# emerge -pqv '=sci-libs/hdf5-1.14.4_p2::gentoo' [ebuild N ] sci-libs/hdf5-1.14.4_p2 USE="cxx examples fortran hl mpi szip threads unsupported zlib -debug -test" # emerge --info '=sci-libs/hdf5-1.14.4_p2::gentoo' Portage 3.0.63 (python 3.12.3-final-0, default/linux/amd64/23.0/desktop/gnome/systemd, gcc-13, glibc-2.39-r2, 6.8.6-gentoo-amd64 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.8.6-gentoo-amd64-x86_64-13th_Gen_Intel-R-_Core-TM-_i7-1360P-with-glibc2.39 KiB Mem: 65395384 total, 57355132 free KiB Swap: 8388604 total, 8388604 free Timestamp of repository gentoo: Wed, 17 Apr 2024 13:30:00 +0000 Head commit of repository gentoo: b721d621363e5f30736fb7a9da422786d65f7148 sh bash 5.2_p26 ld GNU ld (Gentoo 2.42 p3) 2.42.0 ccache version 4.9.1 [disabled] app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p26::gentoo dev-build/autoconf: 2.71-r7::gentoo, 2.72-r1::gentoo dev-build/automake: 1.16.5-r2::gentoo dev-build/cmake: 3.29.2::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-r2::gentoo dev-lang/python: 3.10.14_p1::gentoo, 3.11.9::gentoo, 3.12.3::gentoo dev-lang/rust: 1.77.1::gentoo dev-util/ccache: 4.9.1-r1::gentoo sys-apps/baselayout: 2.15::gentoo sys-apps/sandbox: 2.38::gentoo sys-apps/systemd: 255.4::gentoo sys-devel/binutils: 2.42-r1::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 15.0.7-r3::gentoo, 16.0.6::gentoo, 17.0.6::gentoo, 18.1.3::gentoo sys-devel/gcc: 12.3.1_p20240209::gentoo, 13.2.1_p20240210::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/llvm: 15.0.7-r3::gentoo, 16.0.6::gentoo, 17.0.6::gentoo, 18.1.3::gentoo sys-kernel/linux-headers: 6.8-r1::gentoo (virtual/os-headers) sys-libs/glibc: 2.39-r2::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://gentoo.kopylovs.net/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-max-age: 3 Binary Repositories: gentoobinhost priority: 1 sync-uri: https://distfiles.gentoo.org/releases/amd64/binpackages/23.0/x86-64-v3 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA android AnyDesk-TOS geekbench google-chrome Intel-SDP microsoft-edge Microsoft-vscode NVIDIA-CUDA NVIDIA-SDK OPERA-2018 PUEL-11 RAR TeamViewer Vivaldi" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /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/php/apache2-php8.3/ext-active/ /etc/php/cgi-php8.3/ext-active/ /etc/php/cli-php8.3/ext-active/ /etc/php/fpm-php8.3/ext-active/ /etc/php/phpdbg-php8.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" DISTDIR="/var/cache/distfiles" 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="-march=native -O2 -pipe -fomit-frame-pointer" 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 pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync warn-on-large-env xattr" FFLAGS="-march=native -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://mirror.isoc.org.il/pub/gentoo/ https://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/" LANG="en_US.utf8" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs" LEX="flex" MAKEOPTS="-j10" 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" SHELL="/bin/bash" USE="X a52 aac accessibility acl acpi alsa amd64 audit bash-completion berkdb bidi bluetooth branding brotli btrfs bzip2 cairo cdda cdr cet cli colord crypt cryptsetup cuda cups curl dbus designer device-mapper doc dri drm dts dvd dvdr eds emacs encode evdev evo examples exif experimental ffmpeg flac fortran fuse gamepad gdbm gif git gmp gnome gnome-keyring gnome-online-accounts gnome-shell gnutls go gpg gpm gstreamer gtk gtk-doc gui hscolour html http iconv icu idn introspection iodbc ios ipv6 jack java jemalloc joystick jpeg json kde kerberos keyring lcms ldap libnotify libtirpc lm-sensors lua lvm lz4 lzma lzo mad man mbedtls mng mongodb mp3 