Automatically wrapping with `Clang.jl` #149

jkozdon · 2021-07-15T23:29:54Z

Experimenting to play with #147

Todo

jkozdon · 2021-07-15T23:30:37Z

Doesn't work with everything yet but you can call initialize and finalize.

jkozdon · 2021-07-15T23:41:14Z

Input:

# For some reason you need to initialize MPI before using multiple libraries.
# Need to debug this
using MPI
MPI.Initialized() || MPI.Init()
using PETSc
for petsclib in PETSc.LibPETSc.petsclibs
    println(splitpath(petsclib.petsc_library)[end])
    @show PETSc.initialized(petsclib)
    @show PETSc.initialize(petsclib)
    @show PETSc.initialized(petsclib)
    @show PETSc.finalized(petsclib)
    @show PETSc.finalize(petsclib)
    @show PETSc.initialized(petsclib)
    @show PETSc.finalized(petsclib)
    println()
end

Output:

libpetsc_double_real_Int64.dylib
PETSc.initialized(petsclib) = false
PETSc.initialize(petsclib) = nothing
PETSc.initialized(petsclib) = true
PETSc.finalized(petsclib) = false
PETSc.finalize(petsclib) = nothing
PETSc.initialized(petsclib) = false
PETSc.finalized(petsclib) = true

libpetsc_single_real_Int64.dylib
PETSc.initialized(petsclib) = false
PETSc.initialize(petsclib) = nothing
PETSc.initialized(petsclib) = true
PETSc.finalized(petsclib) = false
PETSc.finalize(petsclib) = nothing
PETSc.initialized(petsclib) = false
PETSc.finalized(petsclib) = true

libpetsc_double_complex_Int64.dylib
PETSc.initialized(petsclib) = false
PETSc.initialize(petsclib) = nothing
PETSc.initialized(petsclib) = true
PETSc.finalized(petsclib) = false
PETSc.finalize(petsclib) = nothing
PETSc.initialized(petsclib) = false
PETSc.finalized(petsclib) = true

libpetsc_single_complex_Int64.dylib
PETSc.initialized(petsclib) = false
PETSc.initialize(petsclib) = nothing
PETSc.initialized(petsclib) = true
PETSc.finalized(petsclib) = false
PETSc.finalize(petsclib) = nothing
PETSc.initialized(petsclib) = false
PETSc.finalized(petsclib) = true

jkozdon · 2021-07-16T02:07:34Z

I guess I still need to sort out the types (But I think it should be possible with more walking of the syntax tree).

psanan · 2021-07-20T07:57:25Z

Lazy question, but what's the high-level procedure here? What is now automatic and what still has to be maintained "by hand"? Are the specific things here related to various PETSc components all of the "by hand" flavor, or are those things that have been generated automatically and are then checked in?

vchuravy · 2021-07-20T09:13:32Z

I think everything in lib is autogenerated.

jkozdon · 2021-07-20T15:19:25Z

As @vchuravy said, the file in lib is generated from the PETSc header files with the code in gen. These produce pretty raw wrappers, that I am then expanding on to make it all a little more friendly to work with.

There is a bunch of stuff we do not currently wrap (look at generator.toml), some of it will need to be sorted out and some of it won't (I think I know / have a plan for how to support most of what will be needed, just waiting to fix it until I am ready to use it / write the test).

There probably some gotchas left in there with respect to system / build dependent types that will need to be sorted out, but right now it does support multiple PETSc builds living side-by-side in Julia.

@psanan shoot me an email if you'd like to VTC to chat about what I am doing, I'd be more than happy to have feedback.

psanan · 2021-08-05T09:02:00Z

Docs suggestion, re our chat our yesterday. Perhaps somewhere like here one could add language like "PETSc.jl's high-level, easy-to-use interface exposes only some of the functionality of PETSc. However, PETSc.jl includes an automatically-generated wrapper layer which directly exposes more of the PETSc API, which may be of use to existing expert users. See (link to minimal example/test of using the wrappers, directly) for an example".

jkozdon · 2021-08-05T15:05:54Z

Thanks for the recommendation. I've put it as part of the PR task list.

jkozdon · 2021-09-08T17:35:37Z

src/viewer.jl

+# ideally we would capture the output directly, but this looks difficult
+# easiest option is to redirect stdout
+# based on suggestion from https://github.com/JuliaLang/julia/issues/32567
+function _show(io::IO, obj)


This still has problems with large matrices.

