A revdep-rebuild run revealed that h5perf was missing a needed library, libh5test.so.0. revdep-rebuild -vv -i -pv Configuring search environment for revdep-rebuild revdep-rebuild environment: SEARCH_DIRS="/usr/qt/3/ /bin/ /sbin/ /usr/bin/ /usr/sbin/ /lib/ /usr/lib/ <snip/> /usr/lib/octave-2.1.72/" SEARCH_DIRS_MASK="/opt/intel/compiler90/bin/iidb /opt/intel/fortran90/bin/iidb" LD_LIBRARY_MASK="libodbcinst.so libodbc.so libjava.so libjvm.so" PORTAGE_ROOT="/" CALLED_OPTIONS="" EMERGE_OPTIONS="-pv" Checking reverse dependencies... Packages containing binaries and libraries broken by a package update will be emerged. Collecting system binaries and libraries... done. (/home/zeekec/.revdep-rebuild.1_files) Collecting complete LD_LIBRARY_PATH... done. (/home/zeekec/.revdep-rebuild.2_ldpath) Checking dynamic linking consistency... broken /usr/bin/h5perf (requires libh5test.so.0) done. (/home/zeekec/.revdep-rebuild.3_rebuild) Assigning files to ebuilds... done. (/home/zeekec/.revdep-rebuild.4_ebuilds) Evaluating package order... done. (/home/zeekec/.revdep-rebuild.5_order) All prepared. Starting rebuild... emerge --oneshot -pv =sci-libs/hdf5-1.6.5 .......... These are the packages that would be merged, in order: Calculating dependencies ... done! [ebuild R ] sci-libs/hdf5-1.6.5 USE="hlapi ssl szip threads zlib -debug -mpi -static" 0 kB Total size of downloads: 0 kB Build finished correctly. Removing temporary files... You can re-run revdep-rebuild to verify that all libraries and binaries are fixed. If some inconsistency remains, it can be orphaned file, deep dependency, binary package or specially evaluated library. emerge --info Portage 2.1_rc2-r3 (default-linux/x86/2006.0, gcc-4.1.1, glibc-2.4-r3, 2.6.16-gentoo-r8 i686) ================================================================= System uname: 2.6.16-gentoo-r8 i686 Intel(R) Pentium(R) 4 CPU 3.00GHz Gentoo Base System version 1.12.0 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] ccache version 2.4 [enabled] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r1 dev-util/confcache: 0.4.2-r1 sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r5 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -mtune=prescott -march=prescott -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-O2 -mtune=prescott -march=prescott -pipe" DISTDIR="/home/gentoo/portage/distfiles" FEATURES="autoconfig candy ccache confcache distlocks metadata-transfer parallel-fetch sandbox sfperms strict userfetch userpriv usersandbox" GENTOO_MIRRORS="http://gentoo.mirrors.pair.com/ http://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ http://gentoo.chem.wisc.edu/gentoo/ http://gentoo.osuosl.org/" LINGUAS="en" MAKEOPTS="-j2" PKGDIR="/home/gentoo/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/home/gentoo/tmp" PORTDIR="/home/gentoo/portage" PORTDIR_OVERLAY="/home/gentoo/local/portage /home/gentoo/local/layman/vmware /home/gentoo/local/layman/science" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="x86 7zip X X509 Xaw3d a52 aac aalib acl acpi activefilter ada aim aio akode alsa amarok amd amr aotuv apache apache2 apm arts artswrappersuid artworkextra asf asm asterisk async atlas auctex audiofile authdaemond automount bash-completion bcmath bcp bdf berkdb binfilter bitmap-fonts bjam bl blas blender-game bonobo boo branding bzip2 c++ cairo calendar cap caps ccache cdda cddb cdf cdio cdparanoia cdr cdrom cgi chm clanJavaScript clanVoice cli clisp cmucl commercial corba cracklib crosscompile crypt cscope css ctype cups curl curlwrappers cvs cvsgraph daap dbm dbus dbx dcc debugger dga dhcp dio directfb discard-path djvu dmi dnd dpms dri dts dv dvd dvdr dvdread dvi dynagraph ecc editor edl eds effects emboss emoticon encode enscript epson erandom esd examples exif expat exscalibar extraicons extramodules fam fame fastbuild fastcgi fat fbcon fbdev fbsplash festival ffmpeg fftw finger firefox fits flac flash flatfile fltk font-server fontconfig foomaticdb force-cgi-redirect fortran fpx freetts ftp fuse gb gcc-libffi gcl gd gdal gdbm geoip geos ggi gif gimp gimpprint ginac gitsendemail gkrellm glade glep glgd glitz glut glx gml gmp gmtfull gmthigh gmtsuppl gmttria gnome gnome-print gnomedb gnuplot gnutls gpg2-experimental gpgme gphoto2 gpm gps graphviz grass gs gsl gssapi gstreamer gstreamer010 gtk gtk2 gtkhtml guile gzip hal haskell hddtemp hdf hdf5 hfs high-ints hlapi hou hpn html httpd i8x0 iconv icq id3 ide idea idn image imagemagick imap imlib imlib2 inifile inkjar input_devices_jamstudio input_devices_keyboard input_devices_mouse insecure-drivers insecure-savers ipv6 isdnlog itcl jack jai java javacomm javascript jbig