Re: fatal: Out of memory, getdelim failed under NFS mounts

From: René Scharfe <l.s.r@web.de>
Date: Aug 10, 2017, 13:27 UTC
Message-ID: <8e307474-d180-6d98-2c6b-062f2181bd14@web.de>
In-Reply-To: <20170809173928.h2ylvg5tp2p5inem@hopa.kiewit.dartmouth.edu>

Am 09.08.2017 um 19:39 schrieb Yaroslav Halchenko:

Show 27 quoted lines

> More context (may be different issue(s)) could be found at
> http://git-annex.branchable.com/forum/git-annex_add_out_of_memory_error/
> but currently I am consistently reproducing it while running
> git (1:2.11.0-3 debian stretch build) within debian stretch singularity
> environment [1].
> 
> External system is Centos 6.9, and git 1.7.1 (and installed in modules
> 2.0.4) do not show similar buggy behavior.
> 
> NFS mounted partitions are bind mounted inside the sinularity space and
> when I try to do some git operations, I get that error inconsistently , e.g.
> 
> 	yhalchen@discovery:/mnt/scratch/yoh/datalad$ git pull --ff-only origin master
> 	fatal: Out of memory, getdelim failed
> 	error: git://github.com/datalad/datalad did not send all necessary objects
> 
> 	yhalchen@discovery:/mnt/scratch/yoh/datalad$ git pull --ff-only origin master
> 	fatal: Out of memory, getdelim failed
> 	error: git://github.com/datalad/datalad did not send all necessary objects
> 
> 	yhalchen@discovery:/mnt/scratch/yoh/datalad$ git pull --ff-only origin master
> 	From git://github.com/datalad/datalad
> 	 * branch              master     -> FETCH_HEAD
> 	fatal: Out of memory, getdelim failed
> 
> and some times it succeeds.  So it smells that some race condition
> somewhere...?

I doubt the type of file system matters. The questions are: How much main memory do you have, what is git trying to cram into it, is there a way to reduce the memory footprint or do you need to add more RAM?

> any recommendations on how to pin point the "offender"? ;)

Running "GIT_TRACE=1 git pull --ff-only origin master" would be a good start, I think, to find out which of the different activities that pull is doing causes the out-of-memory error.

"free" and "ulimit -a" can help you find out how much memory you can use.

Also: What does "wc -L .git/FETCH_HEAD .git/packed-refs" report?
getdelim() is used mostly to read lines from files like these and in
the admittedly unlikely case that they are *really* long such an
error would be expected.

René