Might be better to create a temp file with mktemp(), redirect the PETSC output to an ascii file with PetscViewerASCIIOpenWithFILE, then dump the contents to io.

Or something is wrong with the flush?

ViralBShah · 2024-10-03T17:59:12Z

It would be really cool to get this working and merged. I have no idea what the challenges were (and plan to dive in), but is it possible that improvements in Clang.jl will help us get this done?

boriskaus · 2024-10-03T18:06:03Z

I think there were no real challenges, but it was probably mainly caused by the main developer wanting things to be perfect before merging it back into main.

Clang already used to do a good job in wrapping the functions. Making a nice julia-like interface around this would be good to have, but that had to be done manually which is what took a long time (and was never finished).
I guess Clang can now even take the help into account in the documentation

ViralBShah · 2024-10-03T18:09:09Z

I feel that it would be nice to get it refreshed and merged and it may help others to contribute if all the auto-wrapping is in place. Kind of imagining moving things one step forward.

Since the package is not even loading right now, once that is fixed, this sort of thing may help us find other maintainers.

boriskaus · 2024-10-03T18:12:16Z

Another thing was the interaction with the GC. There was a presentation about how this was solved in python (for firedrake) at this year’s PETSc conference, so I suppose the same method can be used in julia

boriskaus · 2024-10-03T18:16:03Z

I fully agree with you. If the basic functions are wrapped and we have some basic documentation it would motivate others to help.
It probably won’t take professionals that long. I, however, don’t belong to that group. Happy to help with usage examples etc.

ViralBShah · 2024-10-03T18:17:11Z

I'll see how I can help with getting the package back up and running and get this PR merged.

boriskaus · 2024-10-03T18:20:10Z

That would be fantastic!

ViralBShah · 2024-10-14T14:25:36Z

Just leaving this one open to be able to drive work on it.

ViralBShah · 2024-10-14T21:07:28Z

@boriskaus This has a pretty large set of conflicts. Any suggestions on how to get it rebased to main quickly? Are some of these just auto-generated files?

ViralBShah · 2024-10-14T21:55:20Z

Tried to update this branch to Julia 1.11. The package loads fine in Julia 1.11 with some minor tweaks (I checked in my commits).

The clang autowrap stuff prints a few errors (naturally it's been a long time), but it does write a petsc_library.jl. I see this:

┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESObjectiveComputeFunctionDefaultFD, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESObjectiveComputeFunctionDefaultFD(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESComputeJacobianDefault, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESComputeJacobianDefault(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESComputeJacobianDefaultColor, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESComputeJacobianDefaultColor(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeFunction, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeFunction(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeMFFunction, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeMFFunction(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeJacobian, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeJacobian(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:TSComputeRHSFunctionLinear, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) TSComputeRHSFunctionLinear(TS, PetscReal, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:TSComputeRHSJacobianConstant, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) TSComputeRHSJacobianConstant(TS, PetscReal, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.

ViralBShah · 2024-10-14T22:04:52Z

Part of the issue is that the generator seems to be for the default Float64/Int32 combination, and I wonder if it needs to be extended to generate all the type combinations.

boriskaus · 2024-10-15T06:53:43Z

I think we can first focus on getting this working before doing the rest. Part of the problem is likely that some of the PETSc functions have been renamed.

ViralBShah · 2024-10-16T14:23:51Z

I'm going to try to just get this branch working without worrying about rebasing. I am already able to generate the full petsc_library.jl but it doesn't load yet. You can try it out on this branch by running generator.jl.

I don't think major changes have happened since this branch was created and now.

boriskaus · 2024-10-16T14:27:23Z

fine with me; ideally we would change the existing tests that are currently in main to only use the auto-generated wrappers, which would simplify maintaining it.

boriskaus · 2024-10-16T15:28:28Z

We don't have to strictly follow what was done before, since Clang.jl has presumably improved a lot over the last few years.

