When testing MPICH2 I came across a minimal example for MPI which does not link for sys-cluster/mpich2-1.0.3 (x86), but does link with sys-cluster/mpich2-1.0.5_p4 (~x86). #include <mpi.h> int main(int argc, char *argv[]) { int mpiRank; MPI_Init(&argc,&argv); MPI_Comm_rank(MPI_COMM_WORLD,&mpiRank); MPI_Finalize(); return 0; } When linking the example above using the 1.0.3 package, the linker returns this message: /usr/lib/libmpich.so: undefined reference to `MPIU_Free' /usr/lib/libmpich.so: undefined reference to `MPIU_Malloc' collect2: ld returned 1 exit status Using 1.0.5_p4, the program links (and runs) without error. In both cases, I used the standard configuration files in /etc/mpich2. I suggest to stabilize sys-cluster/mpich2-1.0.5_p4. Reproducible: Always Steps to Reproduce: Portage 2.1.3.9 (default-linux/x86/2006.1/desktop, gcc-4.1.2, glibc-2.5-r4, 2.6.22-gentoo-r2 i686) ================================================================= System uname: 2.6.22-gentoo-r2 i686 Intel(R) Pentium(R) 4 CPU 2.80GHz Timestamp of tree: Tue, 25 Sep 2007 08:20:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p17 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.3.5-r3, 2.4.4-r5 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.9-r2 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.61-r1 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-r1 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.21 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -pipe" 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/revdep-rebuild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-O2 -march=pentium4 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://ftp.uni-kl.de/pub/linux/gentoo" LANG="C" LC_ALL="C" LINGUAS="en de" MAKEOPTS="-j2" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage /usr/portage/local/layman/sunrise /usr/local/java-overlay /usr/local/gcj-overlay" SYNC="rsync://rsync.de.gentoo.org/gentoo-portage/" USE="7zip X a52 aac aalib alsa audiofile avi bash-completion berkdb bitmap-fonts bzip2 cdparanoia cdr cli cracklib crypt cups curl cvs d dbus dri dv dvd dvdr dvdread emboss encode exif expad faac faad fam ffmpeg firefox flac foomaticdb gd gdbm gif gnutls gpm graphviz gs hal iconv icq icu idn imagemagick imap imlib isdnlog jabber jbig jpeg jpeg2k kde kipi lame latex lcms ldap libcaca live logrotate lzo mad matroska mbox md5sum midi mikmod mjpeg mmx mng mp3 mpeg mplayer mudflap musicbrainz ncurses network nfs nls nntp nptl nptlonly nsplugin nvidia ogg opengl openmp oss pam pcre pdf perl pic plotutils png ppds pppd python qt qt3 qt4 quicktime readline reflection rtc samba sasl sdl session slang speex spell spl sse sse2 ssl subtitles subversion svg tcpd tetex tga theora threads tiff truetype truetype-fonts type1-fonts unicode usb userlocales v4l v4l2 vim-syntax vorbis win32codec win32codecs wmf x86 xml xorg xscreensaver xv xvid zlib zrtp" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en de" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
I cannot compile sci-biology/mrbayes due to an old mpich2 available for amd64: mpicc -O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o -lncurses -lreadline -lm -o mb /usr/lib64/libmpich.so: undefined reference to `MPIU_Free' /usr/lib64/libmpich.so: undefined reference to `MPIU_Malloc' collect2: ld returned 1 exit status The bug is described also here: http://forums.gentoo.org/viewtopic-p-3996985.html?sid=b930b4fd1de8b4785ad96ed9bbc0b390 Basically, I am asking sys-cluster/mpich2-1.0.6 version bump. The issue is still here because the bugs #173568 and #155920 got closed while no version bump appeared for all platforms. I am using successfully mpich2-1.0.6 on x86 and amd64 to compile mrbayes-3.1.2 on these two platforms. Please unmask mrbayes-3.1.2 afterwards as well. Thanks.
