compiling on macOS

[scfurl]

Hi @jguhlin,

Thanks for all your work on minimap2-rs! I am working on a rust project that would be ideal for minimap2 bindings. I have successfully integrated into my project in a linux environment, but compiling fails on a Mac. I suspect that it is related to SSE4 code that I need to disable when successfully building minimap2 on a Mac using make sse2only=1. I see you have related tasks in your todo list. Have you gotten minimap2-rs to specifically compile on an ARM Mac? Could you share the trick? :) Or do you think something else is causing compilation failure?

Thanks for looking!!

I have output the compilation errors when running cargo build --release below:

Compiling minimap2-sys v0.1.10 Compiling seq_io v0.3.1 Compiling csv v1.2.1 Compiling itertools v0.10.5 Compiling toml v0.5.11 The following warnings were emitted during compilation:

warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: In file included from minimap2/ksw2_ll_sse.c:9: warning: In file included from /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/emmintrin.h:13: warning: In file included from /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/xmmintrin.h:13: warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:50:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_vec_init_v2si(i, 0); warning: ^~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:129:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_packsswb((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:159:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_packssdw((v2si)m1, (v2si)m2); warning: ^~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:189:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_packuswb((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:216:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpckhbw((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:239:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpckhwd((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:260:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpckhdq((v2si)m1, (v2si)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:287:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpcklbw((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:310:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpcklwd((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:331:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_punpckldq((v2si)m1, (v2si)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:352:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddb((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:373:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddw((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:394:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddd((v2si)m1, (v2si)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:416:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddsb((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:439:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddsw((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:461:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddusb((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:483:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_paddusw((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:504:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_psubb((v8qi)m1, (v8qi)m2); warning: ^~~~~~~~~~~~~~~ warning: /Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include/mmintrin.h:525:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size warning: return (m64)builtin_ia32_psubw((v4hi)m1, (v4hi)m2); warning: ^~~~~~~~~~~~~~~ warning: fatal error: too many errors emitted, stopping now [-ferror-limit=] warning: 20 errors generated.

error: failed to run custom build command for minimap2-sys v0.1.10

[jguhlin]

Trying to find a CircleCI config that lets me test mac compilation. I can try and add a feature for sse1only, but for now, can you try simde?

cargo build --release --features simde ?

[scfurl]

Thanks for the quick reply! Hmm. Maybe I am missing something?

cargo build --release --features simde error: none of the selected packages contains these features: simde

[jguhlin]

Are you running the compilation from your own project? You'll have to set up the features in Cargo.toml Otherwise, if you are using the github version maybe do a new pull?

[scfurl]

Yes, I was... And I can confirm that a clone of the minimap2-rs repo will compile fine if I use the --features simde flag, but not without it.

So I guess I need to figure out how to have my project recognize the architecture and compile minimap2-rs appropriately. I tried just putting this in my Cargo.toml file, but it didn't work

[dependencies]
minimap2 = { version = "0.1.11", default-features = false, features = ["simde"] }

(I realize this is now outside the scope of the question so I will close this, but any help would be greatly appreciated)!!

thank you

[jguhlin]

You can leave this open if you'd like. SIMDe is SIMD-everywhere, so you should be good with it always on.

Looks like there is no option yet for per-target features: https://github.com/rust-lang/cargo/issues/1197

[scfurl]

Thanks for clarifying! So including this in my project should technically work everywhere right? But it still doesn't compile on Mac...

[dependencies]
minimap2-sys = { version = "0.1.10", features = ["simde"] }
minimap2 = "0.1.11"

[jguhlin]

Do you need minimap2-sys? If not, you can use

minimap2 = { version = "0.1.11", features = ["simde"] }

[scfurl]

Unfortunately that doesn't work either...

