When trying to emerge Intel MathKernel libraries (sci-libs/mkl-10.0.3.020-r3), the compile process goes smoothly until reaching an specific subdirectory, then the system tries to invoke the command "c" instead of "gcc" (I think). Look for compilation failure log below... Relevant USE Flags for this package are: "debug doc fftw fortran95 int64 mpi". I'm using only "fftw int64 mpi". (And I'm NOT using "fortran95", because I've installed Intel Fortran Compiler v10.1 (dev-lang/ifc-10.1.017).) Note #1: I have proper license files in place for both Intel products. Note #2: The same error happens with sci-libs/mkl-10.0.3.018-r2 Reproducible: Always Steps to Reproduce: 1. emerge -Dv mkl 2. And just wait a minute... Output of "emerge --info": Portage 2.1.4.4 (default-linux/amd64, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-tuxonice-r9 x86_64) ================================================================= System uname: 2.6.24-tuxonice-r9 x86_64 Intel(R) Xeon(TM) CPU 3.60GHz Timestamp of tree: Fri, 01 Aug 2008 21:06:01 +0000 app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r13, 2.5.2-r6 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-r2 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 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="-march=nocona -O3 -pipe" CHOST="x86_64-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 /var/spool/torque" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.dcc.uchile.cl/ http://gentoo.osuosl.org/ http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ ftp://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://distro.ibiblio.org/pub/linux/distributions/gentoo/ http://cudlug.cudenver.edu/gentoo/" LINGUAS="es en" 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" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="7zip X X509 Xaw3d a52 aac aalib accessibility acl acpi activefilter ads akode alsa amazon amd64 amr antlr ao ares arts artswrappersuid artworkextra aspell async asyncns audiofile audit automount bash-completion beagle berkdb bigpatch binary-drivers blas bonjour boost branding bzip2 cairo caps cdaudio cdb cdda cddb cdinstall cdr cdrom cdsound cg chroot cjk cli consolekit cpudetection cracklib crypt cups cupsddk dbus dell device-mapper dga directfb disk-partition divx djbfft djconsole djvu dri dvb dvd dvdarchive dvdchapjump dvdr dvdread dvi dvlfriendlyfnames dvlrecscriptaddon dvlvidprefer eap-tls encode epiphany esd exif expat extensions extra extra-algorithms extra-cardsets fam fasttrack fbcon fbcondecor fbsplash ffmpeg fftw flac fontconfig fontforge foomaticdb fortran fortune fpx freetts fuse galago gcdmaster gd gdbm gedit ggi gif glib glibc-omitfp glitz gmp gnokii gnome gnome-keyring gnome-print gnomecanvas gnomecd gnuplot gnutella gnutls gpac gpg gpgme gphoto2 gpm graphtft graphviz gs gsf gsm gstreamer gtk gtk2 gtkhtml gzip hal hdri hfs hpn ical iceweasel icon icons iconv icu idea idn ieee1394 ifc imagemagick imlib imlib2 immqt-bc imq int64 ipv6 isdnlog jack jack-tmpfs java javacomm javascript jbig jce jingle joystick jpeg jpeg2k jsapi kcal kde kdecards kdeenablefinal kdepim kdm kerberos kig-scripting krb4 ktts l7filter lame lapack latex lcd lcms ldap legacyssl libcaca libedit libffi libgcrypt libnotify libsamplerate libssh2 libvisual lm_sensors logrotate lua lzma lzo mad mbrola midi mikmod mime mixer mjpeg mktemp mmap mng motif mounts-check mouse mozdevelop mozdom mp2 mp3 mp3rtp mp4 mp4live mpeg mpeg2 mpi mudflap multiuser mysql mysqli nas nautilus ncurses neXt net netjack netplay network network-cron networkmanager new-login nls nntp nova nptl nsplugin nss ntfs ntlm objc objc++ objc-gc ocaml odbc offensive ogg ogm openexr openft opengl openmp overlays pam passwdqc pbs pcre pda pdf perl pike pinplugin pixmaps pkcs11 pkinit plasma player plib plotutils plugins png policykit portage portaudio posix povray ppds pppd pth publishers pulseaudio pysolcards pyste python qemu qhull qmax qq qt3 qt3support qt4 quicktime quotas radius rar raw rc5 rdesktop readline reflection rle rpc rplay rpm rrdcgi rtc samba sametime sasl scanner script sdl seamonkey