If I simplify generator.toml to:

[general]
library_name = "$petsc_library"

use_julia_native_enum_type = true
use_deterministic_symbol = true

prologue_file_path = "./prologue.jl"
# epilogue_file_path = "./epilogue.jl"

auto_mutability = true              # Create mutable structures:
auto_mutability_with_new = true     # Allow creating empty structs
auto_mutability_ignorelist = []
auto_mutability_includelist = []

extract_c_comment_style = "doxygen"

export_symbol_prefixes = ["CX", "clang_"]

It essentially compiles the whole library with a few exceptions:

julia> include("generator.jl")
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscbag.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsys.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscconf.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscconf_poison.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscfix.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscmacros.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscversion.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsc/private/petscadvancedmacros.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsystypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscmath.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscerror.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscviewertypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscoptions.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsclog.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsctime.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscbt.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscstring.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsclogtypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsclogdeprecated.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscmatlab.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdraw.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdrawtypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdevice.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdevicetypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsf.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsftypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscvec.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscis.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsectiontypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscistypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscviewer.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsection.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmda.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdm.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscmat.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscmatcoarsen.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmtypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscfetypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdstypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmlabel.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdt.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmdatypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscpf.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscao.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscfe.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscspace.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdualspace.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmcomposite.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmpatch.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmplex.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscpartitioner.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmplextypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscfv.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscfvtypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmfield.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmplextransform.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmplextransformtypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmredundant.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmshell.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmsliced.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmswarm.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmstag.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscdmproduct.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscds.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsccharacteristic.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscts.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsnes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscksp.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscpc.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscpctypes.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscconvest.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsctao.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsctaolinesearch.h
[ Info: Found dependent header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsctao_deprecations.h
[ Info: Parsing headers...
/Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petscsys.h:98:6: error: "PETSc was configured with Open MPI but now appears to be compiling using a non-Open MPI mpi.h"
[ Info: Processing header: /Users/kausb/.julia/artifacts/a69b8f699a39f274f95752394759a3e9973e02b0/lib/petsc/double_real_Int64/include/petsc.h
[ Info: Building the DAG...
┌ Warning: [CollectDependentSystemNode]: found symbols in the system headers: [:MPI_Info, :MPI_Op, :MPI_Status, :MPI_Status, :MPI_Datatype, :off_t, :__darwin_off_t, :MPI_Comm, :MPI_Aint, :MPI_File, :ADIOI_FileD, :MPI_Request, :MPI_Group, :MPI_Offset, :MPI_Win]
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/passes.jl:95
[ Info: Emit Julia expressions...
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESObjectiveComputeFunctionDefaultFD, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESObjectiveComputeFunctionDefaultFD(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESComputeJacobianDefault, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESComputeJacobianDefault(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESComputeJacobianDefaultColor, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESComputeJacobianDefaultColor(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeFunction, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeFunction(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeMFFunction, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeMFFunction(SNES, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:SNESPicardComputeJacobian, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) SNESPicardComputeJacobian(SNES, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:TSComputeRHSFunctionLinear, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) TSComputeRHSFunctionLinear(TS, PetscReal, Vec, Vec, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
┌ Error: missing implementation for ExprNode{Clang.Generators.FunctionDefault, Clang.CLFunctionDecl}(:TSComputeRHSJacobianConstant, Clang.Generators.FunctionDefault(), CLCursor (Clang.CLFunctionDecl) TSComputeRHSJacobianConstant(TS, PetscReal, Vec, Mat, Mat, void *), Expr[], Expr[], Int64[]), please file an issue to Clang.jl.
└ @ Clang.Generators ~/.julia/packages/Clang/uJQ2L/src/generator/codegen.jl:716
[ Info: [ProloguePrinter]: print to /Users/kausb/.julia/dev/PETSc.jl/gen/../lib/petsc_library.jl
[ Info: [GeneralPrinter]: print to /Users/kausb/.julia/dev/PETSc.jl/gen/../lib/petsc_library.jl
[ Info: [EpiloguePrinter]: print to /Users/kausb/.julia/dev/PETSc.jl/gen/../lib/petsc_library.jl
[ Info: Done!
"/Users/kausb/.julia/dev/PETSc.jl/gen/../lib/petsc_library.jl"

boriskaus · 2024-10-16T16:17:25Z

@ViralBShah
I've looked at the tests that are marked with FIXME, and most of the changes are due to PETSc changing the function calls (slightly) during more recent versions. We can port that manually but it probably makes more sense to try and autowrap the full library and use that instead (surely easier to maintain).

Also, this PR is very large. Perhaps it is simpler to start a new one from main?

ViralBShah · 2024-10-16T16:34:11Z

Yes, the simpler thing would be to start the generator on a new PR in main, and just get that running first. And then piecemeal port things over to the new generated API. But not being a user of PETSc, that is where I will start running into my limitations here. Let's push one step forward at least.

