Bug 296132 – sci-libs/hdf5-1.8.4-r1 USE=mpi - hyper.f90:(.text+0x13a): undefined reference to `h5pset_fapl_mpio_f_'

• Product: Gentoo Linux
• Status: RESOLVED NEEDINFO

[Description Juergen Rose 2009-12-07 22:17:57 UTC]

'emerge hdf5' fails with:
...
/bin/sh ../../libtool   --mode=link mpif90 -march=nocona -O2 -pipe   -I../../fortran/src -I../../fortran/test -I../../fortran/src   -Wl,-O1 -o parallel_test ptest.o hyper.o mdset.o ../../fortran/test/libh5test_fortran.la ../../test/libh5test.la ../../fortran/src/libhdf5_fortran.la ../../src/libhdf5.la -lpthread -lsz -lz -lm 
libtool: link: mpif90 -march=nocona -O2 -pipe -I../../fortran/src -I../../fortran/test -I../../fortran/src -Wl,-O1 -o .libs/parallel_test ptest.o hyper.o mdset.o  ../../fortran/test/.libs/libh5test_fortran.a ../../test/.libs/libh5test.a ../../fortran/src/.libs/libhdf5_fortran.so /var/tmp/portage/sci-libs/hdf5-1.8.4-r1/work/hdf5-1.8.4/src/.libs/libhdf5.so ../../src/.libs/libhdf5.so -lpthread /usr/lib64/libsz.so -lz -lm
hyper.o: In function `hyper_':
hyper.f90:(.text+0x13a): undefined reference to `h5pset_fapl_mpio_f_'
hyper.f90:(.text+0x5ff): undefined reference to `h5pset_fapl_mpio_f_'
hyper.f90:(.text+0xb3d): undefined reference to `h5pset_dxpl_mpio_f_'
hyper.f90:(.text+0xb70): undefined reference to `h5pset_dxpl_mpio_f_'
mdset.o: In function `multiple_dset_write_':
mdset.f90:(.text+0x11f): undefined reference to `h5pset_fapl_mpio_f_'
mdset.f90:(.text+0x72d): undefined reference to `h5pset_fapl_mpio_f_'
mdset.f90:(.text+0xd68): undefined reference to `h5pset_dxpl_mpio_f_'
mdset.f90:(.text+0xd9b): undefined reference to `h5pset_dxpl_mpio_f_'
collect2: ld returned 1 exit status
make[2]: *** [parallel_test] Error 1


Reproducible: Always




root@moose:/root(1)# emerge --info
Portage 2.1.7.11 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo x86_64)
=================================================================
System uname: Linux-2.6.32-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.0.1
Timestamp of tree: Mon, 07 Dec 2009 17:30:24 +0000
app-shells/bash:     4.0_p35
dev-java/java-config: 2.1.10
dev-lang/python:     2.6.4, 3.1.1-r1
dev-python/pycrypto: 2.1.0_beta1
dev-util/cmake:      2.8.0
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.5.3
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.64
sys-devel/automake:  1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11
sys-devel/binutils:  2.20
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /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="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch"
FFLAGS="-march=nocona -O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LDFLAGS="-Wl,-O1"
LINGUAS="de fr"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage/layman/zugaina /usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X Xaw3d a52 aac acl acpi administrator afs alsa amd64 amrr ao aotuv apache2 asf aspell audacious audiofile automount bash-completion beagle berkdb bjam blas bluetooth boo boost branding bzip2 c++ cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt cups curl cxx daap dbus device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi dxr3 eds elf emacs emboss encode epiphany evo examples exif expat extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fuse galago garmin gd gdal gdbm geolocation geos gif gimp ginac git glade glib glitz gml gmp gnokii gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphics graphviz gs gsl gsm gstreamer gtk guile hal hardened harness hddtemp hdf hdf5 hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kerberos kexi kpathsea kvm ladspa lame lapack laptop latex lcms ldap libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper math matroska matrox mikmod mmx mmxext mng modules mono motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp pae pam pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl server session slang slp smbclient smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora thinkpad threads thunar thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse                 evdev               " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="ide websvccommon nb harness apisupport groovy gsf j2ee java xml" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" 
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Juergen Rose 2009-12-07 22:20:34 UTC]

/var/tmp/portage/sci-libs/hdf5-1.8.4-r1/temp/build.log has more than 2.2 MB and is therefore not accepted.

[Comment 2 Jeroen Roovers (RETIRED) 2009-12-08 03:16:23 UTC]

(In reply to comment #1)
> /var/tmp/portage/sci-libs/hdf5-1.8.4-r1/temp/build.log has more than 2.2 MB and
> is therefore not accepted.

Even using gzip it should compress to near 100KB and it's fine to attach a compressed log file.

[Comment 3 Juergen Rose 2009-12-08 09:25:08 UTC]

root@moose:/root(47)# emerge -pvq hdf5
[ebuild   R   ] sci-libs/hdf5-1.8.4-r1  USE="cxx fortran mpi* szip threads zlib -examples*" 

[Comment 4 Juergen Rose 2009-12-08 10:51:54 UTC]

Created attachment 212440 [details]
gzipped /var/tmp/portage/sci-libs/hdf5-1.8.4-r1/temp/build.log

[Comment 5 Juergen Rose 2009-12-08 18:52:51 UTC]

At Bug 286492 I got the hint that due to mpi-fortran-wrapper bug you have to erase hdf5 before try to emerge it with the mpi flag. That was succesful for me.