the MIT license (see [LICENSE.md](LICENSE.md)). diff --git a/examples/Project.toml b/examples/Project.toml index 635f102..c961e22 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -1,2 +1,2 @@ [deps] -ParaviewCatalyst = "0fa3a46a-29f8-4c04-a671-08df7e71e505" +ParaViewCatalyst = "0fa3a46a-29f8-4c04-a671-08df7e71e505" diff --git a/examples/test_execute.jl b/examples/test_execute.jl index 47b6eb7..272c7cf 100644 --- a/examples/test_execute.jl +++ b/examples/test_execute.jl @@ -1,4 +1,4 @@ -using ParaviewCatalyst +using ParaViewCatalyst catalyst_initialize() @@ -23,10 +23,10 @@ for t in 1:10 mesh_node["topologies/mesh/elements/shape"] = "hex" mesh_node["topologies/mesh/elements/connectivity"] = [0 1 3 2 4 5 7 6] - mesh_node["fields/pressure/association"] = "element" - mesh_node["fields/pressure/topology"] = "mesh" - mesh_node["fields/pressure/volume_dependent"] = "false" - mesh_node["fields/pressure/values"] = rand(1) + mesh_node["fields/testdata/association"] = "element" + mesh_node["fields/testdata/topology"] = "mesh" + mesh_node["fields/testdata/volume_dependent"] = "false" + mesh_node["fields/testdata/values"] = rand(1) node["catalyst/channels/input/data"] = mesh_node diff --git a/examples/test_init.jl b/examples/test_init.jl index 8391b59..02fd43a 100644 --- a/examples/test_init.jl +++ b/examples/test_init.jl @@ -1,4 +1,4 @@ -using ParaviewCatalyst +using ParaViewCatalyst catalyst_initialize() catalyst_about() catalyst_finalize() diff --git a/src/ParaviewCatalyst.jl b/src/ParaViewCatalyst.jl similarity index 85% rename from src/ParaviewCatalyst.jl rename to src/ParaViewCatalyst.jl index 4dddd3a..84d9797 100644 --- a/src/ParaviewCatalyst.jl +++ b/src/ParaViewCatalyst.jl @@ -1,4 +1,4 @@ -module ParaviewCatalyst +module ParaViewCatalyst import Catalyst_jll @@ -55,12 +55,17 @@ function catalyst_initialize(node::ConduitNode) end function catalyst_initialize(;libpath=nothing, catalyst_pipeline=nothing) - @assert libpath !== nothing || haskey(ENV, "PARAVIEW_CATALYST_PATH") - "please set the PARAVIEW_CATALYST_PATH environment variable to the path of your catalyst library or use the libpath parameter of catalyst_initialize" + @assert libpath !== nothing || haskey(ENV, "CATALYST_IMPLEMENTATION_PATHS") " + set CATALYST_IMPLEMENTATION_PATHS environment variable to the path of your catalyst library + or use the libpath parameter of catalyst_initialize" ConduitNode() do node node["catalyst_load/implementation"] = "paraview" - node["catalyst_load/search_paths/paraview"] = libpath === nothing ? ENV["PARAVIEW_CATALYST_PATH"] : libpath - node["catalyst/scripts/catalyst_pipeline/filename"] = catalyst_pipeline === nothing ? joinpath(@__DIR__, "catalyst_pipeline.py") : catalyst_pipeline + if libpath !== nothing + node["catalyst_load/search_paths/paraview"] = libpath + end + node["catalyst/scripts/catalyst_pipeline/filename"] = + catalyst_pipeline === nothing ? + joinpath(@__DIR__, "catalyst_pipeline.py") : catalyst_pipeline catalyst_initialize(node) end return diff --git a/src/catalyst_pipeline.py b/src/catalyst_pipeline.py index 6657266..ebb7ccf 100644 --- a/src/catalyst_pipeline.py +++ b/src/catalyst_pipeline.py @@ -8,6 +8,7 @@ options = catalyst.Options() options.EnableCatalystLive = 1 +#options.CatalystLiveURL = '192.168.1.1:22222' def catalyst_execute(info): global producer