Please stabilize arpack. The tests should run fine. Thanks.
sci-libs/arpack-96-r2 USE="doc examples mpi -debug" checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking for sgemm_ in -lblas ... yes checking for MPI mode... checking for mpif77... no checking for hf77... no checking for mpxlf_r... no checking for mpxlf... no checking for mpf77... no checking for cmpifc... no checking for MPI_Init... no checking for MPI_Init in -lfmpi... no checking for MPI_Init in -lfmpich... no checking for MPI_Init in -lmpi... no checking for MPI_Init in -lmpich... no configure: error: could not compile an mpi test program !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/arpack-96-r2/work/ARPACK/config.log it builds w/o problems with USE="-mpi". Portage 2.1.4.4 (!../usr/portage/profiles/default-linux/x86/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.23.16 i686) ================================================================= System uname: 2.6.23.16 i686 Genuine Intel(R) CPU T2300 @ 1.66GHz Timestamp of tree: Unknown app-shells/bash: 3.2_p17-r1 dev-lang/python: 2.4.4-r6, 2.5.1-r5 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: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=prescott -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/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -march=prescott -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="collision-protect cvs digest distlocks parallel-fetch sandbox sfperms sign strict test unmerge-orphans userfetch userpriv usersandbox" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" MAKEOPTS="-j3" 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="/home/markus/cvs/gentoo-x86" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acpi alsa avahi berkdb bitmap-fonts cairo cdr cli cracklib crypt cups dbus divx dri dvd dvdr dvdread eds emboss encode evo fam firefox fortran gdbm gif gimp gmedia gnome gpm gtk hal iconv ipv6 isdnlog jpeg kde latex mad midi mikmod mmx mp3 mpeg mudflap ncurses nls nptl nptlonly ogg opengl openmp oss pam pcre pdf perl png pppd python qt3 qt3support qt4 quicktime raw readline realmedia reflection samba sdl session smp spell spl sse sse2 ssl svg tcpd test tetex tiff truetype truetype-fonts type1-fonts unicode vorbis win32codecs wmp x86 xine xml xorg xv zeroconf zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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" USERLAND="GNU" VIDEO_CARDS="i810" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 145240 [details] config.log Same problem here and config.log attached: Portage 2.1.4.4 (default-linux/x86/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r3 i686) ================================================================= System uname: 2.6.24-gentoo-r3 i686 AMD Athlon(tm) X2 Dual Core Processor BE-2400 Timestamp of tree: Mon, 03 Mar 2008 19:30:01 +0000 app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.1.4 dev-lang/python: 2.4.4-r9 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: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /opt/openfire/resources/security/ /opt/openjms/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/lib/hsqldb /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2" DISTDIR="/usr/portage/distfiles" FEATURES="ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch userpriv" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/" LANG="de_DE.utf8" LC_ALL="de_DE.utf8" LINGUAS="de" MAKEOPTS="-j3" 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="/usr/portage/local/layman/sunrise" SYNC="rsync://rsync.informatik.rwth-aachen.de/gentoo-portage" USE="3dnow 3dnowext X a52 acl acpi aiglx alsa apache2 apm applet artworkextra asf audiofile avahi bash-completion beagle berkdb bidi bitmap-fonts bogofilter bootsplash branding bzip2 cairo ccache cdda cddb cdparanoia cdr cli console cracklib crypt css cups curl custom-cflags dbus dga directfb divx4linux dri dts dvd dvdr dvdread dvi eds emacs emboss encode esd evince evo exif fam fat fbcon fdftk ffmpeg firefox flac foomaticdb fortran ftp gb gcj gdbm gif glitz gnome gpm gsf gstreamer gtk gtk2 gtkhtml hal howl iconv icq idn imagemagick imap imlib immqt-bc isdnlog java javascript jpeg jpeg2k kde ldap libnotify lirc lm_sensors mad maildir matroska mbox midi mikmod mime mmx mmxext mng mono mp3 mpeg mpeg2 mudflap mule mysql nautilus ncurses nforce2 nls nocardbus nptl nptlonly nsplugin nvidia objc objc++ objc-gc offensive ogg opengl openmp pam pango pcre pdf perl php plotutils pmu png ppds pppd prediction preview-latex print python qt3 qt3support qt4 quicktime readline reflection samba sdk session slang spell spl sse ssl svg svga t1lib tcl tcpd tetex theora threads thumbnailing tiff tk toolkit-scroll-bars totem tracker truetype truetype-fonts type1-fonts udev unicode usb userlocales vcd videos vorbis win32codecs wmf wxwindows x86 xface xft xine xml xorg xosd xpm xv xvid zlib" 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" 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" CAMERAS="canon ptp2" ELIBC="glibc" INPUT_DEVICES="mouse keyboard" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" LIRC_DEVICES="atiusb" USERLAND="GNU" VIDEO_CARDS="vesa fbdev fglrx" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Hi Markus and Christian, Which mpi are you using? It configures fine with mpich2-1.0.6. I suspect mpich-1 to be buggy with mpif77.
