WIP: Switch to P4est with CBinding v1 #835

sloede · 2021-09-01T04:30:16Z

This PR prepares Trixi for working with trixi-framework/P4est.jl#42 or trixi-framework/P4est.jl#43. To use it, you need to manually dev a local clone of said PRs, e.g., from within a clone of this Trixi branch, execute

julia --project -e 'using Pkg; Pkg.develop("path/to/P4est.jl/clone/on/branch/cbinding-v1")'

sloede · 2021-09-01T04:35:17Z

When running

julia> using Revise, Trixi

julia> trixi_include("examples/p4est_2d_dgsem/elixir_advection_basic.jl")

with the current version (and the appropriate dev'd P4est.jl branch), I get the following error:

ERROR: LoadError: MethodError: no method matching unsafe_convert(::Type{CBinding.Cptr{CBinding.Cconst{Int32}}}, ::Matrix{Int32})
Closest candidates are:
  unsafe_convert(::Type{CBinding.Cptr{T}}, ::Vector{T} where T) where T at /home/mschlott/.julia/packages/CBinding/0akLv/src/pointers.jl:40
  unsafe_convert(::Type{CBinding.Cptr{T}}, ::Ptr) where T at /home/mschlott/.julia/packages/CBinding/0akLv/src/pointers.jl:38
  unsafe_convert(::Type{CBinding.Cptr{T}}, ::Ref) where T at /home/mschlott/.julia/packages/CBinding/0akLv/src/pointers.jl:39
  ...
Stacktrace:
  [1] macro expansion
    @ ./boot.jl:0 [inlined]
  [2] funccall(::Type{CBinding.Cptr{P4est.libp4est.var"c\"struct p4est_connectivity\""}}, ::Type{Tuple{Int32, Int32, Int32, CBinding.Cptr{CBinding.Cconst{Float64}}, CBinding.Cptr{CBinding.Cconst{Int32}}, CBinding.Cptr{CBinding.Cconst{Int32}}, CBinding.Cptr{CBinding.Cconst{Int8}}, CBinding.Cptr{CBinding.Cconst{Int32}}, CBinding.Cptr{CBinding.Cconst{Int32}}, CBinding.Cptr{CBinding.Cconst{Int32}}, CBinding.Cptr{CBinding.Cconst{Int8}}}}, ::Val{:cdecl}, ::P4est.libp4est.Cbinding_p4est_connectivity_new_copy{:p4est_connectivity_new_copy}, ::Int64, ::Int64, ::Int64, ::Ptr{Nothing}, ::Ptr{Nothing}, ::Matrix{Int32}, ::Matrix{Int8}, ::Ptr{Nothing}, ::Vector{Int32}, ::Ptr{Nothing}, ::Ptr{Nothing})
    @ CBinding ~/.julia/packages/CBinding/0akLv/src/functions.jl:32
  [3] macro expansion
    @ ~/.julia/packages/CBinding/0akLv/src/functions.jl:65 [inlined]
  [4] funccall(::P4est.libp4est.Cbinding_p4est_connectivity_new_copy{:p4est_connectivity_new_copy}, ::Int64, ::Int64, ::Int64, ::Ptr{Nothing}, ::Ptr{Nothing}, ::Matrix{Int32}, ::Matrix{Int8}, ::Ptr{Nothing}, ::Vector{Int32}, ::Ptr{Nothing}, ::Ptr{Nothing})
    @ CBinding ~/.julia/packages/CBinding/0akLv/src/functions.jl:46
  [5] (::P4est.libp4est.Cbinding_p4est_connectivity_new_copy{:p4est_connectivity_new_copy})(c"num_vertices"::Int64, c"num_trees"::Int64, c"num_corners"::Int64, c"vertices"::Ptr{Nothing}, c"ttv"::Ptr{Nothing}, c"ttt"::Matrix{Int32}, c"ttf"::Matrix{Int8}, c"ttc"::Ptr{Nothing}, c"coff"::Vector{Int32}, c"ctt"::Ptr{Nothing}, c"ctc"::Ptr{Nothing})
    @ P4est.libp4est ~/.julia/packages/CBinding/0akLv/src/context_c.jl:713
  [6] connectivity_structured(n_cells_x::Int64, n_cells_y::Int64, periodicity::Tuple{Bool, Bool})
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/meshes/p4est_mesh.jl:436
  [7] P4estMesh(trees_per_dimension::Tuple{Int64, Int64}; polydeg::Int64, mapping::Nothing, faces::Nothing, coordinates_min::Tuple{Float64, Float64}, coordinates_max::Tuple{Float64, Float64}, RealT::Type, initial_refinement_level::Int64, periodicity::Bool, unsaved_changes::Bool)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/meshes/p4est_mesh.jl:166
  [8] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/examples/p4est_2d_dgsem/elixir_advection_basic.jl:20
  [9] include
    @ ./Base.jl:387 [inlined]
 [10] #trixi_include#829
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/auxiliary/special_elixirs.jl:33 [inlined]
 [11] trixi_include
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/auxiliary/special_elixirs.jl:33 [inlined]
 [12] #trixi_include#831
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/auxiliary/special_elixirs.jl:36 [inlined]
 [13] trixi_include(elixir::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/auxiliary/special_elixirs.jl:36
 [14] top-level scope
    @ REPL[2]:1
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/examples/p4est_2d_dgsem/elixir_advection_basic.jl:20