sensord session skey slang slp sms sndfile sockets socks5 solver sound soundex sounds speech speedo speex spell spl spoof-source srp srt ssl suid svg svg-experimental svgz swat symlink sysfs syslog t1lib tcl tcltk tcpd tex tex4ht text texteffect textile textures tga tgif themes theora threads tidy tiff timidity tk toolbar tools tracker truetype truetype-fonts twolame type1 type1-fonts unicode unzip urandom usb utempter utils v4l v4l2 vcd vim vim-pager vim-syntax vim-with-x visual visualization vorbis vorbis-psy wav wavpack winbind wininst wmf x264 x86emu xattr xcb xcomposite xforms xft xine xinetd xml xmldoclet xmlreader xmlrpc xmlwriter xmp xmpi xorg xosd xpm xrandr xscreensaver xsettings xsl xulrunner xv xvid xvmc yaepg yahoo yaz zephyr zip zip-external 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 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="*" ELIBC="glibc" INPUT_DEVICES="joystick keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="es en" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Created attachment 162047 [details] Complete log of failed compile (from "/var/log/portage"). Included the complete log, so it will be easy to see any "pattern" in it... ;-)
(In reply to comment #0) > When trying to emerge Intel MathKernel libraries (sci-libs/mkl-10.0.3.020-r3), > the compile process goes smoothly until reaching an specific subdirectory, then > the system tries to invoke the command "c" instead of "gcc" (I think). Look for > compilation failure log below... > The 'c' should have been mpicc if I am not mistaken indicating that there may be a problem with your mpi installation. Everything went smoothly on my machine using openmpi. What mpi implementation do you have installed and if it is not openmpi could you give it a try? Thanks, Markus
O.K... What I have installed is "sys-cluster/lam-mpi-7.1.2". (Latest version available is 7.1.4, anyway.) This was "pulled-in" automatically since I have the "mpi" USE Flag enabled in my "make.conf". Now I'll try uninstalling it and installing "OpenMPI" instead, to see what happens next, and will report here afterwards Now, two little questions: 1-) Since I'll not be using a clustered environment (at least for this semester), I think it will not hurt anyone if I just disable the "mpi" USE Flag. Am I right? 2-) Could this be completely unrelated to MPI altoghether and, just be a matter of "truncated command lines" (due to some unspecified bug in the EBuild or somewhere in the code)? I've seen such a bug in the past (middle 2006), while trying to compile the "Linux Wacom" touchpad drivers. (To resolve that, I had to "Pause" (CTRL-Z) the emerging process, the go and, edit and "swap" two lines in a MakeFile, and then resume emerge.) Regards... JM.
Well, Mr. Markus... You were RIGHT !!! Uninstalling "lam-mpi", and then emerging "openmpi" resolved all problems. Now Intel MathKernel install flawlessly. Thank you very much !!! P.D.: Now playing with "thread" and "no thread" flavours... ;-)
(In reply to comment #4) > Well, Mr. Markus... You were RIGHT !!! > Great and I am glad that it works! I'll have to look into the failure with lam-mpi though since it should, in principle, work with it also. Regarding the questions in the previous comment: 1) If you are not planning on doing any parallel work you can disable the 'mpi' use flag. However, in principle you can take advantage of parallel execution as soon as you have any type of multi-CPU motherboard or multi-Core chip. You don't need a full blown clustered environment. 2) The issue with lam-mpi is probably either with the ebuild or Intel's installer code. Not sure yet. Best, Markus
Great !!! I'm running all this into a neat, big box, wich is a Dell Presicion 670n (from 2 years back): 3.6 Ghz. Intel Pentium 4 Xeon (HT) C.P.U., + 4 GiB. R.A.M. Memory, + 2x 73 GiB. SCSI-III Hard Disk (working in nice "ASR BIOS" RAID-0 mode). And, to make things nicer: 1-) The motherboard have another socket for an additional identical Processor. 3-) In our lab, we have 4 of those boxes. So, cluster sound nice to us... :D Best Regards... JM.
