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HDF5 doesn't work with cross #233

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a1ecbr0wn opened this issue Mar 19, 2023 · 0 comments
Open

HDF5 doesn't work with cross #233

a1ecbr0wn opened this issue Mar 19, 2023 · 0 comments

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@a1ecbr0wn
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a1ecbr0wn commented Mar 19, 2023 •
edited

If you use a custom cross container with a cross compiled version of the hdf5 library, there are a few issues that prevent the build of the hdf5-sys rust library.

e.g.,

  1. create a container with a version of the hdf5 library for another architecture and you tell it to find the package config file:
RUN apt-get install --assume-yes libhdf5-dev:armhf
ENV PKG_CONFIG_PATH_armv7-unknown-linux-gnueabihf=/usr/lib/arm-linux-gnueabihf/pkgconfig \
    PKG_CONFIG_LIBDIR_armv7_unknown_linux_gnueabihf=/usr/lib/arm-linux-gnueabihf \
    PKG_CONFIG_SYSROOT_DIR_armv7_unknown_linux_gnueabihf=/usr/lib/arm-linux-gnueabihf \
    CARGO_TARGET_ARMV7_UNKNOWN_LINUX_GNUEABIHF_LINKER=arm-linux-gnueabihf-gcc \
    CC_armv7_unknown_linux_gnueabihf=arm-linux-gnueabihf-gcc \
    CXX_armv7_unknown_linux_gnueabihf=arm-linux-gnueabihf-g++ \
    BINDGEN_EXTRA_CLANG_ARGS_armv7_unknown_linux_gnueabihf="--sysroot=/usr/arm-linux-gnueabihf" \
    QEMU_LD_PREFIX=/usr/arm-linux-gnueabihf

run

cross build --target=armv7-unknown-linux-gnueabihf

The default looks in the wrong place for the binary, it looks in /usr/lib/arm-linux-gnueabihf/usr/include/hdf5/serial because it cant find the hdf5.pc file:

error: failed to run custom build command for `hdf5-sys v0.8.1`

Caused by:
  process didn't exit successfully: `/target/debug/build/hdf5-sys-c1e87a537622b7ea/build-script-build` (exit status: 101)
  --- stdout
  Attempting to find HDF5 via pkg-config...
  cargo:rerun-if-env-changed=HDF5_NO_PKG_CONFIG
  cargo:rerun-if-env-changed=PKG_CONFIG_ALLOW_CROSS_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_ALLOW_CROSS_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=TARGET_PKG_CONFIG_ALLOW_CROSS
  cargo:rerun-if-env-changed=PKG_CONFIG_ALLOW_CROSS
  cargo:rerun-if-env-changed=PKG_CONFIG_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=TARGET_PKG_CONFIG
  cargo:rerun-if-env-changed=PKG_CONFIG
  cargo:rerun-if-env-changed=HDF5_STATIC
  cargo:rerun-if-env-changed=HDF5_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_STATIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=TARGET_PKG_CONFIG_PATH
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH
  cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR
  cargo:rerun-if-env-changed=SYSROOT
  cargo:rerun-if-env-changed=HDF5_STATIC
  cargo:rerun-if-env-changed=HDF5_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_STATIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=TARGET_PKG_CONFIG
  cargo:rerun-if-env-changed=PKG_CONFIG
  cargo:rerun-if-env-changed=HDF5_STATIC
  cargo:rerun-if-env-changed=HDF5_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_STATIC
  cargo:rerun-if-env-changed=PKG_CONFIG_ALL_DYNAMIC
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=TARGET_PKG_CONFIG_PATH
  cargo:rerun-if-env-changed=PKG_CONFIG_PATH
  cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_armv7_unknown_linux_gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_armv7-unknown-linux-gnueabihf
  cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_armv7_unknown_linux_gnueabihf
  Found HDF5 pkg-config entry
      Include paths:
      - "/usr/lib/arm-linux-gnueabihf/usr/include/hdf5/serial"
      Link paths:
      - "/usr/lib/arm-linux-gnueabihf/usr/lib/arm-linux-gnueabihf/hdf5/serial"
  Unable to locate HDF5 headers from pkg-config info.
  Found HDF5 headers at:
      "/usr/include/hdf5/serial"
  Adding to link path:
      "/usr/lib/x86_64-linux-gnu/hdf5/serial"
  Parsing HDF5 config from:
      "/usr/include/hdf5/serial/H5pubconf.h"
  Looking for HDF5 library binary...
  Adding extra link paths (ld)...
      /usr/local/lib/x86_64-linux-gnu
      /lib/x86_64-linux-gnu
      /usr/lib/x86_64-linux-gnu
      /usr/lib/x86_64-linux-gnu64
      /usr/local/lib64
      /lib64
      /usr/lib64
      /usr/local/lib
      /lib
      /usr/lib
      /usr/x86_64-linux-gnu/lib64
      /usr/x86_64-linux-gnu/lib

  --- stderr
  thread 'main' panicked at 'Unable to infer HDF5 library runtime version (can't find the binary).', /cargo/registry/src/index.crates.io-6f17d22bba15001f/hdf5-sys-0.8.1/build.rs:155:5
  1. If you tell the set parameters to tell hdf5-sys build where to find the the binary anyway, the cross build still failes as it tries to link the library as the wrong architecture:
ENV HDF5_DIR=/usr/lib/arm-linux-gnueabihf/hdf5/serial

run

cross build --target=armv7-unknown-linux-gnueabihf

Complains about the wrong ELF class: ELFCLASS32:

error: failed to run custom build command for `hdf5-sys v0.8.1`

Caused by:
  process didn't exit successfully: `/target/debug/build/hdf5-sys-c1e87a537622b7ea/build-script-build` (exit status: 101)
  --- stdout
  Setting HDF5 root from environment variable:
      HDF5_DIR = "/usr/lib/arm-linux-gnueabihf/hdf5/serial"
  Custom HDF5_DIR provided; rpath can be set via:
      RUSTFLAGS="-C link-args=-Wl,-rpath,/usr/lib/arm-linux-gnueabihf/hdf5/serial/lib"
  Parsing HDF5 config from:
      "/usr/lib/arm-linux-gnueabihf/hdf5/serial/include/H5pubconf.h"
  Looking for HDF5 library binary...
  Adding extra link paths (ld)...
      /usr/local/lib/x86_64-linux-gnu
      /lib/x86_64-linux-gnu
      /usr/lib/x86_64-linux-gnu
      /usr/lib/x86_64-linux-gnu64
      /usr/local/lib64
      /lib64
      /usr/lib64
      /usr/local/lib
      /lib
      /usr/lib
      /usr/x86_64-linux-gnu/lib64
      /usr/x86_64-linux-gnu/lib
  Attempting to load: "/usr/lib/arm-linux-gnueabihf/hdf5/serial/lib/libhdf5.so"
      => /usr/lib/arm-linux-gnueabihf/hdf5/serial/lib/libhdf5.so: wrong ELF class: ELFCLASS32
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