Clang PGO and glibc on x86_64: ld.lld: error: duplicate symbol: __getcwd

[ms178]

I am using the following PKGBUILD for Glibc where I inject the PGO-Flags. Clang version is: bbcfe6f:

# Maintainer: Marcus Seyfarth <marcus85@gmx.de>

pkgbase=glibc
pkgname=(glibc lib32-glibc)
pkgver=2.39
pkgrel=16.1
pkgdesc='GNU C Library'
arch=('x86_64')
url='https://www.gnu.org/software/libc'
license=('GPL' 'LGPL')
depends=('linux-api-headers' 'tzdata')
makedepends=('git' 'gd' 'python' 'lib32-gcc-libs')
optdepends=('perl: for mtrace'
            'gd: graph image generation with memusage')
backup=(etc/gai.conf
        etc/locale.gen
        etc/nscd.conf)
options=('staticlibs' '!lto' 'buildflags')
install=glibc.install
source=("git+https://sourceware.org/git/glibc.git#branch=azanella/clang"
#source=("git+https://sourceware.org/git/glibc.git"
        locale-gen
        locale.gen.txt
        lib32-glibc.conf
        malloc_tune.patch
        mathlto.patch
        #nostackshrink.patch
        tzselect-proper-zone-file.patch
        04-mandriva-va_args.patch
        05-mandriva-zstdcompressedlocals.patch
        06-mandriva-nss-crash.patch
        07-mandriva-nostrictaliasing.patch
        #08-mandriva-float.patch
        nptl.patch
        )
sha256sums=('SKIP'
            )

prepare() {

    mkdir -p glibc-build lib32-glibc-build

  [[ -d glibc-$pkgver ]] && ln -s glibc-$pkgver glibc

    local src
    for src in "${source[@]}"; do
        src="${src%%::*}"
        src="${src##*/}"
        [[ $src = *.patch ]] || continue
        echo "Applying patch $src..."
        patch --directory="glibc" --forward --strip=1 < "$src"
    done
}

build() {

  cd "$srcdir/glibc-build"

  echo "slibdir=/usr/lib" >> configparms
  echo "rtlddir=/usr/lib" >> configparms
  echo "sbindir=/usr/bin" >> configparms
  echo "rootsbindir=/usr/bin" >> configparms

  # Credits @allanmcrae
  # https://github.com/allanmcrae/toolchain/blob/f18604d70c5933c31b51a320978711e4e6791cf1/glibc/PKGBUILD
  # remove fortify for building libraries
  CFLAGS=${CFLAGS/-Wp,-D_FORTIFY_SOURCE=2/}

  "$srcdir/glibc/configure" \
      --prefix=/usr \
      --libdir=/usr/lib \
      --libexecdir=/usr/lib \
      --with-headers=/usr/include \
      --disable-bind-now \
      --without-selinux \
      --disable-fortify-source \
      --disable-systemtap \
      --disable-cet \
      --enable-kernel=6.8.1 \
      --enable-multi-arch \
      --disable-profile \
      --disable-crypt \
      --disable-werror

  # build libraries with fortify disabled
  echo "build-programs=no" >> configparms
  echo "CFLAGS += -g3 -mllvm -vp-counters-per-site=6 -fprofile-generate=/home/marcus/Downloads/glibc-%p.profraw" >> configparms
  echo "LDFLAGS += -g3 -mllvm -vp-counters-per-site=6 -fprofile-generate=/home/marcus/Downloads/glibc-%p.profraw" >> configparms
  make -O

  # re-enable fortify for programs
  sed -i "/build-programs=/s#no#yes#" configparms
  echo "CFLAGS += -Wp,-D_FORTIFY_SOURCE=0" >> configparms
  make -O

