A recent system update (possible eclass) has resulted on packages depending on fortran (eg lapack) to fail to build. lapack and other fortran type packages would fail unless CompilerRT was removed /etc/portage/package.env ... #=== Clang but no RT - Fortran stuff sci-libs/lapack compiler-clang_noCompilerRT dev-python/scipy compiler-clang_noCompilerRT dev-python/numpy compiler-clang_noCompilerRT and compiler-clang_noCompilerRT would include LDFLAGS="-fuse-ld=lld -unwindlib=libunwind -Wl,--as-needed" The normal compiler-clang entry would include: LDFLAGS="${LDFLAGS} -fuse-ld=lld -rtlib=compiler-rt -unwindlib=libunwind -Wl,--as-needed" as you can see it was a significantly stripped back LDFLAGS as this was required to permit fortran type packages to compile Test1 - Compile with previously working package.env: sci-libs/lapack compiler-clang_noCompilerRT ... ...- Check for working C compiler: /usr/lib/llvm/15/bin/clang -- Check for working C compiler: /usr/lib/llvm/15/bin/clang - broken CMake Error at /usr/share/cmake/Modules/CMakeTestCCompiler.cmake:69 (message): The C compiler "/usr/lib/llvm/15/bin/clang" is not able to compile a simple test program. It fails with the following output: Change Dir: /var/tmp/portage/sci-libs/lapack-3.11/work/lapack-3.11_build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/ninja cmTC_4b9ba && [1/2] Building C object CMakeFiles/cmTC_4b9ba.dir/testCCompiler.c.o [2/2] Linking C executable cmTC_4b9ba FAILED: cmTC_4b9ba : && /usr/lib/llvm/15/bin/clang -O3 -pipe -march=x86-64-v3 -mtune=native -flto=thin -fuse-ld=lld -unwindlib=libunwind -Wl,--as-needed -Wl,-O2 -Wl,--as-needed -rdynamic CMakeFiles/cmTC_4b9ba.dir/testCCompiler.c.o -o cmTC_4b9ba && : clang-15: error: --rtlib=libgcc requires --unwindlib=libgcc ninja: build stopped: subcommand failed. CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:3 (project) -- Configuring incomplete, errors occurred! ... Test2 - Compile with commenting out in package.env: #sci-libs/lapack compiler-clang_noCompilerRT ... -- Check for working Fortran compiler: /usr/bin/x86_64-pc-linux-gnu-gfortran -- Check for working Fortran compiler: /usr/bin/x86_64-pc-linux-gnu-gfortran - broken CMake Error at /usr/share/cmake/Modules/CMakeTestFortranCompiler.cmake:61 (message): The Fortran compiler "/usr/bin/x86_64-pc-linux-gnu-gfortran" is not able to compile a simple test program. It fails with the following output: Change Dir: /var/tmp/portage/sci-libs/lapack-3.11/work/lapack-3.11_build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/ninja cmTC_ae2c4 && [1/4] Building Fortran preprocessed CMakeFiles/cmTC_ae2c4.dir/testFortranCompiler.f-pp.f [2/4] Generating Fortran dyndep file CMakeFiles/cmTC_ae2c4.dir/Fortran.dd [3/4] Building Fortran object CMakeFiles/cmTC_ae2c4.dir/testFortranCompiler.f.o [4/4] Linking Fortran executable cmTC_ae2c4 FAILED: cmTC_ae2c4 : && /usr/bin/x86_64-pc-linux-gnu-gfortran -Wl,-O1 -Wl,--as-needed -fuse-ld=lld -rtlib=compiler-rt -unwindlib=libunwind -Wl,--as-needed -Wl,-O2 -Wl,--as-needed -O2 -pipe CMakeFiles/cmTC_ae2c4.dir/testFortranCompiler.f.o -o cmTC_ae2c4 && : x86_64-pc-linux-gnu-gfortran: error: unrecognized command-line option ‘-rtlib=compiler-rt’ ninja: build stopped: subcommand failed. CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:3 (project) -- Configuring incomplete, errors occurred! This is failing for lapack-3.11 (upgrade) and also previous version 3.10.1 qlop -tv lapack | tail -n 1 2022-09-10T00:29:53 >>> sci-libs/lapack-3.10.1: 46s A recent update to toolchain-funcs.eclass ( 8th Oct 2022, after most recent lapack build) now enforces a rtlib, exactly what will cause fortran packages to fail with clang. emerge --info Portage 3.0.38.1 (python 3.10.8-final-0, default/linux/amd64/17.1/desktop, gcc-12, glibc-2.36-r5, 6.0.8-gentoo x86_64) ================================================================= System uname: Linux-6.0.8-gentoo-x86_64-AMD_Ryzen_5_1600_Six-Core_Processor-with-glibc2.36 KiB Mem: 32829964 total, 4134388 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Wed, 16 Nov 2022 22:03:47 +0000 Head commit of repository gentoo: 5cafc5816c679287c7fa3893edad81bd80fab83d sh bash 5.1_p16-r2 ld GNU ld (Gentoo 2.39 p5) 2.39.0 app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.1_p16-r2::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.36.0-r1::gentoo dev-lang/python: 3.10.8_p3::gentoo, 3.11.0_p2::gentoo dev-lang/rust: 1.65.0::gentoo dev-util/cmake: 3.24.3::gentoo dev-util/meson: 0.64.0::gentoo