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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Sat Sep 29, 2012 10:33 pm Post subject: [Memory] Cannot allocate memory with lot of available memory |
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Helo,
The title summarize it, I got frequently error messages like "cannot allocate memory" during compilation of large program (like chromium or libreoffice for example).
It has been a while and i thought it was due to hardware problem but, I recently change everything (CPU RAM and mother board) and i still have the same problem.
Moreover I remark that :
- it rarely use more than a half of my 8G of RAM (without cache)
- it doesn't use SWAP (200M of 5G)
One other thing which can be unrelated, I can't deactivate my swap, even if i got lot of free place in RAM.
Now for example, a free -h gives me :
Code: |
total used free shared buffers cached
Mem: 7,8G 7,2G 599M 0B 1,0G 3,4G
-/+ buffers/cache: 2,8G 5,0G
Swap: 5,0G 174M 4,8G
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And a swapoff -av :
Code: |
swapoff /dev/mapper/vg-Swap
swapoff: /dev/mapper/vg-Swap : échec de swapoff: Ne peut allouer de la mémoire
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Am I the only one with those kind of problem ?
Does anyone has a clue of the origin ? |
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Sun Sep 30, 2012 11:41 am Post subject: |
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pums974,
Please post your
As a WAG, you might have a 32 bit install with PXE enabled but you still only get a 4G address space per process, which will be split 1G/3G for kernel/user.
In fact, depending on your hardware, your per process useful address space may be as little as 3.2G, as memory mapped I/O cannot be mapped out. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Sun Sep 30, 2012 7:04 pm Post subject: |
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Thanks for your answer.
But i do have a 64bit install, I'm sorry I should have precised it sooner.
Here is my emerge --info
Code: |
Portage 2.1.11.23 (default/linux/amd64/10.0/desktop, gcc-4.6.3, glibc-2.15-r3, 3.5.4-gentooPerso x86_64)
=================================================================
System uname: Linux-3.5.4-gentooPerso-x86_64-Intel-R-_Core-TM-_i7-2600_CPU_@_3.40GHz-with-gentoo-2.2
Timestamp of tree: Sun, 30 Sep 2012 11:45:01 +0000
ccache version 3.1.8 [disabled]
app-shells/bash: 4.2_p37
dev-java/java-config: 2.1.12
dev-lang/python: 2.7.3-r2, 3.2.3-r1
dev-util/ccache: 3.1.8
dev-util/cmake: 2.8.9
dev-util/pkgconfig: 0.27.1
sys-apps/baselayout: 2.2
sys-apps/openrc: 0.10.5
sys-apps/sandbox: 2.6
sys-devel/autoconf: 2.13, 2.69
sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.12.4
sys-devel/binutils: 2.22.90
sys-devel/gcc: 4.6.3
sys-devel/gcc-config: 1.7.3
sys-devel/libtool: 2.4.2
sys-devel/make: 3.82-r4::gnome
sys-kernel/linux-headers: 3.5 (virtual/os-headers)
sys-libs/glibc: 2.15-r3
Repositories: gentoo desktop-effects eva gamerlay-stable games kde laurentb multimedia portato retroshare-overlay science systemd ubuntu voyageur x11 vmware virtualization qt mozilla kvm kde-sunset gentoo-guis gnome Local
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe "
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa"
CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CPPFLAGS="-march=native -O2 -pipe "
CXXFLAGS="-march=native -O2 -pipe "
DISTDIR="/usr/portage/tree/../distfiles"
EMERGE_DEFAULT_OPTS="--complete-graph y --with-bdeps y --autounmask y --misspell-suggestions y -D"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs candy config-protect-if-modified distlocks ebuild-locks fixlafiles metadata-transfer news parallel-fetch parallel-install protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch usersandbox xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="ftp://ftp.free.fr/mirrors/ftp.gentoo.org/ http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LANG="fr_FR.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed "
LINGUAS="fr en"
PKGDIR="/usr/portage/tree/../packages"