  # build info pages manually for reproducibility
  make info

  cd "$srcdir/lib32-glibc-build"
  export CC="clang -m32 -mfpmath=sse -mstackrealign"
  export CXX="clang++ -m32 -mfpmath=sse -mstackrealign"

  echo "slibdir=/usr/lib32" >> configparms
  echo "rtlddir=/usr/lib32" >> configparms
  echo "sbindir=/usr/bin" >> configparms
  echo "rootsbindir=/usr/bin" >> configparms

  "$srcdir/glibc/configure" \
      --host=i686-pc-linux-gnu \
      --prefix=/usr \
      --libdir=/usr/lib32 \
      --libexecdir=/usr/lib32 \
      --disable-cet \
      --enable-kernel=6.8.1 \
      --disable-bind-now \
      --without-selinux \
      --disable-fortify-source \
      --disable-systemtap \
      --disable-profile \
      --disable-crypt \
      --disable-sanity-checks \
      --disable-werror \
      "${_configure_flags[@]}"

  # build libraries with fortify disabled
  echo "build-programs=no" >> configparms
  echo "CFLAGS += -g3 -mllvm -vp-counters-per-site=6 -fprofile-generate=/home/marcus/Downloads/glibc-%p.profraw" >> configparms
  echo "LDFLAGS += -g3 -mllvm -vp-counters-per-site=6 -fprofile-generate=/home/marcus/Downloads/glibc-%p.profraw" >> configparms
  make -O

  # re-enable fortify for programs
  sed -i "/build-programs=/s#no#yes#" configparms
  echo "CFLAGS += -Wp,-D_FORTIFY_SOURCE=0" >> configparms
  make -O

  # pregenerate C.UTF-8 locale until it is built into glibc
  # (https://sourceware.org/glibc/wiki/Proposals/C.UTF-8, FS#74864)
  elf/ld.so --library-path "$PWD" locale/localedef -c -f ../glibc/localedata/charmaps/UTF-8 -i ../glibc/localedata/locales/C ../C.UTF-8/
}

# Credits for skip_test() and check() @allanmcrae
# https://github.com/allanmcrae/toolchain/blob/f18604d70c5933c31b51a320978711e4e6791cf1/glibc/PKGBUILD
skip_test() {
  test=${1}
  file=${2}
  sed -i "s/\b${test}\b//" "${srcdir}"/glibc/${file}
}

check() (
  cd glibc-build

  # adjust/remove buildflags that cause false-positive testsuite failures
  sed -i '/FORTIFY/d' configparms                                     # failure to build testsuite
  sed -i 's/-Werror=format-security/-Wformat-security/' config.make   # failure to build testsuite
  sed -i '/CFLAGS/s/-fno-plt//' config.make                           # 16 failures
  sed -i '/CFLAGS/s/-fexceptions//' config.make                       # 1 failure
  LDFLAGS=${LDFLAGS/,-z,now/}                                         # 10 failures

  # The following tests fail due to restrictions in the Arch build system
  # The correct fix is to add the following to the systemd-nspawn call:
  # --system-call-filter="@clock @memlock @pkey"
  _skip_test test-errno-linux        sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-mlock2              sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-ntp_gettime         sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-ntp_gettimex        sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-pkey                sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-process_mrelease    sysdeps/unix/sysv/linux/Makefile
  _skip_test tst-adjtime             time/Makefile

  make -O check
)

package_glibc() {
  pkgdesc='GNU C Library'
  depends=('linux-api-headers>=4.10' tzdata filesystem)
  optdepends=('gd: for memusagestat'
              'perl: for mtrace')
  install=glibc.install
  backup=(etc/gai.conf
          etc/locale.gen
          etc/nscd.conf)

  make -C glibc-build install_root="$pkgdir" install
  rm -f "$pkgdir"/etc/ld.so.cache