mp4 mpeg mpi multilib multimedia mysql nas nautilus ncurses netlink network networkmanager nfs nls nss nvenc odbc offensive ogg opencl opengl openmp openssl pam pango pcap pcre pdf perl pkcs11 plasma plugins png policykit postgres ppds pulseaudio python qml qt5 qt6 readline redis samba sasl screencast sdl seccomp semantic-desktop snmp sound source speech spell sqlite ssl startup-notification svg symlink sysprof systemd tcl telemetry test-rust threads tiff tk tools tpm tracker truetype udev udisks unicode upower usb utils v4l vaapi vala vdpau vim-syntax vnc vorbis vulkan wayland webengine webkit webp wifi wxwidgets x264 xattr xcb xen xft xinerama xml xv xvid yaml zeroconf zip zlib zsh-completion zstd" ABI_X86="64 32" ADA_TARGET="gcc_12" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_core authn_dbd authn_dbm authn_file authn_socache authz_core authz_dbd authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex brotli cache cgi cgid charset_lite dav dav_fs dav_lock dbd deflate dir env expires ext_filter file_cache filter headers http2 ident imagemap include info log_config logio mime mime_magic negotiation ratelimit reqtimeout rewrite session session_cookie session_crypto session_dbd setenvif socache_shmcb speling status substitute tls unique_id unixd userdir usertrack version vhost_alias watchdog xml2enc" APACHE2_MPMS="worker" CALLIGRA_FEATURES="karbon sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 ssse3 vpclmulqdq" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev joystick libinput" KERNEL="linux" L10N="en en-US he ru" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-beanshell scripting-javascript wiki-publisher" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" NGINX_MODULES_HTTP="access addition auth_basic auth_ldap auth_pam auth_request autoindex brotli browser charset dav dav_ext echo empty_gif fancyindex fastcgi flv geo geoip geoip2 grpc gunzip gzip image_filter javascript limit_conn limit_req map memc memcached metrics mirror mp4 perl proxy push_stream referer rewrite scgi split_clients ssi stub_status upload_progress upstream_check upstream_hash upstream_ip_hash upstream_keepalive upstream_least_conn upstream_zone userid uwsgi vhost_traffic_status xslt" NGINX_MODULES_MAIL="imap pop3 smtp" NGINX_MODULES_STREAM="access" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_11 python3_12" RUBY_TARGETS="ruby31 ruby32 ruby33" UWSGI_PLUGINS="alarm_curl cache carbon cheaper_busyness clock_monotonic clock_realtime corerouter curl_cron dumbloop echo emperor_amqp emperor_pg emperor_zeromq fastrouter forkptyrouter geoip graylog2 http ldap legion_cache_fetch logcrypto logfile logpipe logsocket mongodblog nagios notfound pam ping rados rawrouter redislog router_access router_basicauth router_cache router_expires router_hash router_http router_memcached router_metrics router_redirect router_redis router_rewrite router_spnego router_static router_uwsgi router_xmldir rpc rrdtool rsyslog signal spooler sqlite ssi sslrouter stats_pusher_statsd symcall syslog systemd_logger transformation_chunked transformation_gzip transformation_offload transformation_tofile transformation_toupper tuntap ugreen webdav xattr xslt zabbix zergpool" VIDEO_CARDS="intel fbdev vesa nvidia" 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, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
Created attachment 890967 [details] build.log.xz
