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Unable to compile on macOS, ARM64 #126

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victorlin opened this issue Mar 15, 2023 · 7 comments
Closed

Unable to compile on macOS, ARM64 #126

victorlin opened this issue Mar 15, 2023 · 7 comments

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@victorlin
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I am following the compilation guide.

cmake is successful, however make -j gives several warnings/errors. Some notable lines (full output):

clang: error: the clang compiler does not support '-march=native'

clang: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]

vectorclass/vectorclass.h:38:4: error: Please compile for the SSE2 instruction set or higher

vectorclass/vectormath_common.h:65:8: error: unknown type name 'Vec2d'

vectorclass/instrset_detect.cpp:26:10: error: couldn't allocate output register for constraint 'a'

/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"

/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size

Is there something I am missing here?
@victorlin
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I can confirm all the requirements are met:

  • C++

    details 
    % which c++
/usr/bin/c++

  • CMake version >= 2.8.10

    details 
    % cmake --version
cmake version 3.26.0

CMake suite maintained and supported by Kitware (kitware.com/cmake).

  • Boost library

    details

    From the output of cmake:

    -- Found Boost: /opt/homebrew/Caskroom/miniconda/base/envs/build-iqtree/lib/cmake/Boost-1.81.0/BoostConfig.cmake (found version "1.81.0")

  • Eigen3 library

    details 
    % brew info eigen 
==> eigen: stable 3.4.0 (bottled), HEAD
C++ template library for linear algebra
https://eigen.tuxfamily.org/
Conflicts with:
  freeling (because freeling ships its own copy of eigen)
/opt/homebrew/Cellar/eigen/3.4.0_1 (546 files, 8.4MB) *
  Poured from bottle on 2023-03-15 at 16:19:46

  • OpenMP library

    details 
    % brew info libomp
==> libomp: stable 15.0.5 (bottled) [keg-only]
LLVM's OpenMP runtime library
https://openmp.llvm.org/
/opt/homebrew/Cellar/libomp/15.0.5 (7 files, 1.6MB)
  Poured from bottle on 2022-11-28 at 17:19:46

@victorlin
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Oh, I just realized I am using an older version (2.1.2, the latest GitHub Release) which does not include 44bfe3d. I tried using v2.2.2.3 but am now facing a cmake error. I will investigate more tomorrow.

@bqminh
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bqminh commented Mar 16, 2023 via email

@holmrenser holmrenser mentioned this issue Mar 31, 2023
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@corneliusroemer
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corneliusroemer commented May 26, 2023 •
edited
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I managed to compile (on arm 12/13) with the following homebrew recipe (should make it possible to reproduce for anyone without differing local setup): https://github.com/Homebrew/homebrew-core/blob/573b15f29e31ba4143ae8137111cf87a3f181829/Formula/iqtree2.rb

The gist is:

    inreplace "CMakeLists.txt", "--target=arm64-apple-macos10.5", "-mmacosx-version-min=10.7"
    inreplace "CMakeLists.txt", "--target=arm64-apple-macos12.0.1", "-mmacosx-version-min=12.0.1"
    mkdir "build" do
      system "cmake", "..", "-DIQTREE_FLAGS=omp", "-DCMAKE_C_COMPILER=clang", "-DCMAKE_CXX_COMPILER=clang++"
      system "make", "-j"
      bin.install "iqtree2"
    end

But compared with using the official osx-64 binary, iqtree seems to get stuck a lot in substitution model fitting with errors/warnings like:

ERROR: Numerical underflow (lh-derivative). Run again with the safe likelihood kernel via -safe option

Running the official osx-64 binary, I don't get any such warning.

@thomaskf
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thomaskf commented May 27, 2023 via email

@iqtree
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iqtree commented Mar 28, 2024

We now added support for Apple M chips in v2.3.X

@iqtree iqtree closed this as completed Mar 28, 2024
@corneliusroemer corneliusroemer mentioned this issue Mar 28, 2024
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@corneliusroemer
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Thank you, that's great! I managed to compile after experimenting a bit. This is the recipe that worked in the end. Could you check whether that's the same you use? I couldn't find up to date documentation on how exactly you build on arm macs.

This worked for me:

gh repo clone iqtree/iqtree2
cd iqtree2
git submodule init
git submodule update
mkdir build
cd build
cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_CXX_FLAGS="-Dthread_local=" ..
make -j

Also see my docs PR at iqtree/iqtree.github.io#3

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4 participants
@victorlin @bqminh @thomaskf @corneliusroemer