New recipe: catchaMouse16-v0.1.0 #9151

brendanjohnharris · 2024-07-26T04:36:14Z

This pull request contains a new build recipe:

Package name: catchaMouse16
Version: v0.1.0

C/catchaMouse16/build_tarballs.jl

Co-authored-by: Mosè Giordano <[email protected]>

C/catchaMouse16/build_tarballs.jl

Co-authored-by: Mosè Giordano <[email protected]>

giordano · 2024-07-26T13:19:48Z

Error on aarch64 darwin with Clang (which is always the preferred compiler on BSD systems) is

[13:14:33] cc -shared -lm -lgsl -lgslcblas -o "libcatchaMouse16.dylib" main.o fft.o stats.o helper_functions.o histcounts.o CO_AddNoise.o CO_AutoCorr.o CO_HistogramAMI.o CO_NonlinearAutocorr.o CO_TranslateShape.o DN_RemovePoints.o FC_LoopLocalSimple.o IN_AutoMutualInfoStats.o PH_Walker.o SC_FluctAnal.o ST_LocalExtrema.o SY_DriftingMean.o SY_SlidingWindow.o
[13:14:33] ld64.lld: error: undefined symbol: __divdc3
[13:14:33] >>> referenced by helper_functions.c:152
[13:14:33] >>>               helper_functions.o:(symbol _Cdivcc+0x0)
[13:14:33] clang-16: error: linker command failed with exit code 1 (use -v to see invocation)

Sketch of a solution:

Yggdrasil/N/Notcurses/build_tarballs.jl

Lines 48 to 52 in c0ead9c

    
               # Linking FFMPEG requires the function `__divdc3`, which is implemented in 
        
               # `libclang_rt.osx.a` from LLVM compiler-rt. 
        
               FLAGS+=(-DCMAKE_SHARED_LINKER_FLAGS="-L${libdir}/darwin -lclang_rt.osx" 
        
                       -DCMAKE_EXE_LINKER_FLAGS="-L${libdir}/darwin -lclang_rt.osx" 
        
                       )

Yggdrasil/N/Notcurses/build_tarballs.jl

Lines 81 to 84 in c0ead9c

    
           # We need libclang_rt.osx.a for linking FFMPEG, because this library provides the 
        
           # implementation of `__divdc3`. 
        
           BuildDependency(PackageSpec(name="LLVMCompilerRT_jll", uuid="4e17d02c-6bf5-513e-be62-445f41c75a11", version=llvm_version); 
        
                           platforms=[Platform("aarch64", "macos")]),

brendanjohnharris · 2024-07-26T13:24:36Z

Thanks so much 😊

Error on aarch64 darwin with Clang (which is always the preferred compiler on BSD systems) is
[13:14:33] cc -shared -lm -lgsl -lgslcblas -o "libcatchaMouse16.dylib" main.o fft.o stats.o helper_functions.o histcounts.o CO_AddNoise.o CO_AutoCorr.o CO_HistogramAMI.o CO_NonlinearAutocorr.o CO_TranslateShape.o DN_RemovePoints.o FC_LoopLocalSimple.o IN_AutoMutualInfoStats.o PH_Walker.o SC_FluctAnal.o ST_LocalExtrema.o SY_DriftingMean.o SY_SlidingWindow.o
[13:14:33] ld64.lld: error: undefined symbol: __divdc3
[13:14:33] >>> referenced by helper_functions.c:152
[13:14:33] >>>               helper_functions.o:(symbol _Cdivcc+0x0)
[13:14:33] clang-16: error: linker command failed with exit code 1 (use -v to see invocation)
Sketch of a solution:

Yggdrasil/N/Notcurses/build_tarballs.jl

Lines 48 to 52 in c0ead9c

# Linking FFMPEG requires the function `__divdc3`, which is implemented in

# `libclang_rt.osx.a` from LLVM compiler-rt.

FLAGS+=(-DCMAKE_SHARED_LINKER_FLAGS="-L${libdir}/darwin -lclang_rt.osx"