sys-apps/baselayout: 2.9::gentoo sys-apps/openrc: 0.45.2-r1::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r4::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.39-r4::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 15.0.4::gentoo sys-devel/gcc: 12.2.1_p20221008::gentoo sys-devel/gcc-config: 2.8::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/lld: 15.0.4::gentoo sys-devel/llvm: 14.0.6-r2::gentoo, 15.0.4::gentoo sys-devel/make: 4.4::gentoo sys-kernel/linux-headers: 6.0::gentoo (virtual/os-headers) sys-libs/glibc: 2.36-r5::gentoo sys-libs/libselinux: 3.4::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-git-verify-commit-signature: true local location: /var/db/repos/local masters: gentoo Installed sets: @steam ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" AR="llvm-ar" CBUILD="x86_64-pc-linux-gnu" CC="clang" CFLAGS="-O3 -pipe -march=x86-64-v3 -mtune=native -flto=thin" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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 /etc/terminfo" CXX="clang++" CXXFLAGS="-O3 -pipe -march=x86-64-v3 -mtune=native -flto=thin" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--jobs=5 --load-average=5.0 --with-bdeps y" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY 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" 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 metadata-transfer multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://mirror.bytemark.co.uk/gentoo/ http://www.mirrorservice.org/sites/distfiles.gentoo.org/" LANG="en_GB.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -rtlib=compiler-rt -unwindlib=libunwind -Wl,--as-needed -Wl,-O2 -Wl,--as-needed" LINGUAS="en en_GB uk" MAKEOPTS="-j8" NM="llvm-nm" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" 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" RANLIB="llvm-ranlib" SHELL="/bin/bash" USE="X a52 aac acl acpi aiglx alsa amd64 bash-completion binddist branding bzip2 cairo cblas-external cdda cdr clang cleartype cli corefonts crypt dri dts elogind encode eselect-ldso evdev exif ffmpeg flac fortran gcc64 gdbm gegl gif gles1 gles2 gpm graphite gstreamer gtk gui iconv icu imlib introspection ipv6 jpeg lcms libglvnd libnotify libtirpc llvm-libunwind lto mad mng mp3 mp4 mpeg multilib ncurses nls nptl nptlonly nsplugin ogg opengl openmp oss pam pango pcre pdf pgo pipewire png ppds pulseaudio python qt5 readline samba screencast sdl seatd seccomp smbclient spell split-usr ssl startup-notification svg test-rust threads tiff truetype type1 udev udisks unicode upower usb vorbis vulkan wayland wxwidgets xattr xcb xml xulrunner xv xvid zlib" ABI_X86="64 32" ADA_TARGET="gnat_2021" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache 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="f16c mmx mmxext popcnt sse sse2 sse3 sse4a ssse avx sse4_2 sse4_1 ssse3" CURL_SSL="gnutls" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 efi-32" INPUT_DEVICES="keyboard mouse libinput" KERNEL="linux" L10N="en en-GB" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="AMDGPU" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_10" PYTHON_TARGETS="python3_10" RUBY_TARGETS="ruby31" USERLAND="GNU" VIDEO_CARDS="vesa amdgpu radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, ARFLAGS, AS, ASFLAGS, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS Reproducible: Always
Your interpretation seems flawed... When no --rtlib was specified anywhere in any way, then --rtlib=libgcc was always default, and it would require --unwindlib=libgcc, so the following error would always occur: > clang-15: error: --rtlib=libgcc requires --unwindlib=libgcc Your second output shows that Clang-specific options were passed to 'gfortran', which obviously cannot work: > x86_64-pc-linux-gnu-gfortran: error: unrecognized command-line option ‘-rtlib=compiler-rt’ Older versions of sys-devel/clang had USE flags such as "default-compiler-rt", "default-libcxx", "default-lld", and I suspect that your were relying on them. You probably had different LDFLAGS configuration at that time. All your current LDFLAGS settings (global, in "compiler-clang_noCompilerRT" and in "compiler-clang") are invalid for 'gfortran'. (Currently it is rather recommended to set --rtlib=... / --unwindlib=... / --stdlib=... through relevant "default-*" USE flags of sys-devel/clang-common, not in CFLAGS / CXXFLAGS / LDFLAGS.) If you want confirmation, you might attach build log of sci-libs/lapack-3.10.1 from 2022-09-10.