  # Shipped in tzdata
  rm -f "$pkgdir"/usr/bin/{tzselect,zdump,zic}

  cd glibc

  install -dm755 "$pkgdir"/usr/lib/{locale,systemd/system,tmpfiles.d}
  install -m644 nscd/nscd.conf "$pkgdir/etc/nscd.conf"
  install -m644 nscd/nscd.service "$pkgdir/usr/lib/systemd/system"
  install -m644 nscd/nscd.tmpfiles "$pkgdir/usr/lib/tmpfiles.d/nscd.conf"
  install -dm755 "$pkgdir/var/db/nscd"

  install -m644 posix/gai.conf "$pkgdir"/etc/gai.conf

  install -m755 "$srcdir/locale-gen" "$pkgdir/usr/bin"

  # Create /etc/locale.gen
  install -m644 "$srcdir/locale.gen.txt" "$pkgdir/etc/locale.gen"
  sed -e '1,3d' -e 's|/| |g' -e 's|\\| |g' -e 's|^|#|g' \
    "$srcdir/glibc/localedata/SUPPORTED" >> "$pkgdir/etc/locale.gen"

  # install C.UTF-8 so that it is always available
  install -dm755 "$pkgdir/usr/lib/locale"
  cp -r "$srcdir/C.UTF-8" -t "$pkgdir/usr/lib/locale"
  sed -i '/#C\.UTF-8 /d' "$pkgdir/etc/locale.gen"

  # Provide tracing probes to libstdc++ for exceptions, possibly for other
  # libraries too. Useful for gdb's catch command.
  #install -Dm644 "$srcdir/sdt.h" "$pkgdir/usr/include/sys/sdt.h"
  #install -Dm644 "$srcdir/sdt-config.h" "$pkgdir/usr/include/sys/sdt-config.h"
}

package_lib32-glibc() {
  pkgdesc='GNU C Library (32-bit)'
  depends=("glibc=$pkgver")
  options+=('!emptydirs')

  cd lib32-glibc-build

  make install_root="$pkgdir" install
  rm -rf "$pkgdir"/{etc,sbin,usr/{bin,sbin,share},var}

  # We need to keep 32 bit specific header files
  find "$pkgdir/usr/include" -type f -not -name '*-32.h' -delete

  # Dynamic linker
  install -d "$pkgdir/usr/lib"
  ln -s ../lib32/ld-linux.so.2 "$pkgdir/usr/lib/"

  # Add lib32 paths to the default library search path
  install -Dm644 "$srcdir/lib32-glibc.conf" "$pkgdir/etc/ld.so.conf.d/lib32-glibc.conf"

  # Symlink /usr/lib32/locale to /usr/lib/locale
  ln -s ../lib/locale "$pkgdir/usr/lib32/locale"
}

I see the following error:

ld.lld: error: duplicate symbol: __getcwd
>>> defined at getcwd.c:49 (../sysdeps/unix/sysv/linux/getcwd.c:49)
>>>            /tmp/makepkg/glibc/src/glibc-build/elf/dl-allobjs.os:(__getcwd)
>>> defined at getcwd.c:49 (/tmp/makepkg/glibc/src/glibc/io/../sysdeps/unix/sysv/linux/getcwd.c:49)
>>>            getcwd.os:(__GI___getcwd) in archive /tmp/makepkg/glibc/src/glibc-build/libc_pic.a
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [Makefile:1309: /tmp/makepkg/glibc/src/glibc-build/elf/librtld.map] error 1

Flags in /etc/makepkg.conf:

