Merge branch 'main' into refactor_time_integration

trixi-framework · Jun 18, 2024 · 5cdbbc0 · 5cdbbc0
2 parents 5526022 + 16bdaf0
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diff --git a/.zenodo.json b/.zenodo.json
@@ -5,7 +5,7 @@
     "upload_type": "software",
     "creators": [
         {
-            "affiliation": "Applied and Computational Mathematics, RWTH Aachen University, Germany",
+            "affiliation": "High-Performance Scientific Computing, University of Augsburg, Germany",
             "name": "Schlottke-Lakemper, Michael",
             "orcid": "0000-0002-3195-2536"
         },

diff --git a/AUTHORS.md b/AUTHORS.md
@@ -7,8 +7,8 @@ provided substantial additions or modifications. Together, these two groups form
 "The Trixi.jl Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
 
 ## Principal Developers
-* [Michael Schlottke-Lakemper](https://lakemper.eu),
-  RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany
+* [Michael Schlottke-Lakemper](https://www.uni-augsburg.de/fakultaet/mntf/math/prof/hpsc),
+  University of Augsburg, Germany
 * [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner),
   University of Cologne, Germany
 * [Hendrik Ranocha](https://ranocha.de),
@@ -43,3 +43,4 @@ are listed in alphabetical order:
 * Michael Schlottke-Lakemper
 * Toskan Theine
 * Andrew Winters
+* Huiyu Xie
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to
-[Michael Schlottke-Lakemper](mailto:m.schlottke-lakemper@acom.rwth-aachen.de),
+[Michael Schlottke-Lakemper](mailto:michael.schlottke-lakemper@uni-a.de),
 [Hendrik Ranocha](mailto:[email protected]),
 or any other of the principal developers responsible for enforcement listed in
 [AUTHORS.md](AUTHORS.md).

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.7.16-pre"
+version = "0.7.17-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -104,7 +104,7 @@ TimerOutputs = "0.5.7"
 Triangulate = "2.2"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
-TrixiBase = "0.1.1"
+TrixiBase = "0.1.3"
 UUIDs = "1.6"
 julia = "1.8"
 

diff --git a/README.md b/README.md
@@ -259,8 +259,8 @@ In addition, you can also refer to Trixi.jl directly as
 
 ## Authors
 Trixi.jl was initiated by [Michael
-Schlottke-Lakemper](https://lakemper.eu)
-(RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
+Schlottke-Lakemper](https://www.uni-augsburg.de/fakultaet/mntf/math/prof/hpsc)
+(University of Augsburg, Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
 (Johannes Gutenberg University Mainz, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -323,8 +323,8 @@ In addition, you can also refer to Trixi.jl directly as
 
 ## [Authors](@id authors-index-md)
 Trixi.jl was initiated by [Michael
-Schlottke-Lakemper](https://lakemper.eu)
-(RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
+Schlottke-Lakemper](https://www.uni-augsburg.de/fakultaet/mntf/math/prof/hpsc)
+(University of Augsburg, Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
 (Johannes Gutenberg University Mainz, Germany) and [Andrew Winters](https://liu.se/en/employee/andwi94)

diff --git a/docs/src/styleguide.md b/docs/src/styleguide.md
@@ -51,7 +51,7 @@ PRs that verify that running JuliaFormatter.jl again will not change the source
 To format your contributions before created a PR (or, at least, before requesting a review
 of your PR), you need to install JuliaFormatter.jl first by running
 ```shell
-julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
+julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
 ```
 You can then recursively format the core Julia files in the Trixi.jl repo by executing
 ```shell

diff --git a/src/Trixi.jl b/src/Trixi.jl
@@ -64,13 +64,13 @@ using Static: Static, One, True, False
 using StaticArrays: StaticArrays, MVector, MArray, SMatrix, @SMatrix
 using StrideArrays: PtrArray, StrideArray, StaticInt
 @reexport using StructArrays: StructArrays, StructArray
-using TimerOutputs: TimerOutputs, @notimeit, TimerOutput, print_timer, reset_timer!
+using TimerOutputs: TimerOutputs, @notimeit, print_timer, reset_timer!
 using Triangulate: Triangulate, TriangulateIO
 export TriangulateIO # for type parameter in DGMultiMesh
 using TriplotBase: TriplotBase
 using TriplotRecipes: DGTriPseudocolor
 @reexport using TrixiBase: trixi_include
-using TrixiBase: TrixiBase
+using TrixiBase: TrixiBase, @trixi_timeit, timer
 @reexport using SimpleUnPack: @unpack
 using SimpleUnPack: @pack!
 using DataStructures: BinaryHeap, FasterForward, extract_all!

diff --git a/src/auxiliary/auxiliary.jl b/src/auxiliary/auxiliary.jl
@@ -4,19 +4,6 @@
 include("containers.jl")
 include("math.jl")
 
-# Enable debug timings `@trixi_timeit timer() "name" stuff...`.
-# This allows us to disable timings completely by executing
-# `TimerOutputs.disable_debug_timings(Trixi)`
-# and to enable them again by executing
-# `TimerOutputs.enable_debug_timings(Trixi)`
-timeit_debug_enabled() = true
-
-# Store main timer for global timing of functions
-const main_timer = TimerOutput()
-
-# Always call timer() to hide implementation details
-timer() = main_timer
-
 # By default, Julia/LLVM does not use fused multiply-add operations (FMAs).
 # Since these FMAs can increase the performance of many numerical algorithms,
 # we need to opt-in explicitly.
@@ -249,33 +236,6 @@ macro threaded(expr)
                end)
 end
 
-#     @trixi_timeit timer() "some label" expression
-#
-# Basically the same as a special case of `@timeit_debug` from
-# [TimerOutputs.jl](https://github.com/KristofferC/TimerOutputs.jl),
-# but without `try ... finally ... end` block. Thus, it's not exception-safe,
-# but it also avoids some related performance problems. Since we do not use
-# exception handling in Trixi.jl, that's not really an issue.
-macro trixi_timeit(timer_output, label, expr)
-    timeit_block = quote
-        if timeit_debug_enabled()
-            local to = $(esc(timer_output))
-            local enabled = to.enabled
-            if enabled
-                local accumulated_data = $(TimerOutputs.push!)(to, $(esc(label)))
-            end
-            local b₀ = $(TimerOutputs.gc_bytes)()
-            local t₀ = $(TimerOutputs.time_ns)()
-        end
-        local val = $(esc(expr))
-        if timeit_debug_enabled() && enabled
-            $(TimerOutputs.do_accumulate!)(accumulated_data, t₀, b₀)
-            $(TimerOutputs.pop!)(to)
-        end
-        val
-    end
-end
-
 """
     @autoinfiltrate
     @autoinfiltrate condition::Bool