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nottledim
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PostPosted: Fri Feb 16, 2018 5:39 pm    Post subject: New install missing kernel makefile Reply with quote

I'm having trouble installing kernel on new system. I'm following the handbook by rote as I'm not that familiar with Gentoo - starting with minimal install on x86 32bit system.

I emerged sys-kernel/gentoo-sources but it failed without giving a reason. The /usr/src directory looks correct but there's no symlink to linux and there's no Makefile.

I tried emerging vanilla-sources and that installed without error but again there's no Makefile so it can't be compiled.

eselect kernel list says no symling targets found.

The running system is 4.9.76-gentoo-r1 gentoo-sources is the same, vanilla-sources is 4.15.3.

I don't know what to do. I'd appreciate some help.
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NeddySeagoon
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PostPosted: Fri Feb 16, 2018 6:22 pm    Post subject: Reply with quote

nottledim,

The /usr/src/linux symlink is used by tools to find the the kernel to build and by packages that install out of kernel modules to find the kernel to build against.
Sometimes its used by the user too.

It plays no part in the operation of the system, so in many cases its not required.

If you have newer kernels in the same series (vanillia-sources, gentoo-sources ..) and you run
Code:
emerge --depclean
all the files provided in the tarball we be removed from all the kernels except the newest. That means the Makefile will be removed too.

Newest has a special meaning to portage, thats what it means above too.
It might not be what you consider newest.

Code:
cd /usr/src
ls ./*/Makefile
should list all your kernel Makefiles.
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nottledim
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PostPosted: Sat Feb 17, 2018 11:27 am    Post subject: Reply with quote

Thanks for your help however the problem is there are no Makefiles. When I emerge
sys-kernel/gentoo-sources or vanilla-sources no symlink to /usr/src/linux is created and also the
directory containing kernel source has no Makefile.

The documentation says a symling will be created. It isn't. The documentation says run make menuconfig but there's no Makefile.

I've done nothing to remove anything and the system seems blissfully unaware that it installed anything.

This is the log of the emerge sys-kernel/gentoo-sources

Code:

1518805306: Started emerge on: Feb 16, 2018 18:21:45
1518805306:  *** emerge --ask sys-kernel/gentoo-sources
1518805319:  >>> emerge (1 of 1) sys-kernel/gentoo-sources-4.9.76-r1 to /
1518805319:  === (1 of 1) Cleaning (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources-4.9.76-r1.ebuild)
1518805355:  === (1 of 1) Compiling/Merging (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources-4.9.76-r1.ebuild)
1518805929:  === (1 of 1) Merging (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources-4.9.76-r1.ebuild)
1518809060:  *** Finished. Cleaning up...
1518809061:  *** exiting unsuccessfully with status '1'.
1518809062:  *** terminating.


After that when I look in /usr/src/linux-4.9.76-gentoo-r1 there is no Makefile, or any other file, just directories.
Is emerge doing the depclean?

Notice *** exiting unsuccessfully with status '1'.

Trying to install vanilla-kernel didn't help. According to logs same error. How do I install something which will work?

I'm perplexed and stuck. What should I do?
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NeddySeagoon
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PostPosted: Sat Feb 17, 2018 2:01 pm    Post subject: Reply with quote

nottledim,

We need to see the emerge log.

Below the message you quoted is some text about reporting a bug. It tells the path to the build log.
Use wgetpaste to put it onto a pastebin and post the link.

If you want a wild guess ... the kernel is a large number of small files and you are out of inodes on your filesystem.
What does
Code:
df -h
df -hi
show ?

