Created attachment 894345 [details] build.log scipy-1.13.0 fails to build with lto enabled for me. After disabling lto it compiles fine. emerge --info: Portage 3.0.64 (python 3.11.9-final-0, default/linux/amd64/23.0, gcc-13, glibc-2.39-r6, 6.9.1-gentoo x86_64) ================================================================= System uname: Linux-6.9.1-gentoo-x86_64-AMD_Ryzen_9_7950X3D_16-Core_Processor-with-glibc2.39 KiB Mem: 64960100 total, 29642504 free KiB Swap: 16777212 total, 16777212 free Timestamp of repository gentoo: Fri, 24 May 2024 18:33:53 +0000 Head commit of repository gentoo: cac69b44b8d40e2dd7bdecc3aa75e0882075881b Timestamp of repository guru: Fri, 24 May 2024 18:48:47 +0000 Head commit of repository guru: 0de0f6054ef2a9b5aa68dc747d653ace6ded722f Head commit of repository local: 71df98c5b80fe853fa48b78ba9495214a90e683f Timestamp of repository steam-overlay: Mon, 20 May 2024 17:23:25 +0000 Head commit of repository steam-overlay: 3aa8d3201d7bce32a1a0fffdf4afd9dbd0583048 sh bash 5.2_p26-r3 ld GNU ld (Gentoo 2.42 p3) 2.42.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p26-r3::gentoo dev-build/autoconf: 2.13-r8::gentoo, 2.72-r1::gentoo dev-build/automake: 1.16.5-r2::gentoo dev-build/cmake: 3.29.3::gentoo dev-build/libtool: 2.4.7-r4::gentoo dev-build/make: 4.4.1-r1::gentoo dev-build/meson: 1.4.0-r1::gentoo dev-java/java-config: 2.3.3-r1::gentoo dev-lang/perl: 5.38.2-r5::gentoo dev-lang/python: 3.11.9-r1::gentoo, 3.12.3-r1::gentoo, 3.13.0_beta1_p2::gentoo dev-lang/rust: 1.77.1::gentoo sys-apps/baselayout: 2.15::gentoo sys-apps/openrc: 0.54::gentoo sys-apps/sandbox: 2.38::gentoo sys-devel/binutils: 2.42-r1::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 17.0.6::gentoo, 18.1.6::gentoo sys-devel/gcc: 13.2.1_p20240503::gentoo, 14.1.1_p20240518::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/lld: 17.0.6::gentoo, 18.1.6::gentoo sys-devel/llvm: 17.0.6::gentoo, 18.1.6::gentoo sys-kernel/linux-headers: 6.9::gentoo (virtual/os-headers) sys-libs/glibc: 2.39-r6::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://github.com/gentoo-mirror/gentoo priority: -1000 volatile: False sync-git-verify-commit-signature: true guru location: /var/db/repos/guru sync-type: git sync-uri: https://github.com/gentoo-mirror/guru.git masters: gentoo volatile: False local location: /var/db/repos/local sync-type: git sync-uri: git://s2/local.git masters: gentoo volatile: False steam-overlay location: /var/db/repos/steam-overlay sync-type: git sync-uri: https://github.com/gentoo-mirror/steam-overlay.git masters: gentoo volatile: False crossdev location: /var/db/repos/crossdev masters: gentoo priority: 10 volatile: False Installed sets: @g_base, @g_base_openrc, @g_base_tools, @g_dev_tools, @x2 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=znver4 -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=1024 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/openldap/ldap.conf /etc/ssh/sshd_config /etc/sssd/sssd.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d" CXXFLAGS="-O2 -pipe -march=znver4 -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=1024 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--oneshot --jobs=4 --with-bdeps=y --keep-going" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-O2 -pipe -march=znver4 -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=1024 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=znver4 -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=32 --param=l2-cache-size=1024 -flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -fuse-ld=mold" LEX="flex" LINGUAS="en" MAKEOPTS="-j32" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--info=progress2,name0,del0" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" SHELL="/bin/bash" USE="acl alsa amd64 bzip2 cet crypt dbus elogind flac gdbm iconv ipv6 jpeg libtirpc lto mp3 multilib ncurses nls openmp pam pcre pgo pipewire png readline seccomp ssl svg test-rust threads tiff udev unicode vim-syntax vulkan wayland webp xattr xml zlib zstd" ABI_X86="64" ADA_TARGET="gcc_12" AMDGPU_TARGETS="gfx1100" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 aes avx avx2 avx512bw avx512cd avx512dq avx512f avx512vbmi avx512vl f16c fma3 pclmul popcnt rdrand sha sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 ntrip navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" QEMU_SOFTMMU_TARGETS="riscv64 x86_64" QEMU_USER_TARGETS="riscv64" RUBY_TARGETS="ruby31 ruby32" VIDEO_CARDS="radeon amdgpu radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
btw, also just tried it with gcc-14. fails there too.
I have been unable to reproduce this failure at all. gcc 13, ld.bfd.
Hmm, i've just tried it again, but it still fails with the same error. I'm on gcc-14.1.1_p20240615 now Please note that scipy-1.13.1 builds fine with lto enabled. Only 1.13.0 fails.
scipy-1.14.0 also refuses to build with lto.
$ emerge --info | grep FLAGS CFLAGS="-pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Werror=int-conversion -Werror=incompatible-pointer-types" CXXFLAGS="-pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wformat -Werror=format-security" FCFLAGS="-pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" FFLAGS="-pipe -march=native -fstack-protector-all -O2 -fdiagnostics-color=always -frecord-gcc-switches -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -flto=4 -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing -Wl,--defsym=__gentoo_check_ldflags__=0" $ emerge -pv scipy [ebuild U ~] dev-python/scipy-1.14.0::gentoo [1.13.0::gentoo] USE="fortran (test-rust) -debug -doc -test" PYTHON_TARGETS="python3_12 -pypy3 -python3_10 -python3_11*" 0 KiB $ CC=gcc-14 CXX=g++-14 FC=gfortran-14 ebuild scipy-1.14.0.ebuild clean install >>> Install dev-python/scipy-1.14.0 into /var/tmp/portage/dev-python/scipy-1.14.0/image * python3_12: running distutils-r1_run_phase distutils-r1_python_install * Using python3.12 in global scope * python3_12: running distutils-r1_run_phase python_install_all >>> Completed installing dev-python/scipy-1.14.0 into /var/tmp/portage/dev-python/scipy-1.14.0/image ... I cannot reproduce with GCC 14 either.
I reproduced it. It works when numpy is 1.26.4 and fails when numpy is 2.0.0
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=852a312f7cea343a2ada68e427171954ca56b420 commit 852a312f7cea343a2ada68e427171954ca56b420 Author: Patrick McLean <chutzpah@gentoo.org> AuthorDate: 2024-06-27 18:53:43 +0000 Commit: Patrick McLean <chutzpah@gentoo.org> CommitDate: 2024-06-27 18:53:43 +0000 dev-python/scipy: Filter LTO with numpy-2.0.0 (bug #932721) Bug: https://bugs.gentoo.org/932721 Signed-off-by: Patrick McLean <chutzpah@gentoo.org> dev-python/scipy/scipy-1.14.0.ebuild | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-)
