cross compiling to linux android

[jianshu93]

Hi @jguhlin,

I am not sure whether this is interesting to others but I want to report here. I was trying to import and compile many Rust software packages to Linux-based android device so that we can run them on phones for a mobile bioinformatic era (CPU for phones are now quite powerful, like SnapDragon 3 generation). For pure Rust based packages, I have no problems for example, my GSearch crate, sourmash crate, rust-mDBG crate and many others. However, when I was trying to compiling minimap2-rs, there are tons of problems:

install android studio first and deploy it for rust in .bash_profile like this:

android compiling and ld library

export CARGO_TARGET_AARCH64_LINUX_ANDROID_LINKER="/Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/aarch64-linux-android35-clang" export CXX_aarch64_linux_android="/Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/aarch64-linux-android35-clang++" export CC_aarch64_linux_android="/Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/aarch64-linux-android35-clang" export AR_aarch64_linux_android="/Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/llvm-ar"

$ rustup target add aarch64-linux-android $ cargo build --target aarch64-linux-android --release

error: linking with /Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/aarch64-linux-android35-clang failed: exit status: 1 | = note: LC_ALL="C" PATH="/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/bin:/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/bin:/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/bin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Users/jianshuzhao/Github/SPAdes-4.0.0-Darwin/bin:/Users/jianshuzhao/.cargo/bin:/Library/Java/JavaVirtualMachines/jdk-21.jdk/Contents/Home/bin:/Users/jianshuzhao/perl5/bin:/usr/local/bin:/opt/homebrew/bin:/Users/jianshuzhao/bin:/opt/homebrew/opt/bzip2/bin:/Users/jianshuzhao/Github/mummer-4.0.0beta5/bin:/Users/jianshuzhao/go/bin:/Users/jianshuzhao/Github/hmmer-3.4/bin:/opt/homebrew/opt/llvm/bin:/opt/homebrew/opt/openjdk/bin:/opt/homebrew/Cellar/coreutils/9.1/bin:/opt/homebrew/opt/ruby/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/X11/bin:/Library/TeX/texbin:/usr/local/go/bin" VSLANG="1033" "/Users/jianshuzhao/Library/Android/sdk/ndk/27.0.12077973/toolchains/llvm/prebuilt/darwin-x86_64/bin/aarch64-linux-android35-clang" "-Wl,--version-script=/var/folders/mr/8qybn91j5fgdbrcdmq7ckftw0000gn/T/rustcOO9CIw/list" "-Wl,--no-undefined-version" "/var/folders/mr/8qybn91j5fgdbrcdmq7ckftw0000gn/T/rustcOO9CIw/symbols.o" "/Users/jianshuzhao/Github/minimap2-rs-test/target/aarch64-linux-android/release/deps/minimap2_sys-48223b1ce1d5498d.minimap2_sys.49addbfa3dae579b-cgu.0.rcgu.o" "/Users/jianshuzhao/Github/minimap2-rs-test/target/aarch64-linux-android/release/deps/minimap2_sys-48223b1ce1d5498d.035gy82oxncw2556qjxih17mk.rcgu.o" "-Wl,--as-needed" "-Wl,-Bdynamic" "-lm" "-lpthread" "-Wl,-Bstatic" "-llibminimap" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libstd-e8850eccf2f3dd32.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libpanic_unwind-a094c6be714bf5e8.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libobject-bd105c046d7d3f4a.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libmemchr-b65977fbd4d13b26.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libaddr2line-c59b235c1428dacb.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libgimli-4dc541cf9acc0f28.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/librustc_demangle-fcbcb6953c2582a4.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libstd_detect-a5c6c9bf9652d1e7.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libhashbrown-402a49b850a42e97.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/librustc_std_workspace_alloc-19962e45d6dd8556.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libminiz_oxide-778d7232beb22b27.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libadler-ce6b56ec013571c3.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libunwind-7757d29c205c9e38.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libcfg_if-439f5a2fb94b85f2.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/liblibc-cbc1d2077079a2d7.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/liballoc-cbbe8b3cfeaabbd2.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/librustc_std_workspace_core-d80ded003c259869.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libcore-556f2758be89c720.rlib" "/Users/jianshuzhao/.rustup/toolchains/nightly-aarch64-apple-darwin/lib/rustlib/aarch64-linux-android/lib/libcompiler_builtins-bb1d92eb991222e1.rlib" "-Wl,-Bdynamic" "-ldl" "-llog" "-lunwind" "-ldl" "-lm" "-lc" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/Users/jianshuzhao/Github/minimap2-rs-test/target/aarch64-linux-android/release/build/minimap2-sys-47359202de654a64/out" "-o" "/Users/jianshuzhao/Github/minimap2-rs-test/target/aarch64-linux-android/release/deps/libminimap2_sys-48223b1ce1d5498d.so" "-Wl,--gc-sections" "-shared" "-Wl,-soname=libminimap2_sys-48223b1ce1d5498d.so" "-Wl,-z,relro,-z,now" "-Wl,-O1" "-Wl,--strip-debug" "-nodefaultlibs" = note: ld.lld: error: unable to find library -lpthread clang: error: linker command failed with exit code 1 (use -v to see invocation)

The following warnings were emitted during compilation:

warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: [email protected]+minimap2.2.28: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument]

I can see that android clang does not support -lpthread, which is only for linux. However the android libc (bionic) does support many pthread functions: In Android, all pthread functionality is directly available through the Bionic libc without requiring explicit linking. This means that while you can use pthread functions like pthread_create or pthread_mutex_init, you don't add -lpthread to your linker flags.

I am wondering whther it is possible to add a conditional compiling for android devices so that -phthread is not used but it is actually functioning.

I also want to hear how @lh3 thinks, https://github.com/jguhlin/minimap2-rs/issues/63#issuecomment-2269003167_

Thanks,

Jianshu