-DCMAKE_EXE_LINKER_FLAGS="-L${libdir}/darwin -lclang_rt.osx"

)

Yggdrasil/N/Notcurses/build_tarballs.jl

Lines 81 to 84 in c0ead9c

# We need libclang_rt.osx.a for linking FFMPEG, because this library provides the

# implementation of `__divdc3`.

BuildDependency(PackageSpec(name="LLVMCompilerRT_jll", uuid="4e17d02c-6bf5-513e-be62-445f41c75a11", version=llvm_version);

platforms=[Platform("aarch64", "macos")]),

giordano · 2024-07-26T13:25:06Z

C/catchaMouse16/build_tarballs.jl

+.PHONY: all;
+all: ${TARGET_LIB}
+$(TARGET_LIB): $(OBJS)
+	$(CC) ${LDFLAGS} -o $@ $^


Linking order is important, see for example https://wiki.gentoo.org/wiki/Project:Quality_Assurance/As-needed#Importance_of_linking_order (this may fix the issue on Windows):

Suggested change

$(CC) ${LDFLAGS} -o $@ $^

$(CC) -o $@ $^ $(LDFLAGS)

giordano · 2024-07-26T13:25:36Z

C/catchaMouse16/build_tarballs.jl

+clean:-${RM} ${TARGET_LIB} ${OBJS} $(SRCS:.c=.d)
+.PHONY: install
+install:
+	install -Dvm 755 "./lib${SRC_NAME}.$(dlext)" "$(libdir)/lib$(SRC_NAME).$(dlext)"


Suggested change

clean:-${RM} ${TARGET_LIB} ${OBJS} $(SRCS:.c=.d)

.PHONY: install

install:

install -Dvm 755 "./lib${SRC_NAME}.$(dlext)" "$(libdir)/lib$(SRC_NAME).$(dlext)"

clean:-$(RM) $(TARGET_LIB) $(OBJS) $(SRCS:.c=.d)

.PHONY: install

install:

install -Dvm 755 "./lib$(SRC_NAME).$(dlext)" "$(libdir)/lib$(SRC_NAME).$(dlext)"

giordano · 2024-07-26T13:25:45Z

C/catchaMouse16/build_tarballs.jl

+cd $WORKSPACE/srcdir
+cd catchaMouse16/C/src/


Suggested change

cd $WORKSPACE/srcdir

cd catchaMouse16/C/src/

cd ${WORKSPACE}/srcdir/catchaMouse16/C/src/

giordano · 2024-07-26T13:49:33Z

C/catchaMouse16/build_tarballs.jl

+RM = rm -f
+TARGET_LIB = "lib$(SRC_NAME).$(dlext)"
+
+SRCS = main.c fft.c stats.c helper_functions.c histcounts.c CO_AddNoise.c CO_AutoCorr.c CO_HistogramAMI.c CO_NonlinearAutocorr.c CO_TranslateShape.c DN_RemovePoints.c FC_LoopLocalSimple.c IN_AutoMutualInfoStats.c PH_Walker.c SC_FluctAnal.c ST_LocalExtrema.c SY_DriftingMean.c SY_SlidingWindow.c


Maybe do https://github.com/DynamicsAndNeuralSystems/catchaMouse16/blob/56ad41b669a750df3be60d008010c8a84a5cf4bd/C/Makefile#L18 instead of listing the files manually? This isn't very sustainable if the source code upstream changes.

brendanjohnharris · 2024-07-26T14:38:16Z

Thanks for your help, will pick this up again in the morning :)

giordano · 2024-07-30T11:15:44Z

Uhm https://buildkite.com/julialang/yggdrasil/builds/12165#01910162-a083-4498-8f3f-aa33363f4411/674-871

