Hi, using sys-cluster/lam-mpi-7.1.1 I get some strange 'undefined references'-errors from 'mpicc' while compiling trivial mpi-examples. Regards Georg Sauthoff P.S.: The ebuild doesn't install the examples, which are provided by the lam-mpi distribution. P.P.S.: Why does the ebuild use slot 6 for program version 7? Reproducible: Always Steps to Reproduce: 1.cd src/lam-7.1.1/examples/hello 2.mpicc -Wall hello.c 3. Actual Results: /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Malloc_request' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Get_eof_offset' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Shfp_fname' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Init' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_DFLT_ERR_HANDLER' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Close' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Init_keyval' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Set_shared_fp' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Set_lock' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Free_fn' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Get_position' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Open' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Get_byte_offset' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Datatype_iscontig' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_End_call' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_Get_shared_fp' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIO_ResolveFileType' /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/../../../liblammpio.so: undefined reference to `ADIOI_Malloc_fn' collect2: ld returned 1 exit status mpicc: No such file or directory Portage 2.0.51.19 (default-linux/x86/2005.0, gcc-3.3.4, glibc-2.3.4.20040808-r1, 2.6.11.2 i686) ================================================================= System uname: 2.6.11.2 i686 Intel(R) Pentium(R) M processor 1300MHz Gentoo Base System version 1.4.16 Python: dev-lang/python-2.2.2,dev-lang/python-2.3.4 [2.3.4 (#1, Feb 1 2005, 22:09:30)] distcc 2.16 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [enabled] dev-lang/python: 2.2.2, 2.3.4 sys-apps/sandbox: [Not Present] sys-devel/autoconf: 2.59-r6, 2.13 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.5, 1.4_p6, 1.6.3, 1.9.4 sys-devel/binutils: 2.14.90.0.8-r1 sys-devel/libtool: 1.5.10-r4 virtual/os-headers: 2.6.8.1-r2 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CFLAGS="-march=pentium4 -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.4/env /usr/kde/3.4/share/config /usr/kde/3.4/shutdown /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/ /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-march=pentium4 -O2 -pipe" DISTDIR="/mnt/platz/distfiles" FEATURES="autoaddcvs autoconfig ccache distcc distlocks sandbox sfperms strict" GENTOO_MIRRORS=" ftp://ftp.tu-clausthal.de/pub/linux/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo " MAKEOPTS="-j4" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="x86 X aalib acpi alsa apache2 apm avi bash-completion berkdb bitmap-fonts cdr crypt cscope cups curl dga directfb doc dvd emboss encode ethereal f77 fam fbcon flac foomaticdb fortran gcj gdbm gif gimpprint gstreamer gtk2 guile icc imagemagick imap imlib ipv6 java jpeg junit kde kerberos ldap libg++ libwww mad maildir mbox mikmod mmx motif mp3 mpeg ncurses nls noplugin ogg oggvorbis opengl oss pam pcmcia pdflib perl png pnp postgres ppds python qt quicktime readline sasl scanner sdl slang speex spell sse ssl tcltk tetex tiff truetype truetype-fonts trusted type1-fonts usb vorbis xine xinerama xml xml2 xmms xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS
Kugelfang: Your patch, your problems. =) Georg: One bug per issue please -- file new bugs if you'd like further action on your PS's. As for the examples, a patch to the ebuild would likely be accepted. The SLOT is 6 because the original SLOT was 6 for whatever reason and it's designed to not be slottable, so we keep it the same regardless of version.
Hi, > Georg: One bug per issue please -- file new bugs if you'd like further > action on your PS's. As for the examples, a patch to the ebuild would > likely be accepted. you are right. You can find the patch for this at bug #96537. Regards Georg Sauthoff
I have been having the same problem on AMD64 when trying to compile any MPI program or package. I have not patched or changed lam-mpi in any way. This problem is reproducable always. mpicc -o mpi_netperf mpi_netperf.c /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Malloc_request' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Get_eof_offset' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Ftable_max' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Reqtable_ptr' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Shfp_fname' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Init' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_DFLT_ERR_HANDLER' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Close' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Init_keyval' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Set_shared_fp' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Set_lock' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Reqtable' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Free_fn' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Get_position' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Ftable_ptr' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Open' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Reqtable_max' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Realloc_fn' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Get_byte_offset' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Datatype_iscontig' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_End_call' /usr/lib64/liblammpio.so: undefined reference to `ADIO_Get_shared_fp' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Ftable' /usr/lib64/liblammpio.so: undefined reference to `ADIO_ResolveFileType' /usr/lib64/liblammpio.so: undefined reference to `ADIOI_Malloc_fn' collect2: ld returned 1 exit status mpicc: No such file or directory Portage 2.0.51.19 (default-linux/amd64/2005.0, gcc-3.4.3, glibc-2.3.4.20041102-r1, 2.6.11-gentoo-r7 x86_64) ================================================================= System uname: 2.6.11-gentoo-r7 x86_64 AMD Athlon(tm) 64 Processor 2800+ Gentoo Base System version 1.6.12 Python: dev-lang/python-2.3.5 [2.3.5 (#1, Jun 13 2005, 19:05:12)] distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] dev-lang/python: 2.3.5 sys-apps/sandbox: [Not Present] sys-devel/autoconf: 2.13, 2.59-r6 sys-devel/automake: 1.8.5-r3, 1.5, 1.7.9-r1, 1.6.3, 1.4_p6, 1.9.5 sys-devel/binutils: 2.15.92.0.2-r10 sys-devel/libtool: 1.5.16 virtual/os-headers: 2.6.8.1-r4 ACCEPT_KEYWORDS="amd64" AUTOCLEAN="yes" CFLAGS="-march=k8 -pipe -O2" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/share/config /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/env.d" CXXFLAGS="-march=k8 -pipe -O2" DISTDIR="/usr/portage/distfiles" FEATURES="autoaddcvs autoconfig ccache distlocks sandbox sfperms strict" GENTOO_MIRRORS="http://mirrors.acm.cs.rpi.edu/gentoo/ http://gentoo.mirrors.pair.com/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://node01.offbyone.local/gentoo-portage" USE="amd64 acpi alsa berkdb bitmap-fonts crypt font-server fortran gif gpm ipv6 jp2 jpeg lzw lzw-tiff mp3 ncurses nls opengl oss pam perl png python readline ssl tcpd tiff truetype truetype-fonts type1-fonts usb userlocales xml2 xpm xrandr xv zlib userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CBUILD, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTDIR_OVERLAY
Sorry, i broke it with my romio patch. I took the romio patch out and bumped lam-mpi to 7.1.1-r1, which fixes this bug, but leaves #88110 open.