   Compiling minimap2-sys v0.1.10
   Compiling minimap2 v0.1.11
   Compiling scrHLAtag v0.0.1 (/Users/sfurlan/develop/scrHLAtag)
warning: unused imports: `Command`, `Stdio`
  --> src/scrHLAtag.rs:49:20
   |
49 | use std::process::{Command, Stdio};
   |                    ^^^^^^^  ^^^^^
   |
   = note: `#[warn(unused_imports)]` on by default

error: linking with `cc` failed: exit status: 1
  |
  = note: LC_ALL="C" PATH="/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/bin:/Users/sfurlan/.gem/ruby/3.1.2/bin:/Users/sfurlan/.rubies/ruby-3.1.2/lib/ruby/gems/3.1.0/bin:/Users/sfurlan/.rubies/ruby-3.1.2/bin:/opt/homebrew/opt/ruby/bin:/Users/sfurlan/miniforge3x86/bin:/Users/sfurlan/miniforge3x86/condabin:/Users/sfurlan/.local/bin:/Users/sfurlan/.cargo/bin:/Users/sfurlan/.pyenv/shims:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/sfurlan/.cargo/bin" VSLANG="1033" ZERO_AR_DATE="1" "cc" "-arch" "arm64" "/var/folders/bs/c21jznv97xv0cqtbkz8qb6yw0000gr/T/rustcLrYlU9/symbols.o" "/Users/sfurlan/develop/scrHLAtag/target/release/deps/scrHLAtag-2472820d4ffe8973.scrHLAtag.92c46941-cgu.0.rcgu.o" "/Users/sfurlan/develop/scrHLAtag/target/release/deps/scrHLAtag-2472820d4ffe8973.scrHLAtag.92c46941-cgu.1.rcgu.o" 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"/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/librustc_demangle-dcaa4442c7b0af52.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/libstd_detect-c9336c0badc0444f.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/libhashbrown-808b5de2e4735936.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/libminiz_oxide-5e2f3f7f80f17910.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/libadler-bb0de43b6a37ba94.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/librustc_std_workspace_alloc-d1c021689f193e6a.rlib" "/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib/libunwind-b235019e73283224.rlib" 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"/Users/sfurlan/.rustup/toolchains/stable-aarch64-apple-darwin/lib/rustlib/aarch64-apple-darwin/lib" "-o" "/Users/sfurlan/develop/scrHLAtag/target/release/deps/scrHLAtag-2472820d4ffe8973" "-Wl,-dead_strip" "-nodefaultlibs"
  = note: Undefined symbols for architecture arm64:
            "_ksw_extz2_sse", referenced from:
                _mm_align_pair in libminimap2_sys-40fef831d385dba0.rlib(align.o)
            "_ksw_exts2_sse", referenced from:
                _mm_align_pair in libminimap2_sys-40fef831d385dba0.rlib(align.o)
            "_ksw_extd2_sse", referenced from:
                _mm_align_pair in libminimap2_sys-40fef831d385dba0.rlib(align.o)
          ld: symbol(s) not found for architecture arm64
          clang: error: linker command failed with exit code 1 (use -v to see invocation)

[jguhlin]

Hmm, thanks for that. What about a cargo clean, then try again?

Otherwise, that's helpful info; I need to get a way to test mac builds automatically!

[scfurl]

Same result after clean and retry :(

[jguhlin]

Ok thanks for that. I've got some meetings right now but will try to get to this later today / tomorrow and reach back to you!

[jguhlin]

Still working on this, been busy! Any luck on your end?

[scfurl]

Thanks for checking in! No, I admittedly put it aside and just have been calling the minimap executable from rust for now as I need the cigar string. Look forward to eventually getting it working though!

[jguhlin]

It took me way too long to get Github actions to test on MacOS, but it's working now, so once that's finished I'll push this release out.

[Adoni5]

@jguhlin - did you find a way of testing GitHUb actions for this on Arm based architectures for MacOS? We're having issues compiling mappy-rs on M1/M2 Macs on arm, and have to use x86 emulation.

Unfortunately I'm a linux lover, and have no access to an Arm based CPU, so would be great if I could find an environment to test in!

[jguhlin]

@Adoni5 Hmm, it compiles on macos with the latest github workflow, but I think that runs on x86_64. I'm trying cross (https://github.com/cross-rs/cross) now, but under wsl2. It won't do aarch64 + macos but I guess if they are tested independently, it may work?

My work machine's ubuntu install has died during an upgrade. I'm going in on Monday with a gentoo install, but it puts me behind a bit. :/

Edit to add: Gentoo was going to take several days to build. Back on Ubuntu, but open to recommendations. Maybe Arch?