Not sure what would cause this. Nut -fortran should work I guess? libtool: link: mpif90 -shared -fPIC .libs/H5fortran_types.o .libs/H5f90global.o .libs/H5_ff.o .libs/H5Aff.o .libs/H5Dff.o .libs/H5Eff.o .libs/H5ESff.o .libs/H5Fff.o .libs/H5Gff.o .libs/H5Iff.o .libs/H5Lff.o .libs/H5Off.o .libs/H5Pff.o .libs/H5Rff.o .libs/H5Sff.o .libs/H5Tff.o .libs/H5VLff.o .libs/H5Zff.o .libs/H5_gen.o .libs/H5fortkit.o .libs/H5f90kit.o .libs/H5_f.o .libs/H5Af.o .libs/H5Df.o .libs/H5Ef.o .libs/H5Ff.o .libs/H5Gf.o .libs/H5If.o .libs/H5Lf.o .libs/H5Of.o .libs/H5Pf.o .libs/H5Rf.o .libs/H5Sf.o .libs/H5Tf.o .libs/H5Zf.o .libs/HDF5.o -Wl,-rpath -Wl,/var/tmp/portage/sci-libs/hdf5-1.14.4_p2/work/hdf5-1.14.4-2/src/.libs -Wl,-rpath -Wl,//usr/lib64 -Wl,-rpath -Wl,//usr/lib/gcc/x86_64-pc-linux-gnu/13 -Wl,--as-needed ../../src/.libs/libhdf5.so -lsz -lz -ldl -L/usr/lib64 -L=usr/lib64 -L=usr/lib -L=/usr/lib64 -L=/usr/lib/gcc/x86_64-pc-linux-gnu/13 -l -L/usr/lib/gcc/x86_64-pc-linux-gnu/13 -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../.. //usr/lib64/libmpifort.so //usr/lib64/libmpi.so -lhwloc -lpthread -lgfortran //usr/lib/gcc/x86_64-pc-linux-gnu/13/libquadmath.so -lm -lc -lgcc_s -O3 -march=native -O2 -Wl,-O1 -Wl,-z -Wl,pack-relative-relocs -Wl,-soname -Wl,libhdf5_fortran.so.311 -o .libs/libhdf5_fortran.so.311.2.0 /usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -l-L/usr/lib/gcc/x86_64-pc-linux-gnu/13: No such file or directory
(In reply to Paul Zander from comment #2) > Not sure what would cause this. Nut -fortran should work I guess? > libtool: link: mpif90 -shared -fPIC .libs/H5fortran_types.o > .libs/H5f90global.o .libs/H5_ff.o .libs/H5Aff.o .libs/H5Dff.o .libs/H5Eff.o > .libs/H5ESff.o .libs/H5Fff.o .libs/H5Gff.o .libs/H5Iff.o .libs/H5Lff.o > .libs/H5Off.o .libs/H5Pff.o .libs/H5Rff.o .libs/H5Sff.o .libs/H5Tff.o > .libs/H5VLff.o .libs/H5Zff.o .libs/H5_gen.o .libs/H5fortkit.o > .libs/H5f90kit.o .libs/H5_f.o .libs/H5Af.o .libs/H5Df.o .libs/H5Ef.o > .libs/H5Ff.o .libs/H5Gf.o .libs/H5If.o .libs/H5Lf.o .libs/H5Of.o > .libs/H5Pf.o .libs/H5Rf.o .libs/H5Sf.o .libs/H5Tf.o .libs/H5Zf.o > .libs/HDF5.o -Wl,-rpath > -Wl,/var/tmp/portage/sci-libs/hdf5-1.14.4_p2/work/hdf5-1.14.4-2/src/.libs > -Wl,-rpath -Wl,//usr/lib64 -Wl,-rpath > -Wl,//usr/lib/gcc/x86_64-pc-linux-gnu/13 -Wl,--as-needed > ../../src/.libs/libhdf5.so -lsz -lz -ldl -L/usr/lib64 -L=usr/lib64 > -L=usr/lib -L=/usr/lib64 -L=/usr/lib/gcc/x86_64-pc-linux-gnu/13 -l > -L/usr/lib/gcc/x86_64-pc-linux-gnu/13 > -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../lib64 -L/lib/../lib64 > -L/usr/lib/../lib64 > -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../x86_64-pc-linux-gnu/lib > -L/usr/lib/gcc/x86_64-pc-linux-gnu/13/../../.. //usr/lib64/libmpifort.so > //usr/lib64/libmpi.so -lhwloc -lpthread -lgfortran > //usr/lib/gcc/x86_64-pc-linux-gnu/13/libquadmath.so -lm -lc -lgcc_s -O3 > -march=native -O2 -Wl,-O1 -Wl,-z -Wl,pack-relative-relocs -Wl,-soname > -Wl,libhdf5_fortran.so.311 -o .libs/libhdf5_fortran.so.311.2.0 > /usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../x86_64-pc-linux-gnu/bin/ld: > cannot find -l-L/usr/lib/gcc/x86_64-pc-linux-gnu/13: No such file or > directory USE=-fortran - builds without problem
I can't reproduce that with USE=fortran and sys-cluster/openmpi-4.1.6[cuda,cxx,fortran,ipv6,romio].
As i understand, it is due to stray -l in ... > -L=usr/lib -L=/usr/lib64 -L=/usr/lib/gcc/x86_64-pc-linux-gnu/13 -l > -L/usr/lib/gcc/x86_64-pc-linux-gnu/13 ...
And it traces back to stray -l in postdeps variable in ${WORKDIR}/libtool script
Created attachment 891985 [details, diff] Return code that removes "-l" For unknown reason they removed the code that removes these "-l". I am attaching a patch that returns this code.
(In reply to Michael Uleysky from comment #7) > Created attachment 891985 [details, diff] [details, diff] > Return code that removes "-l" > > For unknown reason they removed the code that removes these "-l". I am > attaching a patch that returns this code. patch allows to build with USE=fortran without problem
