Bug 407155 – sys-cluster/openmpi - Rmpi fails to install under dev-lang/R-2.14.2 due to undefined symbol: mca_base_param_reg_int in /usr/lib64/openmpi/mca_paffinity_hwloc.so

• Product: Gentoo Linux
• Status: RESOLVED TEST-REQUEST

[Description Juergen Rose 2012-03-06 19:09:00 UTC]

> install.packages("Rmpi", dependencies=TRUE)
fails with:
...
** testing if installed package can be loaded
/usr/lib64/R/bin/exec/R: symbol lookup error: /usr/lib64/openmpi/mca_paffinity_hwloc.so: undefined symbol: mca_base_param_reg_int
ERROR: loading failed

'ldd -r /usr/lib64/openmpi/mca_paffinity_hwloc.so' gives:
root@lynx:/root(3)# ldd -r /usr/lib64/openmpi/mca_paffinity_hwloc.so
        linux-vdso.so.1 =>  (0x00007fff1e541000)
        libhwloc.so.5 => /usr/lib64/libhwloc.so.5 (0x00007f7f1d455000)
...
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f7f19aaa000)
undefined symbol: mca_base_param_find   (/usr/lib64/openmpi/mca_paffinity_hwloc.so)
undefined symbol: mca_base_param_reg_string     (/usr/lib64/openmpi/mca_paffinity_hwloc.so)
undefined symbol: mca_base_param_reg_int        (/usr/lib64/openmpi/mca_paffinity_hwloc.so)
undefined symbol: mca_base_param_lookup_int     (/usr/lib64/openmpi/mca_paffinity_hwloc.so)


Could it be, that openmpi-1.5.4-r3 does not play with hwloc-1.4.1:

root@lynx:/root(4)# genlop -t openmpi | tail

     Fri Jan 27 10:20:54 2012 >>> sys-cluster/openmpi-1.5.4-r2
       merge time: 5 minutes and 42 seconds.

     Sun Feb  5 09:08:36 2012 >>> sys-cluster/openmpi-1.5.4-r3
       merge time: 5 minutes and 33 seconds.

     Tue Mar  6 19:37:47 2012 >>> sys-cluster/openmpi-1.5.4-r3
       merge time: 5 minutes and 6 seconds.

root@lynx:/root(5)# genlop -t hwloc | tail

     Thu Dec 22 09:56:09 2011 >>> sys-apps/hwloc-1.3.1
       merge time: 32 seconds.

     Thu Jan 26 20:29:36 2012 >>> sys-apps/hwloc-1.4
       merge time: 35 seconds.

     Tue Mar  6 11:03:37 2012 >>> sys-apps/hwloc-1.4.1
       merge time: 41 seconds.





root@lynx:/root(6)# emerge --info
Portage 2.1.10.49 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.14.1-r2, 3.2.9-gentoo x86_64)
=================================================================
System uname: Linux-3.2.9-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.1
Timestamp of tree: Tue, 06 Mar 2012 13:30:01 +0000
app-shells/bash:          4.2_p20
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.2-r3::sage-on-gentoo, 3.2.2
dev-util/cmake:           2.8.7-r3
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1
sys-apps/openrc:          0.9.9.2
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.68
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.3
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2
sys-devel/gcc-config:     1.5.1
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.2-r1 (virtual/os-headers)
sys-libs/glibc:           2.14.1-r2
Repositories: gentoo lordvan x11 bicatali sage-on-gentoo java-overlay sunrise proaudio science dilfridge arcon ibormuth local x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/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="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/lordvan /var/lib/layman/x11 /var/lib/layman/bicatali /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/pro-audio /var/lib/layman/science /var/lib/layman/dilfridge /var/lib/layman/arcon /var/lib/layman/ibormuth /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdrive kerberos kpathsea kqemu kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc live lua lzo mad mail maildir mapnik math matroska media-library mkl mmx mmxext mng modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thinkpad threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter vaapi video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml 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 cgid 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="usb-wt220u" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Juergen Rose 2012-04-03 13:15:56 UTC]

Any news? I hit this error again, doing update.packages() under R-2.15.0.

[Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) 2012-05-11 11:44:42 UTC]

I've found thread on upstream's mailing list (see $URL). However they don't offer anything besides static linking :/

[Comment 3 Kacper Kowalik (Xarthisius) (RETIRED) 2012-05-11 12:13:24 UTC]

looking at Rmpi source:
src/Rmpi.c:	dlopen("libmpi.so.0", RTLD_GLOBAL | RTLD_LAZY);

changing RTLD from LAZY to NOW could help.

[Comment 4 Alexey Shvetsov 2014-04-08 08:21:29 UTC]

Is it still valid?