Any idea what could be wrong or where I might need to poke around, @krrutkow? To be honest, I have no clue where to even start...

krrutkow · 2021-09-01T12:55:49Z

Good find! The automatic array-to-pointer conversion was only defined on a Vector, not AbstractArray. If you define this, does it work?

Base.unsafe_convert(::Type{Cptr{T}}, x::AbstractArray) where {T} = Core.Intrinsics.bitcast(Cptr{T}, Base.unsafe_convert(Ptr{eltype(x)}, x))

If so, I will add that to the next update to CBinding.

sloede · 2021-09-01T16:15:56Z

Good find! The automatic array-to-pointer conversion was only defined on a Vector, not AbstractArray. If you define this, does it work?
Base.unsafe_convert(::Type{Cptr{T}}, x::AbstractArray) where {T} = Core.Intrinsics.bitcast(Cptr{T}, Base.unsafe_convert(Ptr{eltype(x)}, x))
If so, I will add that to the next update to CBinding.

This seems to be working, I added it to https://github.com/krrutkow/P4est.jl/tree/cbinding-v1 in krrutkow/P4est.jl@0a95340. Thanks!

I'll continue fixing up Trixi until I run into the next inexplicable issue...

sloede · 2021-09-01T16:31:41Z

OK, so one thing I can already report is that the REPL regularly keeps dying on me: either during errors, or when I rerun a previously failing and now hopefully fixed example, or just when I exit the REPL. The error messages usually look something like this

julia> 
munmap_chunk(): invalid pointer

signal (6): Aborted
in expression starting at none:0
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f9028c513ed)
unknown function (ip: 0x7f9028c5947b)
unknown function (ip: 0x7f9028c596cb)
p4est_connectivity_destroy at /workspace/srcdir/p4est-2.3.2/src/p4est_connectivity.c:413
macro expansion at /home/mschlott/.julia/packages/CBinding/0akLv/src/functions.jl:0 [inlined]
funccall at /home/mschlott/.julia/packages/CBinding/0akLv/src/functions.jl:32 [inlined]
macro expansion at /home/mschlott/.julia/packages/CBinding/0akLv/src/functions.jl:65 [inlined]
funccall at /home/mschlott/.julia/packages/CBinding/0akLv/src/functions.jl:46 [inlined]
Cbinding_p4est_connectivity_destroy at /home/mschlott/.julia/packages/CBinding/0akLv/src/context_c.jl:713 [inlined]
destroy_mesh at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/meshes/p4est_mesh.jl:46
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1703 [inlined]
run_finalizer at /buildworker/worker/package_linux64/build/src/gc.c:278
jl_gc_run_finalizers_in_list at /buildworker/worker/package_linux64/build/src/gc.c:365
run_finalizers at /buildworker/worker/package_linux64/build/src/gc.c:394 [inlined]
jl_gc_run_all_finalizers at /buildworker/worker/package_linux64/build/src/gc.c:480
jl_atexit_hook at /buildworker/worker/package_linux64/build/src/init.c:240
repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:703
main at julia (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4007d8)
Allocations: 95786701 (Pool: 95749172; Big: 37529); GC: 64
Aborted (core dumped)

Any idea where this might come from? Can this related be to analytech-solutions/CBinding.jl#61? Or is this related to some finalizer funny business?

sloede · 2021-09-01T16:44:37Z

OK, another weird issue: Directly using the macro version @P4EST_MAXLEVEL sometimes fails, sometimes it doesn't. What didn't work:

Trixi.jl/src/solvers/dgsem_p4est/containers_2d.jl

Lines 53 to 54 in 6ab71e9

    
           p4est_root_len = 1 << @P4EST_MAXLEVEL 
        
           p4est_quadrant_len(l) = 1 << (@P4EST_MAXLEVEL - l)

with error message (during using Trixi already!):

no method matching var"@c\"P4EST_MAXLEVEL\""(::LineNumberNode, ::Module, ::Expr)