jce jikes jimi jit jpeg jpeg2k junit jython kcal kde kdeenablefinal kdepim kdexdeltas kqemu ladcca lame lapack largeterminal latex lcms libcaca libclamav libdsk libg++ libgda libsamplerate libwww live lm_sensors logitech-mouse logrotate logwatch lzo lzw mad mail maildir mailwrapper mapeditor maps math matroska mbrola md5sum mhash mikmod mime ming mixer mjpeg mmap mmx mmxext mng mod modplug mopac7 motif moznocompose moznoirc moznomail mozsha1 mozsvg mp3 mp4 mp4live mpeg mpeg2 mplayer mpqc multiprocess multitarget musepack music musicbrainz mysql nas ncurses net netcdf network new-login nfs nls no-old-linux nocd nolvm1 nowin nptl nptlonly nsplugin ntfs ntlm numarray numeric oav ocaml octave offensive ofx ogdi ogg openal openbabel openexr opengl osc oss pager pam parse-clocks pascal patch patented pcntl pcre pdf perl php physfs pic player plotutils plugin png pnp pop portaudio postfix povray ppds pppd print pyste python qemu-fast qhull qt quicktime quotas quotes rar rdesktop readline real reflection remix rle rogue rpc rrdtool rss rtc rtsp ruby samba sasl sbcl scanner scp screen sdk sdl session sftp shared sharedext sharedmem shorten shout skins slp smime smp sndfile softmmu sou sounds speedo speex spell spl sql sqlite sse sse-filters sse2 ssl stencil-buffer stream subject-rewrite subp subtitles subversion suid svg svgz svn-mirror swat symlink sysfs syslog sysvipc szip t1lib tcltk tcpd test tetex tga theora thesaurus threads tidy tiff timidity tokenizer toolbar tools transcode truetype truetype-fonts type1 type1-fonts ucs2 ucs4 udev unicode urandom usb userlocales utf8 uudeview v4l v4l2 vcd vcdimager vfat video_cards_i810 videos vidix vim vim-pager vim-with-x virus-scan visualization vlm vnc voice vorbis vorbis-psy webdav win32codecs wmf wordperfect wv wxwindows x264 xanim xatrix xcomposite xface xforms xine xinetd xml xmldoclet xmms xorg xosd xpm xprint xscreensaver xsl xslt xtended xv xvid xvmc yv12 zip zlib elibc_glibc input_devices_linuxinput input_devices_ps2mouse input_devices_serialmouse kernel_linux linguas_en userland_GNU video_cards_i830" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Same here. # emerge --info Gentoo Base System version 1.12.0 Portage 2.1_rc2-r3 (default-linux/x86/2006.0, gcc-4.1.1, glibc-2.4-r2, 2.6.16-suspend2-r6 i686) ================================================================= System uname: 2.6.16-suspend2-r6 i686 Mobile AMD Athlon(tm) XP 2600+ ccache version 2.4 [enabled] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r1 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r2 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r5 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=athlon-xp -O3 -pipe -fomit-frame-pointer -funroll-loops" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/grass60/etc /usr/lib/mozilla/defaults/pref /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-march=athlon-xp -O3 -pipe -fomit-frame-pointer -funroll-loops" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="ftp://130.59.10.34/mirror/gentoo/ ftp://130.59.10.35/mirror/gentoo/ ftp://ftp.wwc.edu/pub/mirrors/ftp.gentoo.org ftp://ftp.ecc.u-tokyo.ac.jp/GENTOO ftp://mirror.isp.net.au/pub/gentoo/" LANG="it_IT" LC_ALL="it_IT.utf8" LINGUAS="it" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="x86 3dnow 7zip X aac aalib acpi aim alsa apache2 audiofile avi berkdb bitmap-fonts bzip2 caps cdparanoia cdr cli crypt cups dba dbase dbus dga dio dri dts dvb dvd dvdr dvdread emboss encode esd fbcon ffmpeg fftw firefox flac flatfile foomaticdb fortran ftp gcj gdbm geoip gif gnutls gpm gps gstreamer gtk gtk2 hal iconv icq ieee1394 imagemagick imap imlib isdnlog jabber jack javascript jpeg jpeg2k lcms lesstif libcaca libg++ libgda libwww mad matroska mbox md5sum mhash mikmod mime mmap mmx mng motif mp3 mpeg msn nas ncurses nis nls nptl nsplugin odbc offensive ogg opengl oscar oss pam pcmcia pcre pdf pdflib perl php pic png posix postgres ppds pppd python qt quicktime readline reflection samba sdl session sharedmem sndfile soap sockets sox spell spl sse ssl svg sysvipc szip tcltk tcpd tetex theora threads tiff timidity truetype truetype-fonts type1-fonts udev unicode usb v4l vcd vorbis win32codecs wmf wxwindows xinerama xml xml2 xmlrpc xorg xosd xpm xprint xsl xv xvid yahoo zlib elibc_glibc input_devices_keyboard input_devices_mouse input_devices_synaptics kernel_linux linguas_it userland_GNU video_cards_via video_cards_vesa video_cards_fbdev video_cards_v4l" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS
Upgrading to hdf5-1.6.5-r1 fixes the bug, thank you all. Solved for me.
Fixed in the above version (and back-ported to 1.6.5).