[jguhlin]

Froze on building tokio on my machine, will have to try on Monday.

[jguhlin]

@scfurl @Adoni5 New version is out, I can build on aarch64 but the cfg flags do not properly propagate for my cross compilation. Can you give it a try?

[leiste375]

@scfurl @Adoni5 New version is out, I can build on aarch64 but the cfg flags do not properly propagate for my cross compilation. Can you give it a try?

Hi

I encountered the same issue while trying to compile chopper.

I tested it by cloning the github repo, and minimap2 compiles on its own, however the error still persists when not using the "--features simde" flag mentioned above.

When trying to compile chopper I fail with the same error message as encountered by scfurl.

[jguhlin]

Hey thanks. Could you post your error logs?

On Mon, 17 Jul 2023, 10:12 pm leiste375, @.***> wrote:

@scfurl https://github.com/scfurl @Adoni5 https://github.com/Adoni5 New version is out, I can build on aarch64 but the cfg flags do not properly propagate for my cross compilation. Can you give it a try?

Hi

I encountered the same issue while trying to compile chopper. I tested it by cloning the github repo, however the error still persists when not using the "--features simde" flag mentioned above.

— Reply to this email directly, view it on GitHub https://github.com/jguhlin/minimap2-rs/issues/30#issuecomment-1638002626, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOA2CBSQOBB4S2QKSQXVOTXQUT2FANCNFSM6AAAAAAWQOEIJY . You are receiving this because you were mentioned.Message ID: @.***>

[leiste375]

Hey thanks. Could you post your error logs?

The error messages were exactly the same as encountered by @scfurl. Without simde the one at the top, and with simde the one further below (Undefined symbols for architecture arm64...).

When turning default-features off completely and only using simde, as suggested above, I run into a versioning error. I was able to resolve that by playing around with the .toml but ended up with the latter error.

PS: On a side-note, cross-compile (x86_64-apple-darwin) works fine for now, and at least as far as chopper goes, the performance is fine.

PPS: minimap2 itself compiles succesfully, albeit with a couple of warnings about unused flags, and generates all the *.o files, but the final program, chopper in my case, then fails to compile.

Here are the warnings: warning: clang: warning: -lm: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: -lpthread: 'linker' input unused [-Wunused-command-line-argument] warning: clang: warning: argument unused during compilation: '-mfpu=neon' [-Wunused-command-line-argument]

From what I can gather, minimap2 uses neon for the ARM instruction set, but this is not properly translated in the build.rs. I haven't figured out the proper way to do it tho, or whether the issue lies with my own compiler, minimap2 or minimap2-rs...

[jguhlin]

Cool thanks. Good to know. I'll dig into it more next week. Cheers

On Tue, 18 Jul 2023, 4:14 pm leiste375, @.***> wrote:

Hey thanks. Could you post your error logs?

The error messages were exactly the same as encountered by @scfurl https://github.com/scfurl. Without simde the one at the top, and with simde the one further below (Undefined symbols for architecture arm64...).

I also tried loading the crate directly via GitHub. When doing so I have to manually turn default-features off and separately specify flate2 (in the chopper .toml) in addition to simde (as a feature of minimap2), only to end up at the latter error message (Undefined symbols...).

— Reply to this email directly, view it on GitHub https://github.com/jguhlin/minimap2-rs/issues/30#issuecomment-1639555523, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOA2CGRCQ22THDTNZBLIGDXQYSSVANCNFSM6AAAAAAWQOEIJY . You are receiving this because you were mentioned.Message ID: @.***>

[jguhlin]

@leiste375 I think it's the build.rs not taking in the proper options. I've sorted a mac to borrow for a few weeks to get it sorted (hopefully it takes an afternoon!). It's my first FFI project so am surprised it has worked this well even.

[jguhlin]

I did not get an aarch64 mac to test on. :/ Still trying.

[Adoni5]

Thanks @jguhlin - I'll have a think and see what I can do as well.

[leiste375]

I did not get an aarch64 mac to test on. :/ Still trying.

Let me know if there is anything I can try from my end. I hope I'll find time to look at it again soon

[leiste375]

Managed to compile. Will test it and create a pull request later on if that's ok with you

[Adoni5]

🔥 Thanks @leiste375