sci-libs/netcdf-4.0.1 fails to build with -j2. Emerging with MAKEOPTS="-j1" works just fine. Reproducible: Always Steps to Reproduce: MAKEOPTS="-j4" emerge netcdf Actual Results: Fatal Error: Can't delete temporary module file 'netcdf.mod0': No such file or directory
I cannot reproduce that. Please attach the entire build log and post your `emerge --info =sci-libs/netcdf-4.0.1' in a comment.
Created attachment 212656 [details] netcdf build log I accidentally rm'ed original build log and also was unable to reproduce issue under normal conditions. It takes some system load to get into race condition for make process to fail. This failure build log was produced by running updatedb in background (high disk load). Without any system load netcdf compiles with -j6 just fine.
emerge -pqv =sci-libs/netcdf-4.0.1 [ebuild R ] sci-libs/netcdf-4.0.1 USE="fortran -doc -hdf5 -mpi -szip" emerge --info =sci-libs/netcdf-4.0.1 Portage 2.1.7.11 (default/linux/amd64/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_P9500_@_2.53GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 10 Dec 2009 09:45:01 +0000 app-shells/bash: 4.0_p35 dev-java/java-config: 2.1.10 dev-lang/python: 2.4.6, 2.5.4-r2, 2.6.4, 3.1.1-r1 dev-python/pycrypto: 2.1.0_beta1 dev-util/cmake: 2.8.0 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.5.3 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.64 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.20 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -ggdb" 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/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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=nocona -O2 -pipe -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests collision-protect distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.tups.lv/source" LANG="lv_LV" LC_ALL="lv_LV.utf8" LDFLAGS="-Wl,-O1" LINGUAS="lv" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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/local/portage/layman/x11 /home/maris/soft/portage" SYNC="rsync://gentoo.tups.lv/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdr cli clucene consolekit cracklib crypt cups cxx dbus dell dhcpcd dri dts dvd dvdr eap-tls eds emboss encode evo exif fam firefox flac fortran gdal gdbm geos gif gpm gstreamer hal iconv idn inotify ipv6 jpeg json kde laptop ldap libnotify mad mikmod mmx mmxext mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nsplugin offensive ogg opengl openmp pam pcre pdf perl png ppds pppd proj python qt3support qt4 quicktime readline reflection sasl sdl semantic-desktop session slp spell spl sqlite sse sse2 sse3 ssl ssse3 startup-notification svg sysfs tcpd theora thunar tiff truetype unicode usb utf-8 vdpau vorbis x264 xcomposite xinerama xml xmp xorg xulrunner xv xvid 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="authz_host autoindex dir headers mime vhost_alias" APACHE2_MPMS="prefork" ELIBC="glibc" INPUT_DEVICES="synaptics mouse keyboard evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="lv" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-libs/netcdf-4.0.1 was built with the following: USE="fortran (multilib) -doc -hdf5 -mpi -szip"
I cannot reproduce it either with -j2,-j4 or -j30. Since it seems it compiles fine now for you, I will close it for now. Re-open with a reproducible scenario if you still face failures. Thanks.
Created attachment 241051 [details] Build log of 4.1.1 fail netcdf-4.1.1 still fails with "Fatal Error: Can't rename module file 'netcdf.mod0' to 'netcdf.mod': No such file or directory" Steps to reproduce - just run emerge -Du world and continue to work with Your Gentoo system. Success or failure will depend on what You are doing, Your system software versions and phase of the Moon (last one being most important).
