When compiled with gcc-10, sci-libs/scipy-1.4.1 fails with error x86_64-pc-linux-gnu-gfortran:f77: scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaitr.f scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaitr.f:666:35: 383 | call svout (logfil, 1, rnorm, ndigit, | 2 ...... 666 | call svout (logfil, 2, rtemp, ndigit, | 1 Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1) scipy/sparse/linalg/eigen/arpack/ARPACK/SRC/cnaitr.f:737:39: 383 | call svout (logfil, 1, rnorm, ndigit, | 2 ...... 737 | call svout (logfil, 2, rtemp, ndigit, | 1 Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1) A workaround is available: adding "-fallow-argument-mismatch" to F{,C}FLAGS fixes the issue. See https://gcc.gnu.org/gcc-10/changes.html (Fortran changes) Reproducible: Always Portage 2.3.99 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r2, 5.6.11 x86_64) ================================================================= System uname: Linux-5.6.11-x86_64-Intel-R-_Core-TM-_i7-7700_CPU_@_3.60GHz-with-gentoo-2.7 KiB Mem: 32592860 total, 25195968 free KiB Swap: 33554428 total, 33554428 free Head commit of repository gentoo: 0818344e4dfe29af3a8e6e18d53611b61467799d Head commit of repository libressl: ad08d4df67f1e2235ae1847448ed4e2c35d87ab5 sh bash 5.0_p17 ld GNU gold (Gentoo 2.34 p1 2.34.0) 1.16 app-shells/bash: 5.0_p17::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.30.2::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.2-r2::gentoo dev-util/cmake: 3.17.2::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.13.4-r2::gentoo, 1.16.2::gentoo sys-devel/binutils: 2.34::gentoo sys-devel/gcc: 10.1.0::gentoo sys-devel/gcc-config: 2.2.1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r2::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://github.com/gentoo/gentoo.git priority: -1000 kernelpanic location: /var/db/repos/kernelpanic masters: gentoo priority: 0 libressl location: /var/db/repos/libressl sync-type: git sync-uri: https://github.com/gentoo/libressl.git masters: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE @BINARY-REDISTRIBUTABLE @EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mtune=native -O2 -pipe" 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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -mtune=native -O2 -pipe" DISTDIR="/var/cache/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-march=native -mtune=native -O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs cgroup clean-logs compress-build-logs config-protect-if-modified distlocks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -mtune=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="it_IT.UTF-8" LDFLAGS="-Wl,-O2 -Wl,--as-needed" MAKEOPTS="-j9" 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" USE="X a52 aac acl acpi alsa amd64 ao berkdb blas bluray branding bzip2 cairo cdda cjk clang cli crypt cups curl dbus djvu dri dvb dvd elogind encode eselect-ldso exif ffmpeg fftw flac fontconfig fortran gdbm gif gimp gmp gnome-keyring gsm harfbuzz heif iconv icu imlib inotify ipv6 jbig jemalloc jit jpeg jpeg2k lapack latex lcms libass libnotify libressl libtirpc lto lz4 lzma lzo mms mng mp3 mpeg multilib natspec ncurses nls nptl nss offensive ogg openal opencl opencv openexr opengl openmp opus pam pango pcre pdf plotutils png policykit postproc postscript pulseaudio raw readline scanner seccomp smp sndfile sound sox speex spell spice split-usr ssl startup-notification svg theora threads tiff truetype udev udisks unicode usb vaapi vim-syntax vorbis vpx vulkan wavpack webp wmf x264 xattr xcb xcomposite xml xmp xpm xv xvid zip zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="libressl" 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" INPUT_DEVICES="libinput" KERNEL="linux" L10N="it en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby27" SANE_BACKENDS="hp" USERLAND="GNU" VIDEO_CARDS="intel i965 iris" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 637042 [details] build log (MAKEOPTS="-j1"
Hi, I can confirm both bug and workaround on default/linux/amd64/17.1/no-multilib/hardened.
The workaround works for me (although it's only FFLAGS that should be set as there is no equivalent CFLAGS switch). However, there's a worse problem here. scipy lists sci-libs/arpack as a dependency, but the ebuild uses an internal copy of arpack. sci-libs/arpack has the same bug and workaround for all released versions, including 3.7.0 which is not in the tree). The live version works, though. I have filed a bug with upstream arpack asking for a new release.
PR to add the flag to ebuild: https://github.com/gentoo/gentoo/pull/16093 @Joel Berendzen: fwiw, here's a arpack-3.7.0.ebuild that I might PR: https://github.com/acolinisi/casper-ebuilds/blob/master/sci-libs/arpack/arpack-3.7.0.ebuild
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d80e7eafbdb6184a289564ca15d5976d67bf8d17 commit d80e7eafbdb6184a289564ca15d5976d67bf8d17 Author: Alexei Colin <acolin@isi.edu> AuthorDate: 2020-06-06 20:04:51 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2020-06-07 21:03:31 +0000 sci-libs/scipy: -fallow-argument-mismatch for gfortran v10 Already fixed in upstream master: https://github.com/scipy/scipy/pull/11842 Closes: https://bugs.gentoo.org/721860 Signed-off-by: Alexei Colin <acolin@isi.edu> Closes: https://github.com/gentoo/gentoo/pull/16093 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-libs/scipy/scipy-1.4.1.ebuild | 3 +++ 1 file changed, 3 insertions(+)
Reverting, this breaks gcc-9.
(In reply to Michał Górny from comment #6) > Reverting, this breaks gcc-9. And what do you think about something conditional, like [ $(gcc-major-version) -ge 10 ] && append-fflags -fallow-argument-mismatch using toolchain-funcs?
Sure but please figure out how to check gfortran version.
(e.g. people may have CC/CXX set to clang)
(In reply to Michał Górny from comment #8) > Sure but please figure out how to check gfortran version. In bug #721860 (which you marked FIXED?!?) I already mentioned a solution by replacing: append-fflags -fallow-argument-mismatch with: append-fflags $(test-flag-FC -fallow-argument-mismatch) I was only able to test this on amd64 with gcc-9.3/gcc-10.
(In reply to Stephan Hartmann from comment #10) > (In reply to Michał Górny from comment #8) > > Sure but please figure out how to check gfortran version. > > In bug #721860 (which you marked FIXED?!?) I already mentioned a solution by > replacing: > append-fflags -fallow-argument-mismatch > with: > append-fflags $(test-flag-FC -fallow-argument-mismatch) > > I was only able to test this on amd64 with gcc-9.3/gcc-10. Oops, it is actually bug #727590
(In reply to Michał Górny from comment #9) > (e.g. people may have CC/CXX set to clang) Also, other fortran compilers are available. So, maybe, a combination of tc-getFC() and gcc-major-version(): [[ $(tc-getFC) == *gfortran* ]] && [ $(gcc-major-version) -ge 10 ] && append-fflags -fallow-argument-mismatch Is this viable?
test-flag-FC sounds like a better solution.
According to Github; this may be fixed upstream in the next release as well: https://github.com/scipy/scipy/issues/11611
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c695c8ece7b823d102964684c5642f17389cba72 commit c695c8ece7b823d102964684c5642f17389cba72 Author: David Seifert <soap@gentoo.org> AuthorDate: 2020-06-16 22:01:58 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2020-06-16 22:01:58 +0000 sci-libs/scipy: Conditionally add -fallow-argument-mismatch Closes: https://bugs.gentoo.org/721860 Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org> sci-libs/scipy/scipy-1.1.0.ebuild | 6 ++++++ sci-libs/scipy/scipy-1.4.1.ebuild | 6 ++++++ 2 files changed, 12 insertions(+)
