Created attachment 655890 [details] /var/log/genkernel.log, partial output While building kernel using genkernel 4.1.0-r2 program zombie processes are generated during kernel compilation. Trying to kill zombie process using command # kill -9 <pid> does not work as the process does not disappear, kill program does not return any error. The only solution is to run # kill -s SIGCHLD <parent pid> on parent and hope it would not break program operation. Installation media: install-amd64-minimal-20200819T214503Z.iso from official mirror, booted on a virtual machine Virtualization software: VirtualBox 6.1.12, Host cpu: Intel Pentium(R) Dual-Core CPU E6300 @ 2.80GHz Configuration during boot: - optional: enter gentoo vga=ask on boot: command line, select screen resolution smaller than screen, e.g. 800x600x32 - select default keymap when prompted Commands executed upon initial boot, running kernel version: 5.4.48, entered according to instructions from amd64 handbook, with comments where needed tty1# cfdisk /dev/sda #created a DOS label, 1G swap and used remaining space for root partition tty1# mkswap /dev/sda1 tty1# mkfs.ext4 /dev/sda2 tty1# swapon /dev/sda1 tty1# mount /dev/sda2 /mnt/gentoo tty1# cd /mnt/gentoo tty1# links https://www.gentoo.org #download amd64 stage3 archive and save to folder /mnt/gentoo tty1# tar xpvf stage3-amd64-20200819T214503Z.tar.xz --xattrs-include='*.*' --numeric-owner tty1# rm stage3-amd64-20200819T214503Z.tar.xz tty1# nano -w /mnt/gentoo/etc/portage/make.conf #add modifications listed below tty1# mirrorselect -i -o >> /mnt/gentoo/etc/portage/make.conf tty1# mkdir --parents /mnt/gentoo/etc/portage/repos.conf tty1# cp /mnt/gentoo/usr/share/portage/config/repos.conf /mnt/gentoo/etc/portage/repos.conf/gentoo.conf tty1# cp --dereference /etc/resolv.conf /mnt/gentoo/etc/ tty1# mount --types proc /proc /mnt/gentoo/proc tty1# mount --rbind /sys /mnt/gentoo/sys tty1# mount --make-rslave /mnt/gentoo/sys tty1# mount --rbind /dev /mnt/gentoo/dev tty1# mount --make-rslave /mnt/gentoo/dev tty1# chroot /mnt/gentoo /bin/bash tty1 chroot# source /etc/profile tty1 chroot# export PS1="(chroot) ${PS1}" tty1 chroot# emerge-webrsync tty1 chroot# eselect news read tty1 chroot# emerge --sync --quiet tty1 chroot# emerge --ask --verbose --update --deep --newuse @world tty1 chroot# exit tty1# reboot #a package update recommended a reboot after updating it Commands executed right after reboot: tty1# swapon /dev/sda1 tty1# mount /dev/sda2 /mnt/gentoo tty1# mount --types proc /proc /mnt/gentoo/proc tty1# mount --rbind /sys /mnt/gentoo/sys tty1# mount --make-rslave /mnt/gentoo/sys tty1# mount --rbind /dev /mnt/gentoo/dev tty1# mount --make-rslave /mnt/gentoo/dev tty1# chroot /mnt/gentoo /bin/bash tty1 chroot# source /etc/profile tty1 chroot# export PS1="(chroot) ${PS1}" tty1 chroot# emerge --ask sys-kernel/gentoo-sources #version 5.4.48 tty1 chroot# emerge --ask sys-kernel/genkernel #license file for a dependency needs to be updated tty1 chroot# etc-update # update any configuration files (accept license) tty1 chroot# emerge --ask sys-kernel/genkernel tty1 chroot# emerge --ask --deep --newuse sys-boot/grub tty1 chroot# grub-install /dev/sda tty1 chroot# nano -w /etc/locale.gen #input your locales here (e.g. en_US.UTF-8 UTF-8) tty1 chroot# locale-gen tty1 chroot# eselect locale list tty1 chroot# eselect locale set <number> tty1 chroot# genkernel all --no-nice #faster compilation Commands run before and after reboot tty2# links https://www.gentoo.org #visit Gentoo site to open amd64 handbook tty3# top #watch for any zombie process, shown on top row Related configuration changes: /etc/portage/make.conf: COMMON_FLAGS="-march=native -02 -pipe" MAKEOPTS="j2" added to /etc/fstab: #/dev/sda1 UUID=d706258b-6d44-493f-bed1-092b866aa8c4 swap swap sw 0 0 #/dev/sda2 UUID=e269842a-a12a-4aab-a235-b7a1aed8283f / ext4 errors=remount-ro 0 1
Created attachment 655892 [details] lscpu output
Created attachment 655894 [details] kernel .config file
Created attachment 655896 [details] lspci -k
Created attachment 655898 [details] /var/log/messages from livecd
Created attachment 655900 [details] lsmod
Created attachment 655902 [details] dmesg capture
Created attachment 655904 [details] ps -Alf
Created attachment 655906 [details] Screenshot of top program showing zombie process created by genkernel while in process tree mode
Virtualbox VM Configuration VM Type: Linux, Gentoo (64-bit) 992 MB ram on host with 2GB ram PIIX3 Chipset, PS2 Mouse emulation I/O APIC on, 2 processors, PAE/NX on 128 MB video ram, VMSVGA with 3D acceleration on Network: Bridged Adapter
Where did you run genkernel? From ps tree it looks like within the livecd environment so I guess you run out of space. You are supposed to do that in chroot...
I run it from chrooted environment entered from within livecd. On main livecd environment genkernel cannot be installed as there's no portage tools such as emerge coming with livecd, also ps -Alf shows all processes even when on livecd.
(In reply to Juozas Pocius from comment #11) > I run it from chrooted environment entered from within livecd. On main > livecd environment genkernel cannot be installed as there's no portage tools > such as emerge coming with livecd, also ps -Alf shows all processes even > when on livecd. Clarification: ^__ ps -Alf on chroot, not livecd
I cannot reproduce: I run your commands in HyperV instead of VirtualBox. Had a problem with grub (grub-install: error: cannot find EFI directory.) so I had to specify "--target=i386-pc" but this is unrelated. Yes, during kernel build and even initramfs creation, zombie counter in top will change from 0 to >=0. But for me it went down to 0 again and when genkernel was finished, no zombies were left. System was able to boot. So, are you really having a problem or are you just only concerned?
Some zombies would remain, but I was able to get arround by issuing SIGCHLD signal to the parent of zombie process and that fixed it. The kernel boots fine after running grub-mkconfig -o /boot/grub/grub.cfg while in chroot to generate config file.
> Some zombies would remain Did they block you in any way? I.e. did genkernel hang until you killed them? Or did genkernel just normally like expected but you noticed the zombies?
(In reply to Thomas Deutschmann from comment #15) > > Some zombies would remain > > Did they block you in any way? I.e. did genkernel hang until you killed > them? Or did genkernel just normally like expected but you noticed the > zombies? Genkernel would hang if no jobs were left free w/o killing the zombies or sending SIGCHLD to their parent.
Sorry, I don't know what to do with this bug report. I cannot reproduce. If this is happening as described, it shouldn't have any negative impact until you run genkernel in loop and will run out of PIDs at one point (that you cannot kill zombies is normal). Feel free to suggest a patch if you can reproduce and find the root cause.
