installation error with rust on macOS #35
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just an update-- still haven't gotten themisto to install on my mac laptop, but I did get the themisto binary installed on our compute cluster. so will probably just work with that. But here's the progress I made to get themisto working on my laptop-- changing rust versions didn't help, so I went back to nightly Rust as default: Then, I went into the ggcat directory, and ran the following to update rust dependencies: I then went into the build directory, and ran the following: (I installed gcc with homebrew on mac-- gcc links to clang and g++ links to clang++, so to avoid breaking things, homebrew installs gcc as gcc-13 and g++ as g++-13, where 13 is the current version number) I then ran make. I no longer get the "stdsimd" error, but get some other errors. Here is the full output I get from running these steps-- my apologies if this is overwhelming and not helpful... it does look like I can get themisto working on our cluster, but it would be nice if I can get it working on my mac laptop too! $ themisto % cd ggcat Update the VERSION argument value or use a ... suffix to tell -- Compiler is recent enough to support C++14. Update the VERSION argument value or use a ... suffix to tell CMake Warning (dev) at SBWT/sdsl-lite/external/libdivsufsort/CMakeLists.txt:7 (project): The following variable(s) would be set to empty: This warning is for project developers. Use -Wno-dev to suppress it. -- Performing Test HAVE_GCC_WALL Update the VERSION argument value or use a ... suffix to tell -- Submodule update Update the VERSION argument value or use a ... suffix to tell CMake Deprecation Warning at build/_deps/roaring-src/tools/cmake/FindCTargets.cmake:2 (cmake_policy): Update the VERSION argument value or use a ... suffix to tell -- BENCHMARK_DATA_DIR: /Users/rohan/Bioinformatics/themisto/build/_deps/roaring-src/benchmarks/realdata/ warning: call to warning: call to Compiling approx v0.5.1 Compiling newtype_derive v0.1.6 Compiling wyz v0.5.1 Compiling ggcat_querier v0.1.1 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/querier) For more information about this error, try error[E0599]: no method named error[E0599]: no method named error[E0609]: no field error[E0599]: no method named Some errors have detailed explanations: E0599, E0609. |
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OS X binaries are now available with the latest version: https://github.com/algbio/themisto/releases/tag/v3.2.2 |
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Hello, thanks for releasing MacOS binaries! Unfortunately, neither binary is working for me. I am running MacOS Sonoma 14.2.1 With the x86_64 binary I get this error message: With the aarch64 binary I get: |
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Hi, I'm looking into this; it looks like some of the dependencies are not built with the correct compiler flags.. |
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@tmaklin set(CMAKE_SYSTEM_PROCESSOR X86)while CMake documentation says:
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It's probably not the toolchain file as the x86 binary doesn't work on my x86 mac either but it might affect the arm64 macs I suppose. Though I have used the same approach to cross compile other C++ projects for arm64 macs and they seem to work (see eg https://github.com/PROBIC/mSWEEP/releases) (I don't have an arm64 mac to test these myself tho). |
Your arm64 mac toolchain used in that project has: set(CMAKE_SYSTEM_PROCESSOR ARM64)rather than: set(CMAKE_SYSTEM_PROCESSOR X86)like in Themisto's toolchain. Themisto arm64 binary doesn't work on my arm64 Mac, while arm64 binary from your project worked. otool -L mSWEEP
mSWEEP (architecture x86_64):
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.8)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1300.36.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1319.0.0)
mSWEEP (architecture arm64):
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.8)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1300.36.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1319.0.0) |
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I think I figured it out -- KMC was using static linking for everything which messed up the compiled library, and the whole project additionally needs to link the GCC C++ library statically because it's not available on macs. New scripts at https://github.com/algbio/themisto/tree/update-macos-build Also changed New mac binaries are available here https://github.com/algbio/themisto/releases/tag/v3.2.2 @iosfwd can you check if the aarch64 binary still gives the linker error? The x86 binary does not do that anymore on my machine. |
New aarch64 binary works on my machine now. @tmaklin |
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Thanks! @rohanmaddamsetti this should hopefully be fixed now. |
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Both MacOS binaries work on my computer now. Thanks guys!
…On Wed, Jun 12, 2024 at 7:25 AM Tommi Mäklin ***@***.***> wrote:
Thanks! @rohanmaddamsetti <https://github.com/rohanmaddamsetti> this
should hopefully be fixed now.
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Hello,
When I run "make" to install themisto on my mac laptop, I get the following error:
error[E0635]: unknown feature
stdsimd--> /Users/rohan/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ahash-0.8.3/src/lib.rs:99:42
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99 | #![cfg_attr(feature = "stdsimd", feature(stdsimd))]
| ^^^^^^^
For more information about this error, try
rustc --explain E0635.error: could not compile
ahash(lib) due to 1 previous errorwarning: build failed, waiting for other jobs to finish...
make[3]: *** [lib/libggcat_cpp_bindings.a] Error 101
make[2]: *** [CMakeFiles/ggcat_cpp_api] Error 2
make[1]: *** [CMakeFiles/ggcat_cpp_api.dir/all] Error 2
make: *** [all] Error 2
Based on these links, it looks like the stdsimd feature was removed from Rust on February, breaking the themisto installation:
https://users.rust-lang.org/t/error-e0635-unknown-feature-stdsimd/106445
tkaitchuck/aHash#200
following some of these discussions, hoping to find a workaround by installing a Rust version dated February 4.
The text was updated successfully, but these errors were encountered: