Setting the lammps-memalign use flag defines an empty LAMMPS_MEMALIGN macro when compiling. This causes a segmentation fault when executing lammps, because the value of LAMMPS_MEMALIGN is used for the alignment argument in the posix_memalign function in memory.cpp. In some example make files, the alignment value is set to 64, but this is obviously very hardware dependant.
Thank you for reporting. I could not reproduce the segfault here. Can you provide more information when does it crash? How do you start lammps, do you load a special example file? Could you add emerge --info too?
(In reply to Jonas Stein from comment #1) > Thank you for reporting. I could not reproduce the segfault here. Can you > provide more information when does it crash? How do you start lammps, do you > load a special example file? > > Could you add emerge --info too? Strange, simply executing lmp without any input script at the command line causes a segfault for me. It started working properly when I modified the ebuild in the following manner: @@ -69,7 +69,7 @@ lmp_emake() { local LAMMPS_INCLUDEFLAGS LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN=64' '')" # The lammps makefile uses CC to indicate the C++ compiler. emake \ I'll attach ebuild info in the next post.
Portage 2.2.20 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop, gcc-4.8.4, glibc-2.20-r2, 4.0.5-gentoo x86_64) ================================================================= System uname: Linux-4.0.5-gentoo-x86_64-Intel-R-_Core-TM-_i7-3540M_CPU_@_3.00GHz-with-gentoo-2.2 KiB Mem: 8023376 total, 262796 free KiB Swap: 8388628 total, 8388628 free Timestamp of repository gentoo: Tue, 11 Aug 2015 09:15:01 +0000 sh bash 4.3_p33-r2 ld GNU ld (Gentoo 2.24 p1.4) 2.24 app-shells/bash: 4.3_p33-r2::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r1::gentoo, 3.4.1::gentoo dev-util/cmake: 3.2.2::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.17::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.15::gentoo sys-devel/binutils: 2.24-r3::gentoo sys-devel/gcc: 4.8.4::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 anders-larsson location: /var/lib/layman/anders-larsson masters: gentoo priority: 0 MyStuff location: /usr/local/portage masters: gentoo priority: 1 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -fomit-frame-pointer -fno-stack-protector" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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="-O2 -pipe -march=native -fomit-frame-pointer -fno-stack-protector" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://de-mirror.org/gentoo/ http://de-mirror.org/gentoo/ rsync://de-mirror.org/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo http://gentoo.mneisen.org/ http://mirror.netcologne.de/gentoo/ ftp://mirror.netcologne.de/gentoo/ rsync://mirror.netcologne.de/gentoo/ http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ ftp://ftp.halifax.rwth-aachen.de/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/ rsync://ftp.halifax.rwth-aachen.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp-stud.hs-esslingen.de/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi aes alsa amd64 avx berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif glamor gpm gtk iconv icu ipv6 jpeg lcms ldap libnotify lm_sensors mad mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses networkmanager nls nptl ogg opengl openmp pam pango pcre pdf png policykit popcnt ppds pulseaudio qt3support qt4 readline sdl session spell sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid zlib" ABI_X86="64 32" 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" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel i965" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
I have the ebuild fixed already, but am still working out issues that I don't seem to be able to push right now. This is the first time I am using the new git repository.
Ok, finally got it to work. Please have a look and let me know whether this fixes the segfaults you saw.
Yes, it works fine now, thank you.
Closing.