PORTAGE_COMPRESS="bzip2"
PORTAGE_COMPRESS_FLAGS="-9"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_EXTRA_OPTS=""
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage/tree"
PORTDIR_OVERLAY="/var/lib/layman/desktop-effects /var/lib/layman/eva /var/lib/layman/gamerlay /var/lib/layman/games /var/lib/layman/kde /var/lib/layman/laurentb /var/lib/layman/multimedia /var/lib/layman/portato /var/lib/layman/retroshare-overlay /var/lib/layman/science /var/lib/layman/systemd /var/lib/layman/ubuntu /var/lib/layman/voyageur /var/lib/layman/x11 /var/lib/layman/vmware /var/lib/layman/virtualization /var/lib/layman/qt /var/lib/layman/mozilla /var/lib/layman/kvm /var/lib/layman/kde-sunset /var/lib/layman/gentoo-guis /var/lib/layman/gnome /usr/portage/local"
SYNC="rsync://rsync.fr.gentoo.org/gentoo-portage"
USE="32bit 64bit X a52 aac acl acpi alsa amd64 apache2 apm avahi bash-completion berkdb branding btrfs bzip2 cairo cli colord consolekit cxx dbus directfb dri emboss encode exif fam fat fbcon fbcondecor ffmpeg fftw firefox flac fontconfig fortran g3dvl gdbm gif git glew gnome gnome-keyring gpm gsl gstreamer gtk gtk3 iconv icu introspection ipv6 java joystick jpeg kde lcms libnatspec libnotify lm_sensors lto lzma mad minimal mmx mmxext mng modules mp3 mp4 mpeg mpi mpi-threads mudflap multilib mysql nautilus ncurses networkmanager nls nptl nsplugin nspluginwrapper ntfs nvidia offensive ogg opencl opengl openmp openvg pam pango pcre pdf pdo phonon php plasma pmu png policykit ppds pppd pulseaudio python python3 qt3support qt4 readline sdl semantic-desktop session smp spell sql sqlite sqlite3 sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssse3 startup-notification svg system-sqlite systemd tcpd theora threads tiff truetype udev udisks unicode upnp upower usb vdpau vorbis wayland webgl webkit wxwidgets x264 xattr xcb xinerama xml xulrunner xv xvid xvmc zeitgeist zeroconf 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 mmap_emul 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 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="flow karbon krita sheets stage words" ELIBC="glibc" GRUB_PLATFORMS="pc efi-64" INPUT_DEVICES="evdev mouse keyboard" KERNEL="linux" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="fr en" PHP_TARGETS="php5-3 php5-4" PYTHON_TARGETS="python3_2 python2_7" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby19" SANE_BACKENDS="lexmark" USERLAND="GNU" VIDEO_CARDS="nvidia fglrx"
Unset: CTARGET, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, USE_PYTHON
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Sun Sep 30, 2012 8:03 pm Post subject: |
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pums974,
Please post your df output. Your emerge --info looks good. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Sun Sep 30, 2012 8:24 pm Post subject: |
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here is my df :
Code: | Sys. fich. 1K-blocks Util. Disponible Uti% Monté sur
rootfs 103212320 31267056 66702384 32% /
udev 10240 8 10232 1% /dev
/dev/mapper/vg-Root 103212320 31267056 66702384 32% /
tmpfs 4102952 872 4102080 1% /run
cgroup_root 10240 4 10236 1% /sys/fs/cgroup
shm 4102952 2492 4100460 1% /dev/shm
/dev/mapper/vg-Boot 1032088 103376 876284 11% /boot
/dev/sdc1 201633 1 201633 1% /boot/efi
/dev/mapper/vg-Portage 20642428 6328972 13264880 33% /usr/portage
/dev/mapper/vg-Home 103212320 14460964 83508476 15% /home
/dev/mapper/vg-Temp 41284928 32987244 6200532 85% /temp
/dev/mapper/vg-Data 686486944 436544172 215071272 67% /Data
curlftpfs#ftp://freebox:freebox@mafreebox.freebox.fr/ 999999999 0 999999999 0% /media/freebox
/dev/sr0 7923158 7923158 0 100% /media/cdrom
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Last edited by pums974 on Mon Oct 01, 2012 6:26 am; edited 1 time in total |
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Sun Sep 30, 2012 8:34 pm Post subject: |
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pums974,
I was wondering about /dev/shm being full as its allocated half your RAM and allowed to use swap space too.
Its not that.
Does top show anything hogging RAM. That might point to an application with a 'memory leak'. That would be a bug. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Mon Oct 01, 2012 8:21 am Post subject: |
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Not particularly no.
In general, with gnome shell and chromium, around 3G are used wich should leave enough for compilling libreoffice or chromium. |
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BitJam Advocate
Joined: 12 Aug 2003 Posts: 2508 Location: Silver City, NM
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Posted: Mon Oct 01, 2012 9:02 am Post subject: |
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This is a strange problem. It is theoretically possible that your RAM becomes highly fragmented which would make it impossible to allocate large blocks of RAM even though most of the RAM is free. The /proc/buddyinfo file will let you know if this is the problem. Use "getconf PAGESIZE" to find the page size. It's 4096 on my system. My /proc/buddyinfo tells me I have 93 4-meg chunks available and this is the majority of my free RAM.
More realistically: is it possible your kernel is somehow mis-configured? I can't even imagine exactly how a kernel mis-configuration could cause such a problem but after you swapped out hardware this seems to be one of the few common denominators that's left. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Mon Oct 01, 2012 9:24 am Post subject: |
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Quote: | This is a strange problem. |
I agree
I have the same PAGESIZE as you, but doesn't understand buddyinfo.
Code: | tux ~ # getconf PAGESIZE
4096
tux ~ # cat /proc/buddyinfo
Node 0, zone DMA 3 2 0 1 3 2 0 0 1 1 3
Node 0, zone DMA32 60727 50075 26540 9815 2291 550 158 32 3 1 0
Node 0, zone Normal 109563 41269 2590 62 0 0 0 0 0 0 1 |
Quote: | is it possible your kernel is somehow mis-configured? |
That's also what I have in mind, but I can't find what could cause this. |
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BitJam Advocate
Joined: 12 Aug 2003 Posts: 2508 Location: Silver City, NM
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Posted: Mon Oct 01, 2012 10:21 am Post subject: |
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pums974 wrote: | I have the same PAGESIZE as you, but doesn't understand buddyinfo.
Code: | tux ~ # getconf PAGESIZE
4096
tux ~ # cat /proc/buddyinfo
Node 0, zone DMA 3 2 0 1 3 2 0 0 1 1 3
Node 0, zone DMA32 60727 50075 26540 9815 2291 550 158 32 3 1 0
Node 0, zone Normal 109563 41269 2590 62 0 0 0 0 0 0 1 |
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Imagine there is a "size" row like this: Code: | SIZE --> 1 2 4 8 16 32 64 128 256 512 1024
----------------------------------------------------------------------------
Node 0, zone DMA 3 2 0 1 3 2 0 0 1 1 3
Node 0, zone DMA32 60727 50075 26540 9815 2291 550 158 32 3 1 0
Node 0, zone Normal 109563 41269 2590 62 0 0 0 0 0 0 1 |
Look at the columns on the far right. You only have a total of 4 (3 + 0 + 1) blocks that have size 1024 * PAGESIZE and only 2 (1 + 1 + 0) with size 512 * PAGESIZE. So it does appear that you may be running out of the larger blocks of memory. Here are a couple of snapshots from my system:
Code: | Node 0, zone DMA 1 1 1 0 2 1 1 0 1 1 3
Node 0, zone DMA32 6896 6395 2148 693 397 100 67 32 34 3 88
Node 0, zone Normal 167 201 136 88 39 20 7 7 3 2 2 |
and then later (after watching HD movie via Adobe Flash):
Code: | Node 0, zone DMA 1 1 1 0 2 1 1 0 1 1 3
Node 0, zone DMA32 50302 34545 11103 2964 1141 549 266 112 85 45 12
Node 0, zone Normal 402 263 140 76 35 13 5 4 9 2 1 |
It does seems that your "Normal" memory is almost completely fragmented with only one block available that is larger than 8 * PAGESIZE. Processes that need blocks of normal memory 64K or larger will be simply out of luck and will probably give you the "cannot allocate memory" error that you are getting.
I don't know if the problem stems from your kernel or user-space programs. I'm not an expert on how to track this down further. One approach would be to kill off programs while keeping an eye on /proc/buddyinfo and see if the situation improves. You should probably try to free your caches as you go along so blocks of memory can be reclaimed (I'm not absolutely certain this is required).
Running "watch cat /proc/buddyinfo" in one terminal and "watch free -m" in another may be useful. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Mon Oct 01, 2012 1:14 pm Post subject: |
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At the moment I killed everything (gdm chromium...) and I access my computer via ssh.
I have freed my caches (echo 3 > /proc/sys/vm/drop_caches) but I wasn't able to put it back at 0 ("-bash: echo: erreur d'écriture : Argument invalide" wich mean "bash: echo: write error: Invalid argument ")
So my memory is completely free (230M in RAM and 26M in swap).
Then I tried to emerge libreoffice. As usual, it failed claiming that he doesnt have enough memory ("Could not reserve enough space for object heap").
The result of buddyinfo I gave you was just after this failure.
Now, few hours later (not doing anything on this machine), my buddyinfo looks just fine :
Code: | Node 0, zone DMA 3 2 0 1 3 2 0 0 1 1 3
Node 0, zone DMA32 1272 1298 1320 1274 1196 993 896 750 543 403 325
Node 0, zone Normal 10974 10544 9174 7984 6575 4913 3342 1778 650 126 16 |
Si finally, seems to me that fragmented memory is not the cause of my problem, just a residue of the compilation, not the source of the problem. |
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Mon Oct 01, 2012 6:00 pm Post subject: |
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pums974,
Pastebin your kernel .config please.
You could also try one of Pappys seeds. See kernel-seeds.org and the sticky in unsupported software.
If your system still does this with a seed, I'm sure Pappy will be pleased to hear from you. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Mon Oct 01, 2012 7:26 pm Post subject: |
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No problemo : http://pastebin.com/sg8auaGG
I already took a look in seeds kernel, In fact I even started my config from one of him (3years ago).
I may have to restart from a blank kernel soon, but I would prefer to avoid that and understand what cause this problem. |
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Mon Oct 01, 2012 7:44 pm Post subject: |
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pums974,
If building from a kernel seed fixes the problem we can compare yur seed kernel with the one you just posted. Do keep a copy though as pastebins don't live very long.
Regard building a kernel from a seed as a part of the investigation, not a fix.
Did you ever at any time edit the kernel .config with a text editor?
Thats a no-no as many menuconfig options flip several CONF flags in the kernel. When you don't flip them all, you get an illegal .config that may build and give odd, hard to diagnose problems.
The only fix is to start with a new .config.
CONFIG_EXPERT=y should be off. Its only needed on Embedded systems.
CONFIG_PROFILING=y should be off - thats for kernel devs.
CONFIG_SLUB_DEBUG=y should be off
CONFIG_DEBUG_FS=y should be off. Edit. This is harmless
There may be others. _DEBUG optios always cause logspam and may interfere with proper operation.
If you are not debugging the kernel, they should always be off.
Anything with Verbose in its name should be off too unless you really feel you can't live without it.
The exception is verbose boot messages, which only cause logspam at boot. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Tue Oct 02, 2012 8:21 am Post subject: |
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Quote: | Did you ever at any time edit the kernel .config with a text editor? |
Nope. Never.
But in order to be really sure, i restarted my config from the last seed kernel. Reactivating all the options in order to retrieve my previous .config.
I also followed your advice by desactivating all debug and verbose options as well as expert and profiling.
That didn't solve my problem.
