sys-cluster/openmpi-1.3.3 fail every time if i try to compile it ##### Portage 2.1.6.13 (default/linux/amd64/10.0, gcc-4.4.1, glibc-2.10.1-r0, 2.6.31-gentoo-r3 x86_64) ================================================================= System uname: Linux-2.6.31-gentoo-r3-x86_64-Intel-R-_Core-TM-2_Duo_CPU_P9700_@_2.80GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 08 Oct 2009 06:00:01 +0000 app-shells/bash: 4.0_p33 dev-java/java-config: 2.1.9-r1 dev-lang/python: 2.6.3, 3.1.1-r1 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.1 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CXXFLAGS="-march=core2 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LANG="de_DE.UTF-8" LDFLAGS="-Wl,-O1" LINGUAS="de en vi" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="7zip X a52 aac aalib acc accessibility acl acpi adns afs aim alsa amd64 ao apache2 ass audio audiofile avi bash-completion beagle berkdb bidi bluetooth bzip2 cairo caps cdaudio cdda cdio cdparanoia cdr cgi cjk cli clisp consolekit cracklib crypt cs2 cscope css csv cups curl curlwrappers cvs dbus dc1394 dga dia dirac directfb divx dlloader dmx dri dts dv dvd dvdr dvdread dvi emacs enca encode enscript erandom esd exif expat extras faac faad fam fastcgi fbcon ffmpeg firefox flac flash fortran ftp fuse gcj gd gdbm ggi gif gimp git glib gmp gnome gnome-keyring gnutls gphoto2 gpm graphviz gs gstreamer gtk gzip hal hash highlight httpd iconv icq icu idn ieee1394 imagemagick imap imlib ipv6 isdnlog jabber jack java java6 javascript jingle joystick jpeg jpeg2k kde kerberos lame latex lcms ldap libcaca libwww live logrotate lua lzo mad maildir matroska md5sum memlimit mhash midi mikmod mime mjpeg mmap mmx mmxext mng mono motif mp3 mp4 mpeg mpeg2 mplayer msn mudflap mule multilib musepack mysql nas nautilus ncurses network networkmanager nfs nls nptl nptlonly nsplugin nvidia ogg ogg123 openal openexr opengl openmp org oss pam pcre pdf perl php pic pidgin png posix postgres ppds pppd ps pulseaudio pwdb python qt3support qt4 quicktime radio rar raw rdesktop readline realmedia reflection rss rtsp ruby samba sasl schroedinger sdl sdl-image session sip slang slp smp sockets sox spamassassin speex spell spl sqlite sse sse2 ssl stream stun subversion svg swat sysfs syslog sysvipc tcl tcpd tetex theora threads tidy tiff timidity tk truetype ucs2 udev unace unicode urandom url usb userlocales v4l v4l2 vcd vhost video vim-syntax vlc vlm vnc vorbis wav wavpack webkit wifi wma wmf wxwidgets x264 xattr xcb xdm xft xinerama xinetd xlinks xml xmlrpc xorg xpm xprint xscreensaver xsl xulrunner xv xvid xvmc yahoo zip zlib zsh-completion" ALSA_CARDS="hda_intel" 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" 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 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 php5 proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" APACHE2_MPMS="worker" CAMERAS="canon" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de en vi" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa fbdev vga vmware" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Reproducible: Always Steps to Reproduce: Actual Results: /bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_environ.lo -MD -MP -MF $depbase.Tpo -c -o opal_environ.lo opal_environ.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT numtostr.lo -MD -MP -MF .deps/numtostr.Tpo -c numtostr.c -fPIC -DPIC -o .libs/numtostr.o depbase=`echo opal_getcwd.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_getcwd.lo -MD -MP -MF $depbase.Tpo -c -o opal_getcwd.lo opal_getcwd.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo opal_pty.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_pty.lo -MD -MP -MF $depbase.Tpo -c -o opal_pty.lo opal_pty.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_environ.lo -MD -MP -MF .deps/opal_environ.Tpo -c opal_environ.c -fPIC -DPIC -o .libs/opal_environ.o opal_environ.c: In function ‘opal_setenv’: opal_environ.c:107: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result opal_environ.c:109: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result opal_environ.c:139: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result opal_environ.c: In function ‘opal_unsetenv’: opal_environ.c:195: warning: ignoring return value of ‘asprintf’, declared with attribute warn_unused_result libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_getcwd.lo -MD -MP -MF .deps/opal_getcwd.Tpo -c opal_getcwd.c -fPIC -DPIC -o .libs/opal_getcwd.o libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT opal_pty.lo -MD -MP -MF .deps/opal_pty.Tpo -c opal_pty.c -fPIC -DPIC -o .libs/opal_pty.o depbase=`echo os_dirpath.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT os_dirpath.lo -MD -MP -MF $depbase.Tpo -c -o os_dirpath.lo os_dirpath.c &&\ mv -f $depbase.Tpo $depbase.Plo In file included from /usr/include/define.h:48, from /usr/include/util.h:56, from opal_pty.c:95: /usr/include/cmdline.h:47:20: error: config.h: No such file or directory depbase=`echo os_path.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT os_path.lo -MD -MP -MF $depbase.Tpo -c -o os_path.lo os_path.c &&\ mv -f $depbase.Tpo $depbase.Plo make[3]: *** [opal_pty.