[02:07:40] error: /opt/aarch64-apple-darwin20/bin/aarch64-apple-darwin20-install_name_tool: changing install names or rpaths can't be redone for: lib/libcatchaMouse16.dylib (for architecture arm64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names)
[02:07:40] error: /opt/aarch64-apple-darwin20/bin/aarch64-apple-darwin20-install_name_tool: changing install names or rpaths can't be redone for: lib/libcatchaMouse16.dylib (for architecture arm64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names)

giordano · 2024-07-30T12:35:59Z

It doesn't seem to be enough, also, we have the same on x86_64 darwin too.

brendanjohnharris · 2024-08-12T02:01:45Z

@giordano should be ok now, I think; appears to build successfully on all platforms

C/catchaMouse16/build_tarballs.jl

Co-authored-by: Mosè Giordano <[email protected]>

brendanjohnharris and others added 2 commits July 26, 2024 14:31

New recipe: catchaMouse16-v0.1.0

af764e2

Exclude windows

0f2f6a2

brendanjohnharris marked this pull request as draft July 26, 2024 05:28

brendanjohnharris marked this pull request as ready for review July 26, 2024 07:37

giordano reviewed Jul 26, 2024

View reviewed changes

brendanjohnharris and others added 6 commits July 26, 2024 22:36

Change compiler to generic 'cc'

881a1a5

Co-authored-by: Mosè Giordano <[email protected]>

Change to command substitutions

a781228

Co-authored-by: Mosè Giordano <[email protected]>

Set make job count

f450b21

Co-authored-by: Mosè Giordano <[email protected]>

Specify GSL_jll version (~2.7.2)

08a2fd0

Co-authored-by: Mosè Giordano <[email protected]>

Use install instead of cp

7a4e01b

Co-authored-by: Mosè Giordano <[email protected]>

Use make install target and lower Julia compat to LTS

de4a56e

giordano reviewed Jul 26, 2024

View reviewed changes

C/catchaMouse16/build_tarballs.jl Outdated Show resolved Hide resolved

giordano reviewed Jul 26, 2024

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C/catchaMouse16/build_tarballs.jl Outdated Show resolved Hide resolved

brendanjohnharris and others added 4 commits July 26, 2024 23:09

Standardize output name

46efde0

Co-authored-by: Mosè Giordano <[email protected]>

Use command substitutions

e580151

Co-authored-by: Mosè Giordano <[email protected]>

Use c11 to avoid warnings

b7b7bfc

Use gcc for apple (?)

36bf85d

Remove windows again

c8250ee

giordano reviewed Jul 26, 2024

View reviewed changes

Hopeful fix for macos and windows

3446673

brendanjohnharris added 4 commits July 27, 2024 12:19

Enable all platforms

2179afd

Extra flags for macos fix

41b1456

Add extra flags in right place

f2d9cbb

Clean up makefile

7897772

Add headerpad flag

069f8c3

brendanjohnharris added 2 commits July 30, 2024 22:51

Headerpad flag for all machines

b3b5abd

Fix src file finding

4deeb30

giordano reviewed Aug 13, 2024

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brendanjohnharris and others added 2 commits August 13, 2024 21:42

Update C/catchaMouse16/build_tarballs.jl

9fc6681

Co-authored-by: Mosè Giordano <[email protected]>

Merge branch 'master' into catchaMouse16

14ff2cc

giordano merged commit 809e483 into JuliaPackaging:master Aug 13, 2024
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New recipe: catchaMouse16-v0.1.0 #9151

New recipe: catchaMouse16-v0.1.0 #9151

brendanjohnharris commented Jul 26, 2024

giordano commented Jul 26, 2024

brendanjohnharris commented Jul 26, 2024

giordano Jul 26, 2024

giordano Jul 26, 2024

giordano Jul 26, 2024

giordano Jul 26, 2024

brendanjohnharris commented Jul 26, 2024

giordano commented Jul 30, 2024

giordano commented Jul 30, 2024

brendanjohnharris commented Aug 12, 2024

	cd $WORKSPACE/srcdir
	cd catchaMouse16/C/src/
	cd ${WORKSPACE}/srcdir/catchaMouse16/C/src/

New recipe: catchaMouse16-v0.1.0 #9151

New recipe: catchaMouse16-v0.1.0 #9151

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