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

From
Yaroslav Halchenko <yoh@onerussian.com>
Date
Aug 10, 2017, 14:43 UTC
Message-ID
<20170810144305.5d4lcx6oubkemsss@hopa.kiewit.dartmouth.edu>
In-Reply-To
<8e307474-d180-6d98-2c6b-062f2181bd14@web.de>
Thank you René!  comments/answers embedded below
On Thu, 10 Aug 2017, René Scharfe wrote:
Show 6 quoted lines
> Am 09.08.2017 um 19:39 schrieb Yaroslav Halchenko:
> > 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.

So far it has been a very consistent indicator. I did not manage to get this error while performing the same operation under /tmp (bind to local mounted drive), where it also feels going faster (again suggesting that original issue is some kind of a race)

Show 6 quoted lines
> 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?
> ... reordered ...
> "free" and "ulimit -a" can help you find out how much memory you can
> use.
I think those aren't the reason:
yhalchen@discovery:/mnt/scratch/yoh/datalad$ free -h
              total        used        free      shared  buff/cache   available
Mem:           126G        2.5G         90G        652K         33G        123G
Swap:          127G        1.7M        127G
yhalchen@discovery:/mnt/scratch/yoh/datalad$ ulimit
unlimited
> > 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.

samples of bad, and then good runs (from eyeballing -- the same until error message):

yhalchen@discovery:/mnt/scratch/yoh$ cat git_trace_bad.log 14:05:25.782270 git.c:371 trace: built-in: git 'pull' '--ff-only' 'origin' 'master' 14:05:25.795036 run-command.c:350 trace: run_command: 'fetch' '--update-head-ok' 'origin' 'master' 14:05:25.795332 exec_cmd.c:116 trace: exec: 'git' 'fetch' '--update-head-ok' 'origin' 'master' 14:05:25.797212 git.c:371 trace: built-in: git 'fetch' '--update-head-ok' 'origin' 'master' 14:05:25.904088 run-command.c:350 trace: run_command: 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet' 14:05:26.085954 run-command.c:350 trace: run_command: 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11652 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103' 14:05:26.086333 exec_cmd.c:116 trace: exec: 'git' 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11652 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103' 14:05:26.088382 git.c:371 trace: built-in: git 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11652 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103' 14:05:26.133326 run-command.c:350 trace: run_command: 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet' 14:05:26.133688 exec_cmd.c:116 trace: exec: 'git' 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet' 14:05:26.135493 git.c:371 trace: built-in: git 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet' fatal: Out of memory, getdelim failed error: git://github.com/datalad/datalad did not send all necessary objects

14:05:26.138838 run-command.c:350 trace: run_command: 'gc' '--auto' 14:05:26.139131 exec_cmd.c:116 trace: exec: 'git' 'gc' '--auto' 14:05:26.141108 git.c:371 trace: built-in: git 'gc' '--auto'