Please stabilize 1.0.6 for amd64 and x86. Thanks. This version is known to be buggy so why do you keep at all it? Look yourself into your own einfo comments in mpich2-1.0.6.ebuild. ;-)
I just added mpich2-1.0.8 to the science overlay. If you have a spare moment, could you please test and report back? Note that if you were using MPE2 support as part of mpich2, you'll have to emerge sys-cluster/mpe2 separately. Thanks.
(In reply to comment #3) > I just added mpich2-1.0.8 to the science overlay. If you have a spare moment, > could you please test and report back? No, the mpich2-1.0.8 does not work for me whereas 1.0.6 does on amd64 (multilib). Please stabilize 1.0.6. The 1.0.3 is unusable on such systems due to <quote> /usr/lib64/libmpich.so: undefined reference to `MPIU_Free' /usr/lib64/libmpich.so: undefined reference to `MPIU_Malloc' collect2: ld returned 1 exit status </quote>
(In reply to comment #4) > No, the mpich2-1.0.8 does not work for me whereas 1.0.6 does on amd64 > (multilib). > Please stabilize 1.0.6. The 1.0.3 is unusable on such systems due to 1.0.6 has at least two outstanding bugs, both of which are fixed in 1.0.8 https://bugs.gentoo.org/buglist.cgi?query_format=advanced&short_desc_type=allwordssubstr&short_desc=mpich2-1.0.6&long_desc_type=substring&long_desc=&bug_file_loc_type=allwordssubstr&bug_file_loc=&status_whiteboard_type=allwordssubstr&status_whiteboard=&keywords_type=allwords&keywords=&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED&emailassigned_to1=1&emailtype1=substring&email1=&emailassigned_to2=1&emailreporter2=1&emailcc2=1&emailtype2=substring&email2=&bugidtype=include&bug_id=&votes=&chfieldfrom=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Reuse+same+sort+as+last+time&field0-0-0=noop&type0-0-0=noop&value0-0-0= > > <quote> > /usr/lib64/libmpich.so: undefined reference to `MPIU_Free' > /usr/lib64/libmpich.so: undefined reference to `MPIU_Malloc' > collect2: ld returned 1 exit status > </quote> > Compiles fine for me, along with hpl and mpe2 and various other mpi utilities on amd64. Is the emerge --info you posted still current? I don't see LDFLAGS in it, which could be causing this issue. What USE flags are you compiling mpich2 with?
Yes, I still cannot compile mrbayes on stable amd64 against mpich2-1.0.3: node001 ~ # emerge -pv mrbayes These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-biology/mrbayes-3.1.2 USE="mpi readline" 0 kB Total: 1 package (1 reinstall), Size of downloads: 0 kB node001 ~ # emerge mrbayes Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 1) sci-biology/mrbayes-3.1.2 * mrbayes-3.1.2.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mrbayes-3.1.2.tar.gz to /var/tmp/portage/sci-biology/mrbayes-3.1.2/work * Applying mb_readline_312.patch ... [ ok ] >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sci-biology/mrbayes-3.1.2/work/mrbayes-3.1.2 ... make -j1 mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o mb.o mb.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o mcmc.o mcmc.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o bayes.o bayes.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o command.o command.c command.c: In function 'GetToken': command.c:7813: warning: value computed is not used mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o mbmath.o mbmath.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o model.o model.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o plot.o plot.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o sump.o sump.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall -c -o sumt.o sumt.c mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o -lncurses -lreadline -lm -o mb /usr/lib64/libmpich.so: undefined reference to `MPIU_Free' /usr/lib64/libmpich.so: undefined reference to `MPIU_Malloc' collect2: ld returned 1 exit status make: *** [mb] Error 1 * * ERROR: sci-biology/mrbayes-3.1.2 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2129: Called _eapi0_src_compile * ebuild.sh, line 595: Called _eapi2_src_compile # emerge --info Portage 2.1.6.