I do feel that on main, it would be nice to fix all the FIXME things first so that everything that was working in the past is working again now, and tagged - giving a solid baseline for the new stuff.

boriskaus · 2024-10-16T17:06:16Z

I’m a PETSc user (well at least of part of the library). Yet I’m only a beginner when it comes to using clang to port it all.
I did notice in a recent project that it is possible to automatically make julia docs out of doxygen strings (which every routine in petsc has).
It would be fantastic if we can automatically provide help for all of the routines (even when the help is strictly speaking only valid for the c routines)

If you leave out the functions that have ccalls in the current main, there are only a limited number of additional functions remaining that are mainly there to make using petsc more julia-like. Those ones could be gradually expanded to include more functionally, but as long as we call autowrapped routines throughout it will be much easier to maintain this.

ViralBShah · 2024-10-16T17:11:38Z

So with your generated library, did you try doing include petsc_library.jl? Getting it to load cleanly is the first step. I assume you used the generator.toml that is in this branch (which has a lot of stuff to exclude and such).

I see what you are saying about the auto-generated comments for the wrappers. Wouldn't we still need the docs that are in the Julian interface as it stands right now - or are you thinking those could be completely replaced with this auto-generated stuff?

boriskaus · 2024-10-16T17:16:42Z

So with your generated library, did you try doing include petsc_library.jl? Getting it to load cleanly is the first step. I assume you used the generator.toml that is in this branch (which has a lot of stuff to exclude and such).

I didn’t manage to load it just now; I was using a simpler generator.toml shown in one of the comments

I see what you are saying about the auto-generated comments for the wrappers. Wouldn't we still need the docs that are in the Julian interface as it stands right now - or are you thinking those could be completely replaced with this auto-generated stuff?

I think it can be replaced with autogenerated stuff. Multiple dispatch will take care of the rest.

boriskaus · 2024-10-28T14:04:53Z

@ViralBShah, @vchuravy

One of the reasons for the wrapper file to be rather complex is that the different versions of the PETSc libraries have different definitions of PetscInt, PetscScalar, etc. which can be 32bit, 64bit etc.
In the main branch, we handle this by interpolating the values of $PetscInt, $PetscScalar into function calls as can be seen here

Yet, this doesn't work for structures, which are instead defined as:

mutable struct DMSTAGSTENCIL{PetscInt}
    loc::DMStagStencilLocation
    i::PetscInt
    j::PetscInt
    k::PetscInt
    c::PetscInt
end

At the time the initial wrapping was done, it wasn't possible to automatically wrap C structures to give something like above. Instead Clang gives something like:

mutable struct DMStagStencil
    loc::DMStagStencilLocation
    i::PetscInt
    j::PetscInt
    k::PetscInt
    c::PetscInt
    DMStagStencil() = new()
end

Question: do you know whether there is a way to automatically add types to the structures using Clang?
If yes, it would greatly simplify the generator.toml file.

EDIT: @albert-de-montserrat pointed out that this is actually done already in wrap.jl. The disadvantage is that it has to be specified manually for every struct as:

(x, s) -> add_struct_type(x, s, ("MatStencil",), ("PetscInt",)),

jkozdon force-pushed the jek/gen branch from 985a085 to 89a1184 Compare July 16, 2021 21:17

jkozdon mentioned this pull request Jul 16, 2021

Use CBindings.jl or Clang.jl to build raw interface? #147

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This was referenced Jul 20, 2021

DM and DMDA interface #120

Merged

Revisit MPI after / with #149 #150

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jkozdon force-pushed the jek/gen branch 3 times, most recently from 16b5f8e to fe80c8f Compare July 20, 2021 04:03

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boriskaus marked this pull request as ready for review August 3, 2021 21:49

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jkozdon linked an issue Aug 31, 2021 that may be closed by this pull request

Revisit MPI after / with #149 #150

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jkozdon force-pushed the jek/gen branch 2 times, most recently from 4db9766 to 581f379 Compare September 3, 2021 18:48

Fix viewer for long output on stdout

581f379

jkozdon commented Sep 8, 2021

View reviewed changes

jkozdon mentioned this pull request Dec 3, 2021

Update PETSc_jll with more solvers #146

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jkozdon closed this Feb 10, 2023

ViralBShah reopened this Oct 14, 2024

Try to compile with Julia 1.11

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Automatically wrapping with `Clang.jl` #149

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Automatically wrapping with `Clang.jl` #149

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