Try removing -unwindlib from compiler-clang_noCompilerRT.
Created attachment 833181 [details] lapack build log Thankyou for your replied. Those things were added while converting to > 99% clang and also before said defaults were available. Stripping back just in case -- Verifying Fortran/C Compiler Compatibility - Failed CMake Error at /usr/share/cmake/Modules/FortranCInterface.cmake:400 (message): The Fortran compiler: /usr/bin/x86_64-pc-linux-gnu-gfortran and the C compiler: /usr/lib/llvm/15/bin/clang failed to compile a simple test project using both languages. The output was: Change Dir: /var/tmp/portage/sci-libs/lapack-3.11/work/lapack-3.11_build/CMakeFiles/FortranCInterface/VerifyC Run Build Command(s):/usr/bin/ninja VerifyFortranC && [1/7] Building Fortran preprocessed CMakeFiles/VerifyFortran.dir/VerifyFortran.f-pp.f [2/7] Generating Fortran dyndep file CMakeFiles/VerifyFortran.dir/Fortran.dd [3/7] Building C object CMakeFiles/VerifyFortranC.dir/VerifyC.c.o [4/7] Building C object CMakeFiles/VerifyFortranC.dir/main.c.o [5/7] Building Fortran object CMakeFiles/VerifyFortran.dir/VerifyFortran.f.o [6/7] Linking Fortran static library libVerifyFortran.a [7/7] Linking C executable VerifyFortranC FAILED: VerifyFortranC : && /usr/lib/llvm/15/bin/clang -O3 -pipe -march=x86-64-v3 -mtune=native -flto=thin -O3 -DNDEBUG -Wl,-O1 -Wl,--as-needed CMakeFiles/VerifyFortranC.dir/main.c.o CMakeFiles/VerifyFortranC.dir/VerifyC.c.o -o VerifyFortranC libVerifyFortran.a -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lgcc_s -lgcc && : ld.lld: error: undefined symbol: VerifyFortran >>> referenced by main.c >>> lto.tmp:(main) clang-15: error: linker command failed with exit code 1 (use -v to see invocation) ninja: build stopped: subcommand failed. Call Stack (most recent call first): CBLAS/CMakeLists.txt:9 (FortranCInterface_VERIFY) ######################## grep lapack /etc/portage/package.env sci-libs/lapack compiler-clang #################### ie clang with no lto cat /etc/portage/env/compiler-clang COMMON_FLAGS="-O3 -pipe -march=x86-64-v3 -mtune=native"# BASELINE CFLAGS="${COMMON_FLAGS} " CXXFLAGS="${COMMON_FLAGS}" #== CLANG GLOBAL CC="clang" CXX="clang++" AR="llvm-ar" NM="llvm-nm" RANLIB="llvm-ranlib" #LDFLAGS="${LDFLAGS} -fuse-ld=lld -rtlib=compiler-rt -unwindlib=libunwind -Wl,--as-needed" #LDFLAGS="${LDFLAGS} -Wl,-O2 -Wl,--as-needed"
lapack just installed as part of a emerge @world. Scipy is the next fortran package in the list
commit a3ab8231602c8af892facac582b5770f3834c21f Author: Sam James <sam@gentoo.org> Date: Fri Aug 25 00:14:13 2023 +0100 sci-libs/lapack: use fortran-2.eclass Not strictly related to bug #908798 but noticed while looking at it. Bug: https://bugs.gentoo.org/908798 Signed-off-by: Sam James <sam@gentoo.org> commit 5e5c9d5c524871f5af260557dbd2962b8eec5087 Author: Sam James <sam@gentoo.org> Date: Fri Aug 25 00:13:08 2023 +0100 profiles/features/llvm: drop problematic LDFLAGS clang-common already handles setting these for us, and if we set it in profiles, then it gets passed down to gcc via clang for things like Fortran where clang is just acting as the driver. Closes: https://bugs.gentoo.org/908798 Signed-off-by: Sam James <sam@gentoo.org>