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r4-default x86_64) ================================================================= System uname: Linux-2.6.24-gentoo-r4-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q6600_@_2.40GHz-with-glibc2.2.5 Timestamp of tree: Thu, 15 Jan 2009 16:00:01 +0000 distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6-r1 dev-lang/python: 2.4.4-r13, 2.5.2-r7 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" 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="/nfslarge/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d acl acpi amd64 apache2 bash-completion bcmath berkdb blas boost bzip2 cblas clamav cli colordiff compress cpio cracklib crypt cscope css ctype curl curlwrappers cxx dbus djbfft emboss enblend encode enscript expat fam fortran ftp gcj gd gdbm gif glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpm graphviz gs gtk gtkhtml hal icc iconv ifc inifile innodb isdnlog ithreads java javascript jbig jikes jpeg jpeg2k kdtree lapack lcms libedit libwww lzo lzw maildir mhash midi mime ming mjpeg mmap mmx mng mod_python modperl modplug mozilla moznoirc mpeg mpi mpi_njtree mpich2 mudflap mule multilib mxdatetime mysql mysqli ncurses netcdf netpbm network nntp nptl nptlonly numeric openmp pam pcntl pcre pdf perl plotutils png pnm postproc postscript ppds pppd procmail pymol python rar raw readline reflection reiserfs rpm rtc scp seamonkey server session sftp sift smime sndfile sockets spl srt sse sse2 sse3 ssl svg svgz sysfs sysvipc tcl tcpd threads tiff transcode unicode urandom userlocales uuencode vim-syntax vim-with-x wmf xanim xfs xinetd xml xorg xpm xslt xv xvid zip zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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 authn_alias authn_anon 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 deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif 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="en cs cz" USERLAND="GNU" VIDEO_CARDS="nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
mrbayes also compiles for me without issues. Can you make sure that libmpich.so is exporting MPIU_tfree with: objdump -T /usr/lib64/libmpich.so | grep MPIU_trfree
Justin(In reply to comment #7) > mrbayes also compiles for me without issues. > > Can you make sure that libmpich.so is exporting MPIU_tfree with: > objdump -T /usr/lib64/libmpich.so | grep MPIU_trfree > Justin, I think it was mentioned somewhere in Changelog around 1.0.4 but I cannot find it now easily. Maybe this gives a hint? http://www.mcs.anl.gov/~gropp/projects/parallel/MPICH/mpich2/changes/change08-12-2007.html I have already upgraded to mpich2-1.0.6 but after downgrade to 1.0.3 I still cannot compile mrbayes. # objdump -T /usr/lib64/libmpich.so | grep MPIU_trfree 000000000008bc20 g DF .text 00000000000002f8 Base MPIU_trfree # [cut] mpicc -O2 -march=nocona -fomit-frame-pointer -pipe -DUNIX_VERSION -DUSE_READLINE -DMPI_ENABLED -Wall mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o -lncurses -lreadline -lm -o mb /usr/lib64/libmpich.so: undefined reference to `MPIU_Free' /usr/lib64/libmpich.so: undefined reference to `MPIU_Malloc' collect2: ld returned 1 exit status make: *** [mb] Error 1 * * ERROR: sci-biology/mrbayes-3.1.2 failed. [cut] # emerge -pv =sys-cluster/mpich2-1.0.3 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sys-cluster/mpich2-1.0.3 USE="crypt cxx threads -debug -doc -mpe" 0 kB # emerge =sys-cluster/mpich2-1.0.3 Calculating dependencies... done! >>> Verifying ebuild manifests >>> Emerging (1 of 1) sys-cluster/mpich2-1.0.3 * mpich2-1.0.3.