export CC=clang
export CXX=clang++
export CC_LD=lld
export CXX_LD=lld
export AR=llvm-ar
export NM=llvm-nm
export STRIP=llvm-strip
export OBJCOPY=llvm-objcopy
export OBJDUMP=llvm-objdump
export READELF=llvm-readelf
export RANLIB=llvm-ranlib
export HOSTCC=clang
export HOSTCXX=clang++
export HOSTAR=llvm-ar
export CPPFLAGS="-D_FORTIFY_SOURCE=0"
export CFLAGS="-O3 -march=native -mtune=native -maes -mbmi2 -mpclmul -mllvm -inline-threshold=1500 -mllvm -extra-vectorizer-passes -mllvm -enable-cond-stores-vec -mllvm -slp-vectorize-hor-store -mllvm -enable-loopinterchange -mllvm -enable-loop-distribute -mllvm -enable-unroll-and-jam -mllvm -enable-loop-flatten -mllvm -unroll-runtime-multi-exit -mllvm -aggressive-ext-opt -mllvm -enable-interleaved-mem-accesses -mllvm -enable-masked-interleaved-mem-accesses -fno-math-errno -falign-functions=32 -funroll-loops -fomit-frame-pointer -mprefer-vector-width=256 -mllvm -adce-remove-loops -mllvm -enable-ext-tsp-block-placement -mllvm -enable-gvn-hoist -mllvm -enable-dfa-jump-thread -fcf-protection=none -mharden-sls=none -Wno-error -fgnuc-version=6.5.0"
export CXXFLAGS="${CFLAGS} -Wp,-U_GLIBCXX_ASSERTIONS"
export LDFLAGS="-Wl,-O3,--as-needed -Wl,-mllvm -Wl,-extra-vectorizer-passes -Wl,-mllvm -Wl,-enable-cond-stores-vec -Wl,-mllvm -Wl,-slp-vectorize-hor-store -Wl,-mllvm -Wl,-enable-loopinterchange -Wl,-mllvm -Wl,-enable-loop-distribute -Wl,-mllvm -Wl,-enable-unroll-and-jam -Wl,-mllvm -Wl,-enable-loop-flatten -Wl,-mllvm -Wl,-unroll-runtime-multi-exit -Wl,-mllvm -Wl,-aggressive-ext-opt -Wl,-mllvm -Wl,-enable-interleaved-mem-accesses -Wl,-mllvm -Wl,-enable-masked-interleaved-mem-accesses -march=native -maes -mbmi2 -mpclmul -fuse-ld=lld -Wl,-zmax-page-size=0x200000 -Wl,-mllvm -Wl,-adce-remove-loops -Wl,-mllvm -Wl,-enable-ext-tsp-block-placement -Wl,-mllvm -Wl,-enable-gvn-hoist -Wl,-mllvm -Wl,-enable-dfa-jump-thread -Wl,--undefined-version -fcf-protection=none -mharden-sls=none"
export CCLDFLAGS="$LDFLAGS"
export CXXLDFLAGS="$LDFLAGS"
export ASFLAGS="-D__AVX__=1 -D__AVX2__=1 -D__FMA__=1"

[ms178]

@zatrazz To not derail the BOLT thread any further, this is another unique issue at the moment with your Clang/Glibc branch. The idea was to gather PGO data from the test run, but adding the neccessary flags leads to the reported duplicate symbol error.

[ms178]

I've tried mold, bfd and gold which also all error out. Gold throws the best error messages:

/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member GCDAProfiling.c.o at 4640 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfiling.c.o at 44444 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingInternal.c.o at 58096 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingValue.c.o at 64924 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingBuffer.c.o at 105932 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingFile.c.o at 124548 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingMerge.c.o at 175920 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingMergeFile.c.o at 188824 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingNameVar.c.o at 196276 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingVersionVar.c.o at 199500 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingWriter.c.o at 202732 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformAIX.c.o at 224796 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformDarwin.c.o at 227880 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformFuchsia.c.o at 230972 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformLinux.c.o at 234064 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformOther.c.o at 246728 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingPlatformWindows.c.o at 249816 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingRuntime.cpp.o at 252908 is not an ELF object
/usr/bin/ld.gold: error: /usr/lib/clang/19/lib/x86_64-pc-linux-gnu/libclang_rt.profile.a: member InstrProfilingUtil.c.o at 259812 is not an ELF object
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [../Makerules:601: /tmp/makepkg/glibc/src/glibc-build/libc_pic.os] error 1