Reopening as netcdf emerge success or failure depends on Moon phases. Seems like netcdf still is not parallell make safe. emerge --info =sci-libs/netcdf-4.1.1 Portage 2.1.8.3 (default/linux/amd64/10.0/desktop, gcc-4.4.3, glibc-2.11.2-r0, 2.6.34-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.34-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_P9500_@_2.53GHz-with-gentoo-2.0.1 Timestamp of tree: Mon, 02 Aug 2010 07:15:01 +0000 app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11 dev-lang/python: 2.6.5-r3, 3.1.2-r4 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.1-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.10 virtual/os-headers: 2.6.34 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 skype-eula AdobeFlash-10.1 googleearth" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -ggdb" 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/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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=nocona -O2 -pipe -ggdb" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests collision-protect distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms splitdebug strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.tups.lv/source" LANG="lv_LV" LC_ALL="lv_LV.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="lv" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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="/var/lib/layman/kde-sunset /home/maris/soft/portage" SYNC="rsync://gentoo.tups.lv/gentoo-portage" USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdr cli clucene consolekit cracklib crypt cups cxx dbus dell dhcpcd dri dts dvd dvdr eap-tls emboss encode exif fam firefox flac fortran gallium gdal gdbm geos gif glib gpm hal iconv idn inotify ipv6 jpeg json kde laptop lcms ldap libnotify mad mikmod mmx mmxext mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nsplugin offensive ogg opengl openmp pam pango pcre pdf perl png ppds pppd proj python qt3support qt4 readline reflection sasl sdl semantic-desktop session slp spell spl sqlite sse sse2 sse3 ssl ssse3 startup-notification svg sysfs tcpd theora tiff truetype unicode usb utf-8 vdpau vorbis x264 xcb xcomposite xinerama xml xmp xorg xulrunner xv xvid 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 mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="alias authz_host autoindex dir env headers mime rewrite vhost_alias log_config auth_basic authn_file authz_user" APACHE2_MPMS="prefork" ELIBC="glibc" INPUT_DEVICES="synaptics mouse keyboard evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="lv" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa nvidia nouveau" 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, FFLAGS, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Same here. =sci-libs/netcdf-4.1.1.
I can confirm all this. Error ocurred first time compiling. I retried and the second time it worked fine. (no changes, both times with -j5 on a 4 core processor)
*** Bug 347756 has been marked as a duplicate of this bug. ***
+*netcdf-4.1.1-r1 (04 Dec 2010) + + 04 Dec 2010; Kacper Kowalik <xarthisius@gentoo.org> -netcdf-4.0.1-r1.ebuild, + -files/netcdf-4.0.1-as-needed.patch, -files/netcdf-4.0.1-cfortran.patch, + -files/netcdf-4.0.1-pkgconfig.patch, +netcdf-4.1.1-r1.ebuild, + +files/netcdf-4.1.1-implicits.patch, + +files/netcdf-4.1.1-parallel-build.patch: + Fix parallel build wrt #296174 by MarisN <maris.gis@gmail.com>. Fix implicit + function declarations. Drop old. +
Still not solved for 4.1.1-r4. Will attach full build log, still it's same as for bug 187759. Changing MAKEOPTS to -j1 fixes build process. Removed version number from bug summary, as it seems to affect any version up to 4.1.1 including.
Created attachment 260978 [details] netcdf-4.1.1-r4 build log 4.1.1-r4 still fails during parallel make.
(In reply to comment #12) > Created an attachment (id=260978) [details] > netcdf-4.1.1-r4 build log > > 4.1.1-r4 still fails during parallel make. When have you synced your tree? Few days ago I've put newer version of patch without a revbump: 25 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> files/netcdf-4.1.1-parallel-build.patch: Further parallel build fixes wrt #352615 by Juergen Rose <rose@rz.uni-potsdam.de> Could you please check your changelog and see ^^ it's there?
(In reply to comment #13) > (In reply to comment #12) > > Created an attachment (id=260978) [details] [details] > > netcdf-4.1.1-r4 build log > > > > 4.1.1-r4 still fails during parallel make. > When have you synced your tree? Few days ago I've put newer version of patch > without a revbump: > > 25 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> > files/netcdf-4.1.1-parallel-build.patch: > Further parallel build fixes wrt #352615 by Juergen Rose > <rose@rz.uni-potsdam.de> > > Could you please check your changelog and see ^^ it's there? > Yes, it is. When running emerge with low system load - compiles fine, when system is under load (open just some crappy web page with Flash banners ;) - it fails :(
(In reply to comment #14) > Yes, it is. > When running emerge with low system load - compiles fine, when system is under > load (open just some crappy web page with Flash banners ;) - it fails :( + 29 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> + files/netcdf-4.1.1-parallel-build.patch: + Attempt to fix parallel issues once and for all, wrt #296174 c#14 + Hopefully that will do the trick. Cheers, Kacper