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking mpich2-1.0.3.tar.gz to /var/tmp/portage/sys-cluster/mpich2-1.0.3/work [cut] Creating src/pm/smpd/smpd_version.h /usr/lib64/portage/bin/isolated-functions.sh: line 279: failed: command not found [ !! ] /usr/lib64/portage/bin/isolated-functions.sh: line 291: return: Reconfigure: numeric argument required /usr/lib64/portage/bin/isolated-functions.sh: line 301: return: Reconfigure: numeric argument required * Applying mpich2-1.0.3-make.patch ... [ ok ] * Applying mpich2-1.0.3-soname.patch ... [ ok ] >>> Source unpacked. >>> Compiling source in /var/tmp/portage/sys-cluster/mpich2-1.0.3/work/mpich2-1.0.3 ... Configuring MPICH2 version 1.0.3 with --prefix=/usr --enable-sharedlibs=gcc --enable-fast --enable-g=none --with-thread-package=pthreads --enable-rlog=no --enable-slog2=no --enable-cxx --disable-mpe --enable-threads --includedir=/usr/include --libdir=/usr/lib64 --mandir=/usr/share/man --with-docdir=/usr/share/doc/mpich2-1.0.3 --with-htmldir=/usr/share/doc/mpich2-1.0.3/html --sysconfdir=/etc/mpich2 --datadir=/usr/share/mpich2 sourcing /var/tmp/portage/sys-cluster/mpich2-1.0.3/work/mpich2-1.0.3/src/pm/mpd/setup_pm checking for gcc... gcc [cut] # emerge --info Portage 2.1.6.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r4-default x86_64) ================================================================= System uname: Linux-2.6.24-gentoo-r4-default-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q6600_@_2.40GHz-with-glibc2.2.5 Timestamp of tree: Mon, 19 Jan 2009 12:05:01 +0000 distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6-r1 dev-lang/python: 2.4.4-r13, 2.5.2-r7 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" DISTDIR="/nfslarge/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" 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="/nfslarge/usr/portage" PORTDIR_OVERLAY="/nfslarge/usr/portage/local/layman/sunrise /nfslarge/usr/portage/local" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d acl acpi amd64 apache2 bash-completion bcmath berkdb blas boost bzip2 cblas clamav cli colordiff compress cpio cracklib crypt cscope css ctype curl curlwrappers cxx dbus djbfft emboss enblend encode enscript expat fam fortran ftp gcj gd gdbm gif glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpm graphviz gs gtk gtkhtml hal icc iconv ifc inifile innodb isdnlog ithreads java javascript jbig jikes jpeg jpeg2k kdtree lapack lcms libedit libwww lzo lzw maildir mhash midi mime ming mjpeg mmap mmx mng mod_python modperl modplug mozilla moznoirc mpeg mpi mpi_njtree mpich2 mudflap mule multilib mxdatetime mysql mysqli ncurses netcdf netpbm network nntp nptl nptlonly numeric openmp pam pcntl pcre pdf perl plotutils png pnm postproc postscript ppds pppd procmail pymol python rar raw readline reflection reiserfs rpm rtc scp seamonkey server session sftp sift smime sndfile sockets spl srt sse sse2 sse3 ssl svg svgz sysfs sysvipc tcl tcpd threads tiff transcode unicode urandom userlocales uuencode vim-syntax vim-with-x wmf xanim xfs xinetd xml xorg xpm xslt xv xvid zip zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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 authn_alias authn_anon 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 deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif 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="en cs cz" USERLAND="GNU" VIDEO_CARDS="vesa nvidia nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
# objdump -T /usr/lib64/libmpich.so | grep MPIU_Free 0000000000000000 D *UND* 0000000000000000 MPIU_Free # objdump -T /usr/lib64/libmpich.so | grep MPIU_Malloc 0000000000000000 D *UND* 0000000000000000 MPIU_Malloc # equery belongs /usr/lib64/libmpich.so [ Searching for file(s) /usr/lib64/libmpich.so in *... ] sys-cluster/mpich2-1.0.3 (/usr/lib64/libmpich.so -> libmpich.so.0.0) #
Both mpich2-1.0.3 and mpich2-1.0.6 have been removed from the tree and this works fine for me with 1.0.8.