(In reply to comment #3) > Hi Markus and Christian, > > Which mpi are you using? It configures fine with mpich2-1.0.6. > I suspect mpich-1 to be buggy with mpif77. sys-cluster/mpich-1.2.7_p1 and sys-cluster/mpich2 is not installed. Will test with mpich2-1.0.3
Hi Sébastien, At least on amd64, I am pretty sure that we will run into trouble with mpich and it in fact does not compile on my opteron (in general, since mpich only provides static libs, any dynamic lib on amd64 that links against mpich will fail due to non-pic code). arpack compiles fine against lam-mpi on my machine. Hence, we might want to depend only on the mpi implementations that are known to work which unfortunately does not include mpich, the default pulled in by virtual/mpi. cheers, Markus
(In reply to comment #4) > (In reply to comment #3) > > Hi Markus and Christian, > > > > Which mpi are you using? It configures fine with mpich2-1.0.6. > > I suspect mpich-1 to be buggy with mpif77. > > sys-cluster/mpich-1.2.7_p1 > and sys-cluster/mpich2 is not installed. Will test with mpich2-1.0.3 With mpich2-1.03 it fails, too. 1.0.6 is fine though.
So what will you do, sci team? Rework dependencies of arpack?
(In reply to comment #7) > So what will you do, sci team? Rework dependencies of arpack? > Yeah, we'll have to :( Based on our testing it looks like the only viable mpi implementation with an ebuild in ARCH would be lam-mpi-7.1.2 (unless I missed on). Could you please give this a shot. If lam-mpi works I'll hardcode this package instead of virtual/mpi until some of the other mpi implementations have stabled some of their more recent versions. Sorry for the inconvenience! cheers, Markus
> Based on our testing it looks like the only viable mpi > implementation with an ebuild in ARCH would be > lam-mpi-7.1.2 (unless I missed on). Could you please give > this a shot. If lam-mpi works I'll hardcode this package instead of > virtual/mpi until some of the other mpi implementations > have stabled some of their more recent versions. Markus, if you go this way, we need to add another revision bump which depends on the generic virtual/mpi so that the mpich2 or openmpi users are not forced to install the lam-mpi. I'll talk to the cluster team to see the state of mpich-1
> I'll talk to the cluster team to see the state of mpich-1 They are now planning to set openmpi as a default virtual. So probably best would be to try with openmpi.
(In reply to comment #10) > > I'll talk to the cluster team to see the state of mpich-1 > > They are now planning to set openmpi as a default virtual. So probably > best would be to try with openmpi. > arpack + openmpi works for me and is the preferred solution in my opinion since lam-mpi will be phased out. However, in this case we'll have to stable openmpi first since it only has versions in ~ARCH. best, Markus
Recc and reopen once you worked out how to do this. Thanks.