You can have lots of free space but be unable to use it because every file requires at least one inode.
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nottledim
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PostPosted: Sat Feb 17, 2018 2:17 pm    Post subject: Reply with quote

If it worked the build file is: https://paste.pound-python.org/show/GZ3j0uRcWOeZaJn6WU7U/

I assume you meant the build log rather than the /var/log/emerge.log but just in case:
https://paste.pound-python.org/show/dQlhGkDNvMgbDYuknpYF/

Code:

livecd ~ # df -hi
Filesystem              Inodes IUsed IFree IUse% Mounted on
/dev/mapper/vg00-gentoo    13M  354K   13M    3% /
/dev/sda1                  64K   366   64K    1% /boot
cgroup_root                55K     3   55K    1% /sys/fs/cgroup
udev                       54K   464   54K    1% /dev
shm                        55K     1   55K    1% /dev/shm
livecd ~ # df -h
Filesystem               Size  Used Avail Use% Mounted on
/dev/mapper/vg00-gentoo   25G  4.0G   22G  16% /
/dev/sda1                240M   53M  171M  24% /boot
cgroup_root               10M     0   10M   0% /sys/fs/cgroup
udev                      10M  4.0K   10M   1% /dev
shm                      219M     0  219M   0% /dev/shm


Thanks again
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PostPosted: Sat Feb 17, 2018 4:43 pm    Post subject: Reply with quote

According to that build log, you already have substantial portions of that kernel installed (maybe all of it, maybe not), but none of the installed files are owned by the package that is supposed to own them, so Portage considers it an error that the package you are installing tries to overwrite them. This is a rather unusual error. One possible cause is that you previously installed the kernel with a different instance of the Portage package database, so the files you have now are owned by a package in the other /var/db/pkg.

If you just want to proceed without determining how you entered this state, move aside the offending directory and retry. You will likely delete the directory at some point, but you should preserve it for now so that it is easy to undo.

If you want to understand how this happened, there is still more information to collect. If we do not know how this happened, it is possible that there are other as-yet undiscovered problems with the same root cause. During the install, did you do the entire install in a single sitting or did you stop at some point, then return and resume later? If the latter, are you certain that you mounted all the supporting filesystems at the same paths in each sitting? What is the output of cat -n /etc/fstab ; echo ; cat -n /proc/self/mountinfo ; echo ; file -s /dev/sd*, as seen inside the chroot (or live system if you have the system fully operational)? That may not be enough to solve this, but it is a good first step.
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PostPosted: Sat Feb 17, 2018 5:42 pm    Post subject: Reply with quote

I've installed the kernels a few times both overwriting and by deleting the directory first. Yes the system has been rebooted a couple of times but I think the problem I'm seeing started before it was rebooted.
I can start over again if that's a viable solution (it's only 1.2GHz Via computer - it takes forever :-) )

/usr/src/* is owned by root as is /var/db.pkg and, it seems, so is everything else. Is that a problem? What is supposed to own them?

Output requested:

Code:

cat -n /etc/fstab
1  # /etc/fstab: static file system information.
     2  #
     3  # noatime turns off atimes for increased performance (atimes normally aren't
     4  # needed); notail increases performance of ReiserFS (at the expense of storage
     5  # efficiency).  It's safe to drop the noatime options if you want and to
     6  # switch between notail / tail freely.
     7  #
     8  # The root filesystem should have a pass number of either 0 or 1.
     9  # All other filesystems should have a pass number of 0 or greater than 1.
    10  #
    11  # See the manpage fstab(5) for more information.
    12  #
    13
    14  # <fs>                  <mountpoint>    <type>          <opts>          <dump/pass>
    15
    16  # NOTE: If your BOOT partition is ReiserFS, add the notail option to opts.
    17  #
    18  # NOTE: Even though we list ext4 as the type here, it will work with ext2/ext3
    19  #       filesystems.  This just tells the kernel to use the ext4 driver.
    20  #
    21  # NOTE: You can use full paths to devices like /dev/sda3, but it is often
    22  #       more reliable to use filesystem labels or UUIDs. See your filesystem
    23  #       documentation for details on setting a label. To obtain the UUID, use
    24  #       the blkid(8) command.
    25
    26  #LABEL=boot             /boot           ext4            noauto,noatime  1 2
    27  #UUID=58e72203-57d1-4497-81ad-97655bd56494              /               ext4            noatime         0 1
    28  #LABEL=swap             none            swap            sw              0 0
    29  #/dev/cdrom             /mnt/cdrom      auto            noauto,ro       0 0
    30  /dev/sda1 /boot ext4 defaults 0 2

