Emerge hdf5-1.6.5-r1 fails with
...
checking for MPI_File_open in -lmpio... no
checking prefix for running on one processor... none
checking prefix for running in parallel... /usr/bin/mpirun -np $${NPROCS:=3}
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application
in config.log I find:
configure:35224: /usr/bin/mpicc -o conftest -O2 -pipe -march=i686 -march=i686
-std=c99 -Wno-long-long -O -fomit-frame-pointer -fin\
line-functions -D_BSD_SOURCE -D_POSIX_SOURCE -D_FILE_OFFSET_BITS=64
-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -DNDEBUG -UH5_DEBUG\
_API conftest.c -lssl -lcrypto -lz -lm >&5
conftest.c: In function 'main':
conftest.c:120: warning: implicit declaration of function 'MPI_File_open'
/var/tmp/portage/sci-libs/hdf5-1.6.5-r1/temp/cccxTLrQ.o: In function `main':
conftest.c:(.text+0xf): undefined reference to `MPI_File_open'
For hdf5 the mpi USE-flag is set in package.use.
MPI_File_open is not defined in /usr/include/mpi.h.
installed is sys-cluster/mpich2-1.0.3-r1 respectively virtual/mpi-1.0.
root@tiger:/usr/src(76)# emerge --info
Portage 2.1.2_rc4-r2 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.5-r0,
2.6.19.1 i686)
=================================================================
System uname: 2.6.19.1 i686 Pentium II (Klamath)
Gentoo Base System version 1.12.8
Last Sync: Fri, 29 Dec 2006 08:20:01 +0000
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
dev-java/java-config: 1.3.7, 2.0.31
dev-lang/python: 2.4.4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox: 1.2.18.1
sys-devel/autoconf: 2.13, 2.61
sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils: 2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool: 1.5.22
virtual/os-headers: 2.6.19
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=i686"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config
/usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c
"
CXXFLAGS="-O2 -pipe -march=i686"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks fixpackages metadata-transfer sandbox sfperms
strict"
GENTOO_MIRRORS="ftp://ftp.tu-clausthal.de/pub/linux/gentoo/
ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo http://linux.rz
.ruhr-uni-bochum.de/download/gentoo-mirror/
ftp://linux.rz.ruhr-uni-bochum.de/gentoo-mirror/
http://ftp.uni-erlangen.de/pub/mirrors/
gentoo ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo
ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo
ftp://ftp.join.uni-muenster.de/pu
b/linux/distributions/gentoo
http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/
http://ftp-stud.fht-esslingen.de/pub/Mirrors/gent
oo/ "
LINGUAS="de fr"
MAKEOPTS="-j3"
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"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="cdf gs flac unicode nls jpeg graphviz matrox netcdf cdr mysql
libsamplerate gdbm dxr3 auctex mng xvmc iconv samba hal cli daap
gml lapack gtk elf apache2 udev fortran ldap atlas hardened gmp aotuv wmf real
v4l2 postgres xmlrpc python lzw ssl effects lzo xvid
sse X bitmap-fonts sqlite subtitles guile evolution nptl evo dbus fftw rrdcgi
pam zlib session innodb ppds bonobo qhull cairo numeri
c xext xemacs mp4live mmx corba network exif jabber geos devmap cdda id3 cddb
rle esd proj nfs icq nntp cgi imagemagick isdnlog gina
c mozdevelop truetype-fonts asf octave musicbrainz mysqli theora gdal grass
gnome hdf5 mono ocaml glade xine dri epiphany pdf t1lib
tiff mpeg2 kexi zvbi math cups odbc pcre gpm dynagraph xpm automount
type1-fonts snmp perl a52 emacs ipv6 matroska mozsvg cracklib x
ml2 dlloader rrdtool ncurses ogdi mozilla pppd libgda jbig hddtemp cdparanoia
reiserfs berkdb gsl png lm_sensors Xaw3d ffmpeg aac np
tlonly mozcalendar plugin slp hdf gphoto2 svg posix rhythmbox lcms sox nautilus
blas expat tidy ao tcpd plotutils spl tetex mozxmlte
rm sndfile hlapi curl fame gimp bzip2 fltk gnuplot lame crypt libg++ xmlreader
tcltk fpx alsa cdio dga x86 mplayer xorg fits readlin
e jp2 slang latex dvi reflection sse2 dvd numarray dvb mod jpeg2 win32codecs
gsm audiofile" ALSA_CARDS="ali5451 als4000 atiixp atiix
p-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801
hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via
82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare
dsnoop empty extplug file hooks iec958 ioplug ladspa l
float linear meter mulaw multi null plug rate route share shm softvol"
ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" L
INGUAS="de fr" USERLAND="GNU" VIDEO_CARDS="mga vesa fbdev"
Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
