| Summary: | sci-libs/hdf5-1.6.5-r1 with mpich2 fails | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Juergen Rose <rose> |
| Component: | [OLD] Library | Assignee: | Gentoo Linux bug wranglers <bug-wranglers> |
| Status: | VERIFIED DUPLICATE | ||
| Severity: | normal | ||
| Priority: | High | ||
| Version: | 2006.1 | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
*** This bug has been marked as a duplicate of 159389 *** Dupe. |
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