  cat -n /proc/self/mountinfo
     1  27 16 253:1 / / rw,relatime - xfs /dev/mapper/vg00-gentoo rw,attr2,inode64,noquota
     2  28 27 8:1 / /boot rw,relatime - ext4 /dev/sda1 rw,data=ordered
     3  29 27 0:4 / /proc rw,relatime - proc /proc rw
     4  30 27 0:13 / /sys rw,nosuid,nodev,noexec,relatime - sysfs sysfs rw
     5  31 30 0:8 / /sys/kernel/debug rw,nosuid,nodev,noexec,relatime - debugfs debugfs rw
     6  32 30 0:17 / /sys/fs/fuse/connections rw,nosuid,nodev,noexec,relatime - fusectl fusectl rw
     7  33 30 0:18 / /sys/fs/cgroup rw,nosuid,nodev,noexec,relatime - tmpfs cgroup_root rw,size=10240k,mode=755
     8  34 33 0:19 / /sys/fs/cgroup/openrc rw,nosuid,nodev,noexec,relatime - cgroup openrc rw,release_agent=/lib/rc/sh/cgroup-release-agent.sh,name=openrc
     9  35 33 0:20 / /sys/fs/cgroup/unified rw,nosuid,nodev,noexec,relatime - cgroup2 none rw
    10  36 27 0:6 / /dev rw,nosuid,relatime - devtmpfs udev rw,size=10240k,nr_inodes=55213,mode=755
    11  37 36 0:12 / /dev/pts rw,relatime - devpts devpts rw,gid=5,mode=620,ptmxmode=000
    12  38 36 0:16 / /dev/shm rw,nosuid,nodev,noexec,relatime - tmpfs shm rw

file -s /dev/sd*
/dev/sda:  DOS/MBR boot sector
/dev/sda1: Linux rev 1.0 ext4 filesystem data, UUID=0347a7e8-f886-4e0e-b2fc-05dbca7bcf1c (needs journal recovery) (extents) (64bit) (large files) (huge files)
/dev/sda2: LVM2 PV (Linux Logical Volume Manager), UUID: Mtq6eE-dEJb-6q8j-JUyJ-t43s-gIGk-GyRWwh, size: 99760741888
/dev/sdb:  DOS/MBR boot sector; partition 1 : ID=0x17, active, start-CHS (0x0,0,1), end-CHS (0x127,63,32), startsector 0, 606208 sectors
/dev/sdb1: DOS/MBR boot sector; partition 1 : ID=0x17, active, start-CHS (0x0,0,1), end-CHS (0x127,63,32), startsector 0, 606208 sectors


If you can't put your finger on cause then I think I'll start over. I must have done something silly.
.
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PostPosted: Sat Feb 17, 2018 6:01 pm    Post subject: Reply with quote

nottledim,


By owner, Hu was referring to the installed package that owns a file.

When you remove something without using portage, portage doesn't know and still has its record of all the files the package installed.

Your log contains ...
Code:
ecompressdir: bzip2 -9 /usr/share/doc
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at https://bugs.gentoo.org/ unless you report exactly
 * which two packages install the same file(s). See
 * https://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how
 * to solve the problem. And once again, please do NOT file a bug report
 * unless you have completely understood the above message.
 * 
 * Detected file collision(s):

So portage thinks that this kernel is still installed.
The log ends with
Code:
  31;01m * None of the installed packages claim the file(s).
 * 
 * Package 'sys-kernel/gentoo-sources-4.9.76-r1' merged despite file
 * collisions. If necessary, refer to your elog messages for the whole
 * content of the above message.


Which says that it worked. ... but it didn't

Try
Code:
emerge -C =sys-kernel/gentoo-sources-4.9.76-r1
That will remove portages record of the install and all the source files that belong to the package.
After that its safe to remove the directory from /usr/src.

