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philipc / gkl-rs

Rust bindings for Intel Genomics Kernel Library (GKL)
Apache License 2.0
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Compiling with x86_64-unknown-linux-musl #1

Closed rhysnewell closed 2 years ago

rhysnewell commented 2 years ago

Hi Philip,

I've been trying to compile Lorikeet + gkl-rs with x86_64-unknown-linux-musl as the target in order to produce a statically linked binary that can easily be distributed in releases. However, I'm having some difficulties with the custome build script that gkl-rs uses. These are the errors I get when I've attempted it:

The following warnings were emitted during compilation:

warning: In file included from gkl/pairhmm/avx-pairhmm.h:26,
warning:                  from gkl/pairhmm/avx_impl.cc:25:
warning: gkl/pairhmm/Context.h:27:10: fatal error: cmath: No such file or directory
warning:  #include <cmath> // std::isinf
warning:           ^~~~~~~
warning: compilation terminated.

error: failed to run custom build command for `gkl v0.1.0 (https://github.com/philipc/gkl-rs#11a88b99)`

Caused by:
  process didn't exit successfully: `/github/workspace/target/release/build/gkl-3421105fe0419bef/build-script-build` (exit status: 1)
  --- stdout
  cargo:rerun-if-changed=gkl
  TARGET = Some("x86_64-unknown-linux-musl")
  OPT_LEVEL = Some("3")
  HOST = Some("x86_64-unknown-linux-gnu")
  CC_x86_64-unknown-linux-musl = None
  CC_x86_64_unknown_linux_musl = None
  TARGET_CC = None
  CC = None
  CROSS_COMPILE = None
  CFLAGS_x86_64-unknown-linux-musl = None
  CFLAGS_x86_64_unknown_linux_musl = None
  TARGET_CFLAGS = None
  CFLAGS = None
  CRATE_CC_NO_DEFAULTS = None
  DEBUG = Some("false")
  CARGO_CFG_TARGET_FEATURE = Some("fxsr,sse,sse2")
  running: "musl-gcc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" "-o" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/pairhmm/pairhmm_common.o" "-c" "gkl/pairhmm/pairhmm_common.cc"
  exit status: 0
  running: "musl-gcc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" "-o" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/smithwaterman/smithwaterman_common.o" "-c" "gkl/smithwaterman/smithwaterman_common.cc"
  exit status: 0
  AR_x86_64-unknown-linux-musl = None
  AR_x86_64_unknown_linux_musl = None
  TARGET_AR = None
  AR = None
  running: "ar" "cq" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/libgkl-common.a" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/pairhmm/pairhmm_common.o" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/smithwaterman/smithwaterman_common.o"
  exit status: 0
  running: "ar" "s" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/libgkl-common.a"
  exit status: 0
  cargo:rustc-link-lib=static=gkl-common
  cargo:rustc-link-search=native=/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out
  TARGET = Some("x86_64-unknown-linux-musl")
  OPT_LEVEL = Some("3")
  HOST = Some("x86_64-unknown-linux-gnu")
  CC_x86_64-unknown-linux-musl = None
  CC_x86_64_unknown_linux_musl = None
  TARGET_CC = None
  CC = None
  CROSS_COMPILE = None
  CFLAGS_x86_64-unknown-linux-musl = None
  CFLAGS_x86_64_unknown_linux_musl = None
  TARGET_CFLAGS = None
  CFLAGS = None
  CRATE_CC_NO_DEFAULTS = None
  DEBUG = Some("false")
  CARGO_CFG_TARGET_FEATURE = Some("fxsr,sse,sse2")
  running: "musl-gcc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" "-mavx" "-o" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/pairhmm/avx_impl.o" "-c" "gkl/pairhmm/avx_impl.cc"
  cargo:warning=In file included from gkl/pairhmm/avx-pairhmm.h:26,
  cargo:warning=                 from gkl/pairhmm/avx_impl.cc:25:
  cargo:warning=gkl/pairhmm/Context.h:27:10: fatal error: cmath: No such file or directory
  cargo:warning= #include <cmath> // std::isinf
  cargo:warning=          ^~~~~~~
  cargo:warning=compilation terminated.
  exit status: 1

  --- stderr

  error occurred: Command "musl-gcc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-m64" "-mavx" "-o" "/github/workspace/target/x86_64-unknown-linux-musl/release/build/gkl-9101aadbf0ecc6ed/out/gkl/pairhmm/avx_impl.o" "-c" "gkl/pairhmm/avx_impl.cc" with args "musl-gcc" did not execute successfully (status code exit status: 1).

warning: build failed, waiting for other jobs to finish...
error: build failed

I thought this might be something to do with using musl-gcc rather than musl-g++ to compile, but the docker container this in running is meant to use musl-g++ in order to get past this cmath issue. (See: https://github.com/rhysnewell/rust-cargo-musl-action/blob/master/Dockerfile)

Any help would be appreciated! :)

Cheers, Rhys

philipc commented 2 years ago

See if d409df16b7e583ce42cada08b6312d3696028fcd fixes it.

rhysnewell commented 2 years ago

Yep, worked perfectly thanks! Closing now