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Subject: |
sort fails to fork() + execlp(compress_program) if overcommit limit is reached |
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Date: |
Sun, 30 Jun 2013 04:42:34 +0300 |
I was trying to sort a big file (22GB, 5GB gzipped) with `sort
--compress-program=gzip -S40% data`. My /tmp filesystem is a 6GB tmpfs
and the total system RAM is 16GB. The problem was that after a while
sort would write uncompressed temp files in /tmp causing it to fill up
and then crash for having no free space.
After messing around with sort.c I found out that fork() would fail
after the first batches were written successfully in /tmp with errno
ENOMEM. I found out that I was hitting my kernel's VM overcommit limit
as the tmpfs utilisation grew. And indeed, running `sysctl -w
vm.overcommit=1` fixed the problem and the file was sorted.
As sort is a program with high memory consumption and could be running
in environments where overcommit is either unavailable or disabled I
would expect it to use another method for spawning its
compress_program. I'm not a C developer, so I'm not sure this is
possible, but vfork() and clone() that seem to solve this problem.
--
Petros Angelatos
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--- Begin Message ---
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Subject: |
Re: bug#14752: sort fails to fork() + execlp(compress_program) if overcommit limit is reached |
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Date: |
Mon, 01 Jul 2013 09:16:37 +0200 |
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User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:17.0) Gecko/20130329 Thunderbird/17.0.5 |
tag 14752 notabug
close 14752
stop
On 06/30/2013 03:42 AM, Petros Aggelatos wrote:
> I was trying to sort a big file (22GB, 5GB gzipped) with `sort
> --compress-program=gzip -S40% data`. My /tmp filesystem is a 6GB tmpfs
> and the total system RAM is 16GB. The problem was that after a while
> sort would write uncompressed temp files in /tmp causing it to fill up
> and then crash for having no free space.
Thanks for reporting this. However, I think that your system's memory
is just too small for sorting that file (that way, see below).
You already recognized yourself that sort(1) was writing huge chunk files
into the /tmp directory which is a tmpfs file system, i.e., that all that
data is decreasing the memory available for running processes.
The overhead for spawning a new process is negligible compared to such
an amount of data.
In such a case, you're much better off telling sort(1) to use a different
directory for the temporary files.
Here's an excerpt from the texinfo manual
(info coreutils 'sort invocation'):
If the environment variable `TMPDIR' is set, `sort' uses its value
as the directory for temporary files instead of `/tmp'. The
`--temporary-directory' (`-T') option in turn overrides the environment
variable.
...
`-T TEMPDIR'
`--temporary-directory=TEMPDIR'
Use directory TEMPDIR to store temporary files, overriding the
`TMPDIR' environment variable. If this option is given more than
once, temporary files are stored in all the directories given. If
you have a large sort or merge that is I/O-bound, you can often
improve performance by using this option to specify directories on
different disks and controllers.
Have a nice day,
Berny
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