That gets your system into a self consistent state for gentoo-sources-4.9.76-r1. Its not in /usr/src anh its not in portages database either.

Now emerge it again.

Reinstalling never solves anything. Its just a bad habit Gentoo users bring with them from other operating systems.
It may save time in the long run, if you do it correctly. However, the learning opportunity is lost so its quite possible to do the same thing again.
Besides, you might make a new mistake :)
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PostPosted: Sat Feb 17, 2018 6:12 pm    Post subject: Reply with quote

Code:

emerge -C =sys-kernel/gentoo-sources-4.9.76-r1
 * This action can remove important packages! In order to be safer, use
 * `emerge -pv --depclean <atom>` to check for reverse dependencies before
 * removing packages.

--- Couldn't find '=sys-kernel/gentoo-sources-4.9.76-r1' to unmerge.

>>> No packages selected for removal by unmerge


Which doesn't surprise me as eselect kernel list shows nothing.

I'll try emerging gentoo-sources into empty /usr/src and hope!

I appreciate your support, thanks.

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PostPosted: Sat Feb 17, 2018 6:55 pm    Post subject: Reply with quote

nottledim,

I don't yet understand how portage believes the package is installed, which gives rise to the file collisions, yet can't find it to remove.

The can't find it has nothing to do with the content of /usr/src
Portage keeps track of things in /var/db/pkg/<category>/<package>-<version>/
Looking is safe but changing things is not.
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PostPosted: Mon Feb 19, 2018 11:42 am    Post subject: Reply with quote

I tried again to install with no success so I started the install again into a fresh partition. The result is exactly the same: emerge failed after cleanup phase, no Makefiles in /usr/src and /var/db/pkg/sys-kernel contains a directory -MERGING-gentoo-sources-4.9.76-r1 which I assume is named like that to indicate install process is incomplete. There is also a directory called linux-headers-4.13 which was installed by stage3 tarball. The version number puzzles me. And to confirm eselect kernel list shows empty..

How do I install a different version of the kernel?

I can't believe nobody else has had this problem. Could it be related to installing x86 32 bit? It's not so common now.

Could it be a USE flag I'm not setting? I've just taken the defaults.
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PostPosted: Mon Feb 19, 2018 12:26 pm    Post subject: Reply with quote

nottledim,

linux-headers is used by things in userspace that need a stable set of kernel headers to build against.
These headers are not provided by the kernel you happen be be running or building today.

I'm not surprised you have the same error in a new install. Its probably the same problem we still don't understand.
I've not seen this issue before. Similar things happen when you run out of i-nodes or disk space.

Lets try fetching a kernel outside of portage. I expect it to fail too.
Code:
cd /usr/src
wget https://cdn.kernel.org/pub/linux/kernel/v4.x/linux-4.9.82.tar.xz
tar xf linux-4.9.82.tar.xz

This is vanilla-sources-4.9.82 without using portage.

Quote any error messages.

Portage does almost the same thing but may make an extra copy or even two, depending on your partition scheme.
Portage downloads and unpacks the tarball to /var/tmp/portage/...
Then does an install in /var/tmp/portage/ which should only be hardlinks ... no extra disk space.
Next it copies the /var/tmp/portage/ install to /usr/src.
If that works, it removes the /var/tmp/portage/ temporary files.

If /var/tmp/portage/ and /usr/src are on different filesystems, the copy from one to the other is actually a copy, using more disk space, i-nodes and so on.
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PostPosted: Mon Feb 19, 2018 12:55 pm    Post subject: Reply with quote

That worked fine and the directory contains Makefile, README and .git whatever as I would expect.

I can compile that manually but portage won't know about it.