[ Info: Precompiling Trixi [a7f1ee26-1774-49b1-8366-f1abc58fbfcb]
ERROR: LoadError: LoadError: LoadError: LoadError: LoadError: LoadError: LoadError: MethodError: no method matching var"@c\"P4EST_MAXLEVEL\""(::LineNumberNode, ::Module, ::Expr)
Closest candidates are:
  var"@c\"P4EST_MAXLEVEL\""(::LineNumberNode, ::Module) at /home/mschlott/.julia/packages/CBinding/0akLv/src/context_c.jl:798
Stacktrace:
  [1] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
  [2] include(x::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:16
  [3] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/containers.jl:671
  [4] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
  [5] include(x::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:16
  [6] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/dg.jl:47
  [7] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
  [8] include(x::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:16
  [9] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dg.jl:478
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
 [11] include(x::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:16
 [12] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/solvers.jl:8
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:386
 [14] include(x::String)
    @ Trixi /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:16
 [15] top-level scope
    @ /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:95
 [16] include
    @ ./Base.jl:386 [inlined]
 [17] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1213
 [18] top-level scope
    @ none:1
 [19] eval
    @ ./boot.jl:360 [inlined]
 [20] eval(x::Expr)
    @ Base.MainInclude ./client.jl:446
 [21] top-level scope
    @ none:1
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/containers_2d.jl:54
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/containers_2d.jl:5
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/containers.jl:5
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dgsem_p4est/dg.jl:5
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/dg.jl:5
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/solvers/solvers.jl:5
in expression starting at /mnt/ssd/home/mschlott/hackathon/main-Trixi.jl/src/Trixi.jl:1
ERROR: Failed to precompile Trixi [a7f1ee26-1774-49b1-8366-f1abc58fbfcb] to /home/mschlott/.julia/compiled/v1.6/Trixi/jl_AD7AzM.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY)
   @ Base ./loading.jl:1360
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1306
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1021
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:914
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:901

julia>

Funnily, the following does work:

Trixi.jl/src/solvers/dgsem_p4est/containers_2d.jl

Lines 53 to 55 in 9589447

    
           p4est_max_level = @P4EST_MAXLEVEL 
        
           p4est_root_len = 1 << p4est_max_level 
        
           p4est_quadrant_len(l) = 1 << (p4est_max_level - l)

Any idea what's going on here @krrutkow?

…need for Cptr

krrutkow · 2021-09-01T16:57:57Z

The macro parsing of Julia is probably grabbing everything after @P4EST_MAXLEVEL so if you wrap it with parentheses it will prevent that from happening. (@P4EST_MAXLEVEL) - l

krrutkow · 2021-09-02T15:05:15Z

@sloede Regarding #835 (comment), I think the pointer being destroyed mesh.p4est.connectivity is the pointer to the connectivity pointer. You probably need mesh.p4est.connectivity[] to get the pointer you want to destroy.

Currently pointers that are arguments to C functions are automatically converted, but perhaps only conversion to/from void * should be automatic and the rest must be explicitly converted. I suppose being less Julian is actually better in this situation...

ranocha · 2023-01-02T07:41:59Z

Can be closed after merging #1184?

sloede · 2023-01-25T12:55:10Z

Superseded by #1184.

sloede added 2 commits September 1, 2021 06:23

Remove version compat since dev'ed P4est is used

dce6cbd

Use new syntax in auxiliar.jl

be34e32

Dereference CBinding structures appropriately

effab1a

sloede added 2 commits September 1, 2021 18:37

Use macro version of P4EST_MAXLEVEL

6ab71e9

Fix use of macro version of P4EST_MAXLEVEL

9589447

sloede added 2 commits September 1, 2021 18:50

Add CBinding as a dependency, since we do not seem to get around the …

6aae071

…need for Cptr

Use Cptr instead of plain Ptr

e248935

ranocha added the upstream label Oct 19, 2021

sloede closed this Jan 25, 2023

sloede deleted the switch-to-p4est-with-cbinding-v1 branch January 25, 2023 12:55

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WIP: Switch to P4est with CBinding v1 #835

WIP: Switch to P4est with CBinding v1 #835

sloede commented Sep 1, 2021

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ranocha commented Jan 2, 2023

sloede commented Jan 25, 2023

WIP: Switch to P4est with CBinding v1 #835

WIP: Switch to P4est with CBinding v1 #835

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