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT os_dirpath.lo -MD -MP -MF .deps/os_dirpath.Tpo -c os_dirpath.c -fPIC -DPIC -o .libs/os_dirpath.o libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../../opal/include -I../../orte/include -I../../ompi/include -I../../opal/mca/paffinity/linux/plpa/src/libplpa -I../.. -DNDEBUG -march=core2 -O2 -pipe -finline-functions -fno-strict-aliasing -pthread -fvisibility=hidden -MT os_path.lo -MD -MP -MF .deps/os_path.Tpo -c os_path.c -fPIC -DPIC -o .libs/os_path.o make[3]: Leaving directory `/var/tmp/portage/sys-cluster/openmpi-1.3.3/work/openmpi-1.3.3/opal/util' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/var/tmp/portage/sys-cluster/openmpi-1.3.3/work/openmpi-1.3.3/opal/util' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sys-cluster/openmpi-1.3.3/work/openmpi-1.3.3/opal' make: *** [all-recursive] Error 1 * * ERROR: sys-cluster/openmpi-1.3.3 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3295: Called _eapi2_src_compile * ebuild.sh, line 634: Called die * The specific snippet of code: * emake || die "emake failed" * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sys-cluster:openmpi-1.3.3:20091008-063101.log'. * The ebuild environment file is located at '/var/tmp/portage/sys-cluster/openmpi-1.3.3/temp/environment'. * >>> Failed to emerge sys-cluster/openmpi-1.3.3, Log file: >>> '/var/log/portage/sys-cluster:openmpi-1.3.3:20091008-063101.log' * Messages for package sys-cluster/openmpi-1.3.3: * * OpenMPI has an overwhelming count of configuration options. * Don't forget the EXTRA_ECONF environment variable can let you * specify configure options if you find them necessary. * * Messages for package sys-cluster/openmpi-1.3.3: * * OpenMPI has an overwhelming count of configuration options. * Don't forget the EXTRA_ECONF environment variable can let you * specify configure options if you find them necessary. * * * ERROR: sys-cluster/openmpi-1.3.3 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3295: Called _eapi2_src_compile * ebuild.sh, line 634: Called die * The specific snippet of code: * emake || die "emake failed" * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/log/portage/sys-cluster:openmpi-1.3.3:20091008-063101.log'. * The ebuild environment file is located at '/var/tmp/portage/sys-cluster/openmpi-1.3.3/temp/environment'.
*** Bug 288148 has been marked as a duplicate of this bug. ***
In file included from /usr/include/define.h:48, from /usr/include/util.h:56, from opal_pty.c:95: /usr/include/cmdline.h:47:20: error: config.h: No such file or directory To which package do these files belong? equery belongs /usr/include/define.h equery belongs /usr/include/util.h
it belongs to package iat, but the remergening of iat then openmpi bring to me the same error
$ equery f iat * Searching for iat ... * Contents of app-cdr/iat-0.1.3: /usr /usr/bin /usr/bin/iat /usr/share /usr/share/doc /usr/share/doc/iat-0.1.3 /usr/share/doc/iat-0.1.3/AUTHORS.bz2 iat doesn't install these files here. What gives equery f iat for you? Are they still present after re-emerging iat? If so where do they belong to now? Is the build error for openmpi still the same?
# equery f iat * Searching for iat ... * Contents of app-cdr/iat-0.1.7: /usr /usr/bin /usr/bin/iat /usr/include /usr/include/calculate_pregap.h /usr/include/cmdline.h /usr/include/convert_2_iso.h /usr/include/debug.h /usr/include/define.h /usr/include/ecma119.h /usr/include/ecma167.h /usr/include/mkcore.h /usr/include/mkcue.h /usr/include/mktoc.h /usr/include/mmc2r11.h /usr/include/util.h /usr/share /usr/share/doc /usr/share/doc/iat-0.1.7 /usr/share/doc/iat-0.1.7/AUTHORS.bz2 /usr/share/doc/iat-0.1.7/NEWS.bz2 /usr/share/doc/iat-0.1.7/README.bz2 /usr/share/man /usr/share/man/man1 /usr/share/man/man1/iat.1.bz2 y very strange but i got the same errors again
I should sync more often... These are two bugs in one. iat shouldn't install those files in /usr/include and openmpi shouldn't use them even if they are present. @reporter please file a separate bug for iat. As a workaround: downgrade iat.
ok ok i have removed iat and openmpi was emerge fine
This is not fixed.
*** This bug has been marked as a duplicate of bug 288203 ***
No this isn't a duplicate. It's a problem with the openmpi buildsystem!
jlec is correct, please stop closing this.
This isn't openmpi looking for it's own bundled files, rather looking for system headers, as can be verified in configure.ac. Given that the headers it checks for all seem to be pretty standard on various OS's, I'm going to close this. AC_CHECK_HEADERS([alloca.h aio.h arpa/inet.h dirent.h \ dlfcn.h execinfo.h err.h fcntl.h grp.h inttypes.h libgen.h \ libutil.h netdb.h netinet/in.h netinet/tcp.h \ poll.h pthread.h pty.h pwd.h sched.h stdint.h \ string.h strings.h stropts.h sys/fcntl.h sys/ipc.h \ sys/ioctl.h sys/mman.h sys/param.h sys/queue.h \ sys/resource.h sys/select.h sys/socket.h sys/sockio.h \ stdarg.h sys/stat.h sys/statvfs.h sys/time.h sys/tree.h \ sys/types.h sys/uio.h net/uio.h sys/utsname.h sys/wait.h syslog.h \ time.h termios.h ulimit.h unistd.h util.h utmp.h malloc.h \ ifaddrs.h sys/sysctl.h crt_externs.h regex.h \ ioLib.h sockLib.h hostLib.h shlwapi.h sys/synch.h])