Can I use genkernel? Should I use genkernel?
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PostPosted: Mon Feb 19, 2018 1:12 pm    Post subject: Reply with quote

nottledim,

We still don't know what the issue is. I expect other packages will be affected too.

genkernel will build you a kernel with the same settings as the liveCD uses.
Configuring the kernel by hand is probably the hardest part of a Gentoo install. genkernel will allow you to delay that learning step.
However, you may find that genkernel alone will not set up your video or wifi. You can fix that later.
That's a limitation imposed by hardware manufacturers. A one size fits all is not possible as kernel drivers conflict with one another.

You will need to make the linux symlink by hand, then you can use genkernel.

This is only a work around, not a fix. Put the full portage generated kernel install log onto a pastebin site if you still have it, or do it again if you don't.
Post
Code:
df -Th
df -ih
too please.

You can continue your install using this workaround if you wish.
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PostPosted: Mon Feb 19, 2018 1:30 pm    Post subject: Reply with quote

build log: https://paste.pound-python.org/show/XFLCWvvnliqGiJ1ZKDG0/

snippet from emerge.log:
Code:

1518974781: Started emerge on: Feb 18, 2018 17:26:21
1518974781:  *** emerge --ask sys-kernel/gentoo-sources
1518974807:  >>> emerge (1 of 2) sys-devel/bc-1.06.95-r2 to /
1518974807:  === (1 of 2) Cleaning (sys-devel/bc-1.06.95-r2::/usr/portage/sys-devel/bc/bc-1.06.95-r2.ebuild)
1518974808:  === (1 of 2) Compiling/Merging (sys-devel/bc-1.06.95-r2::/usr/portage/sys-devel/bc/bc-1.06.95-r2.ebuild)
1518974897:  === (1 of 2) Merging (sys-devel/bc-1.06.95-r2::/usr/portage/sys-devel/bc/bc-1.06.95-r2.ebuild)
1518974908:  >>> AUTOCLEAN: sys-devel/bc:0
1518974914:  === (1 of 2) Post-Build Cleaning (sys-devel/bc-1.06.95-r2::/usr/portage/sys-devel/bc/bc-1.06.95-r2.ebuild)
1518974914:  ::: completed emerge (1 of 2) sys-devel/bc-1.06.95-r2 to /
1518974914:  >>> emerge (2 of 2) sys-kernel/gentoo-sources-4.9.76-r1 to /
1518974914:  === (2 of 2) Cleaning (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources-4.9.76-r
1.ebuild)
1518974927:  === (2 of 2) Compiling/Merging (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources
-4.9.76-r1.ebuild)
1518975411:  === (2 of 2) Merging (sys-kernel/gentoo-sources-4.9.76-r1::/usr/portage/sys-kernel/gentoo-sources/gentoo-sources-4.9.76-r1
.ebuild)
1518977076:  *** Finished. Cleaning up...
1518977076:  *** exiting unsuccessfully with status '1'.
1518977092:  *** terminating.


Code:

livecd ~ # df -Th
Filesystem            Type      Size  Used Avail Use% Mounted on
/dev/mapper/vg00-gen2 xfs        20G  3.5G   17G  18% /
cgroup_root           tmpfs      10M     0   10M   0% /sys/fs/cgroup
udev                  devtmpfs   10M  4.0K   10M   1% /dev
shm                   tmpfs     219M     0  219M   0% /dev/shm
/dev/sda1             ext4      240M   53M  171M  24% /boot
livecd ~ # df -ih
Filesystem            Inodes IUsed IFree IUse% Mounted on
/dev/mapper/vg00-gen2    10M  333K  9.7M    4% /
cgroup_root              55K     3   55K    1% /sys/fs/cgroup
udev                     54K   470   54K    1% /dev
shm                      55K     1   55K    1% /dev/shm
/dev/sda1                64K   366   64K    1% /boot


and eselect kernel list shows 4.9.82 so clever :-)
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PostPosted: Mon Feb 19, 2018 1:48 pm    Post subject: Reply with quote

nottledim,

Code:
Filesystem            Type      Size  Used Avail Use% Mounted on
/dev/mapper/vg00-gen2 xfs        20G  3.5G   17G  18% /


Your full kernel build log is truncated. There is no error. A kernel install through portage needs at most 3G of space.
The truncated log points to portage not being able to continue ... I would guess for lack of disk space but I don't see any reason for it.