I will restart a new config from seed this week end. |
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Herring42 Guru
Joined: 10 Mar 2004 Posts: 373 Location: Buckinghamshire
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Posted: Tue Oct 02, 2012 11:08 am Post subject: |
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Silly question, but one that has caught me out before:
You are running the kernel you think you are running, right? I once got very frustrated that my new hardware wasn't working, before I realised that I was failing to mount /boot before running make install.
unale -a pointed out my error _________________ "The problem with quotes on the internet is that it is difficult
to determine whether or not they are genuine." -- Abraham Lincoln |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Tue Oct 02, 2012 1:15 pm Post subject: |
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Quote: | Silly question, but one that has caught me out before: You are running the kernel you think you are running, right? |
There is no silly question, everyone make mistakes. By chance, I didn't made that one. |
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NeddySeagoon Administrator
Joined: 05 Jul 2003 Posts: 54236 Location: 56N 3W
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Posted: Tue Oct 02, 2012 6:00 pm Post subject: |
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pums974,
For a quick and dirty test, boot a liveCD, get into the chroot so you are running your apps on top of the liveCD kernel and support.
Does the problem still exist?
IF so, this narrows it down to the kernel, glibc and supporting services. _________________ Regards,
NeddySeagoon
Computer users fall into two groups:-
those that do backups
those that have never had a hard drive fail. |
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pums974 Tux's lil' helper
Joined: 27 Feb 2010 Posts: 78
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Posted: Wed Oct 03, 2012 12:07 pm Post subject: |
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A friend of mine found a solution.
I had "vm.overcommit_memory = 2" in /etc/sysctl.conf.
I don't remember putting it in, and I don't really understand why this is here.
The fact is that since I commented that out, I am able to compile libreoffice without errors anymore.
Can you explain me what does this options mean ?
Is that normal that I had all those problem with it ?
Anyway, thank you for helping me. |
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BitJam Advocate
Joined: 12 Aug 2003 Posts: 2508 Location: Silver City, NM
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Posted: Thu Oct 04, 2012 12:57 am Post subject: |
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man 5 proc says: Code: | /proc/sys/vm/overcommit_memory
This file contains the kernel virtual memory accounting mode. Values
are:
0: heuristic overcommit (this is the default)
1: always overcommit, never check
2: always check, never overcommit
In mode 0, calls of mmap(2) with MAP_NORESERVE are not checked, and the
default check is very weak, leading to the risk of getting a process
"OOM-killed". Under Linux 2.4 any nonzero value implies mode 1. In
mode 2 (available since Linux 2.6), the total virtual address space on
the system is limited to (SS + RAM*(r/100)), where SS is the size of
the swap space, and RAM is the size of the physical memory, and r is
the contents of the file /proc/sys/vm/overcommit_ratio.
/proc/sys/vm/overcommit_ratio
See the description of /proc/sys/vm/overcommit_memory. |
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kernelOfTruth Watchman
Joined: 20 Dec 2005 Posts: 6111 Location: Vienna, Austria; Germany; hello world :)
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Posted: Sun Mar 17, 2013 3:52 pm Post subject: |
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pums974 wrote: | A friend of mine found a solution.
I had "vm.overcommit_memory = 2" in /etc/sysctl.conf.
I don't remember putting it in, and I don't really understand why this is here.
The fact is that since I commented that out, I am able to compile libreoffice without errors anymore.
Can you explain me what does this options mean ?
Is that normal that I had all those problem with it ?
Anyway, thank you for helping me. |
ok, so that's the cause for my similar error
thanks for posting the solution
edit:
a really controversial and contradictive topic (at least when following advice from forum & other posts on the net)
here's some documentation after I finally understood it completely ^^
http://www.novell.com/support/kb/doc.php?id=7002775 _________________ https://github.com/kernelOfTruth/ZFS-for-SystemRescueCD/tree/ZFS-for-SysRescCD-4.9.0
https://github.com/kernelOfTruth/pulseaudio-equalizer-ladspa
Hardcore Gentoo Linux user since 2004 |
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