Your 20G space for everything will not be enough for a desktop install. A few things need 8G to build, then you have the distfiles to store too.
20G is fine for a server. A desktop install wants about 40G for comfort.

There is no need to start over. /usr/portage and /var/tmp/portage can be on their own filesystems and mounted in fstab with very little pain.
/var/tmp/portage is the build space used by emerge.
/usr/portage is the portage repo, distfiles and binary packages if you opted to save binary packages.
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PostPosted: Mon Feb 19, 2018 3:13 pm    Post subject: Reply with quote

I've no idea either.

20G should be plenty. It's only a little server. I can make the partition bigger once it's booted if I want. I was really using it as a means to get to know Gentoo. Now ArchLinux is not supporting 32bit I have to find something else for these old motherboards I have.

genkernel doesn't work. It also has some error. I can't work out what it means but it fails.. So I'm doing a manual compile which so far is going OK. I imagine it'll be several hours.

Thanks again for your help. No doubt you'll hear from me again if/when the kernel is compiled.
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PostPosted: Mon Feb 19, 2018 3:19 pm    Post subject: Reply with quote

nottledim,

I run KVM servers in 20G, as you say it will be fine.
How much RAM and swap do you have?
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PostPosted: Mon Feb 19, 2018 3:56 pm    Post subject: Reply with quote

It looks like 512M ram. I thought it was 1G. No doubt the 1G stick was borrowed. It's only using 60..80M + buffers.

No swap configured. I'll use lvm swap once it's running.

Compile is going OK - so far so good.
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PostPosted: Mon Feb 19, 2018 7:06 pm    Post subject: Reply with quote

nottledim,

Keep an eye on things. That emerge *-sources fails is a pointer to something.
If you run out of RAM, the OOM will kick in an leave messages in dmesg.
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PostPosted: Mon Feb 19, 2018 10:14 pm    Post subject: Reply with quote

Quote:

If you run out of RAM, the OOM will kick in an leave messages in dmesg.


"You dirty, rotten swine, you! You have deaded me!"

Code:

[11138.435292] Out of memory: Kill process 18418 (emerge) score 709 or sacrifice child
[11138.435303] Killed process 18418 (emerge) total-vm:337248kB, anon-rss:326244kB, file-rss:0kB, shmem-rss:0kB
[11138.583608] oom_reaper: reaped process 18418 (emerge),


nuff said. Doh!
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PostPosted: Mon Feb 19, 2018 10:49 pm    Post subject: Reply with quote

nottledim,

:)

Add some swap. Not having swap does not prevent the kernel swapping. It reduces it choices for swapping.
Swap is only ever used for dynamically allocated memory. That's thing that do not have a permanent home on the HDD.
When you run a program, its not loaded into memory. Its mapped into virtual memory. When a piece tries to execute, you get a page fault and that bit is loaded into physical RAM.
When there is not enough RAM, previously loaded code can be dropped and the process repeated next time the code is needed. Its swapping.

This mechanism allows Linux to run programs that are too big to fit into RAM. Its OK for several areas of virtual memory to map to the same physical RAM.
Only one can occupy the physical RAM at a time.

Not having any swap forces the kernel to keep all dynamically allocated RAM in RAM.
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PostPosted: Mon Feb 19, 2018 10:54 pm    Post subject: Reply with quote

I added swap. I'll change the memory tomorrow when the compile has finished.

Funny, your location is very similar to mine. Not a contributor to edlug by any chance?
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PostPosted: Mon Feb 19, 2018 11:04 pm    Post subject: Reply with quote

nottledim,

I subscribe to the edlug list but I've never made it to a meeting.
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PostPosted: Tue Feb 20, 2018 8:26 pm    Post subject: Reply with quote

Sorted out the memory and it's all working fine including emerge sys-kernel/gentoo-sources


Learning experience. Thanks for your invaluable.
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