yhalchen@discovery:/mnt/scratch/yoh$ cat git_trace_good.log
14:05:37.851862 git.c:371               trace: built-in: git 'pull' '--ff-only' 'origin' 'master'
14:05:37.854250 run-command.c:350       trace: run_command: 'fetch' '--update-head-ok' 'origin' 'master'
14:05:37.854527 exec_cmd.c:116          trace: exec: 'git' 'fetch' '--update-head-ok' 'origin' 'master'
14:05:37.856389 git.c:371               trace: built-in: git 'fetch' '--update-head-ok' 'origin' 'master'
14:05:37.954099 run-command.c:350       trace: run_command: 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet'
14:05:38.118652 run-command.c:350       trace: run_command: 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11688 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103'
14:05:38.119011 exec_cmd.c:116          trace: exec: 'git' 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11688 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103'
14:05:38.120924 git.c:371               trace: built-in: git 'index-pack' '--stdin' '--fix-thin' '--keep=fetch-pack 11688 on discovery.hpcc.dartmouth.edu' '--pack_header=2,103'
14:05:38.167508 run-command.c:350       trace: run_command: 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet'
14:05:38.167851 exec_cmd.c:116          trace: exec: 'git' 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet'
14:05:38.169726 git.c:371               trace: built-in: git 'rev-list' '--objects' '--stdin' '--not' '--all' '--quiet'
From git://github.com/datalad/datalad
 * branch              master     -> FETCH_HEAD
   39f80454..1f90ef47  master     -> origin/master
14:05:38.306113 run-command.c:1130      run_processes_parallel: preparing to run up to 1 tasks
14:05:38.306148 run-command.c:1162      run_processes_parallel: done
14:05:38.306313 run-command.c:350       trace: run_command: 'gc' '--auto'
14:05:38.306616 exec_cmd.c:116          trace: exec: 'git' 'gc' '--auto'
14:05:38.308598 git.c:371               trace: built-in: git 'gc' '--auto'
14:05:38.311380 run-command.c:350       trace: run_command: 'merge' '--ff-only' 'FETCH_HEAD'
14:05:38.311645 exec_cmd.c:116          trace: exec: 'git' 'merge' '--ff-only' 'FETCH_HEAD'
14:05:38.313384 git.c:371               trace: built-in: git 'merge' '--ff-only' 'FETCH_HEAD'
14:05:45.092247 run-command.c:350       trace: run_command: 'gc' '--auto'
Updating 39f80454..1f90ef47
Fast-forward
14:05:45.092620 exec_cmd.c:116          trace: exec: 'git' 'gc' '--auto'
14:05:45.095862 git.c:371               trace: built-in: git 'gc' '--auto'
> Also: What does "wc -L .git/FETCH_HEAD .git/packed-refs" report?

"varying" and not consistent with causing an error (first trials, where I did not cat .git/FETCH_HEAD kinda suggested differently):

yhalchen@discovery:/mnt/scratch/yoh/datalad$ cat .git/FETCH_HEAD; wc -L .git/FETCH_HEAD .git/packed-refs; git pull --ff-only origin master
1f90ef474ee200befea19ba77242fa44f16739f0                branch 'master' of git://github.com/datalad/datalad
 107 .git/FETCH_HEAD
  90 .git/packed-refs
 107 total
From git://github.com/datalad/datalad
 * branch              master     -> FETCH_HEAD
Already up-to-date.
yhalchen@discovery:/mnt/scratch/yoh/datalad$ cat .git/FETCH_HEAD; wc -L .git/FETCH_HEAD .git/packed-refs; git pull --ff-only origin master 
1f90ef474ee200befea19ba77242fa44f16739f0                branch 'master' of git://github.com/datalad/datalad
 107 .git/FETCH_HEAD
  90 .git/packed-refs
 107 total
fatal: Out of memory, getdelim failed
error: git://github.com/datalad/datalad did not send all necessary objects
yhalchen@discovery:/mnt/scratch/yoh/datalad$ cat .git/FETCH_HEAD; wc -L .git/FETCH_HEAD .git/packed-refs; git pull --ff-only origin master 
   0 .git/FETCH_HEAD
  90 .git/packed-refs
  90 total
fatal: Out of memory, getdelim failed
error: git://github.com/datalad/datalad did not send all necessary objects
yhalchen@discovery:/mnt/scratch/yoh/datalad$ cat .git/FETCH_HEAD; wc -L .git/FETCH_HEAD .git/packed-refs; git pull --ff-only origin master 
   0 .git/FETCH_HEAD
  90 .git/packed-refs
  90 total
fatal: Out of memory, getdelim failed
error: git://github.com/datalad/datalad did not send all necessary objects
yhalchen@discovery:/mnt/scratch/yoh/datalad$ cat .git/FETCH_HEAD; wc -L .git/FETCH_HEAD .git/packed-refs; git pull --ff-only origin master 
   0 .git/FETCH_HEAD
  90 .git/packed-refs
  90 total
From git://github.com/datalad/datalad
 * branch              master     -> FETCH_HEAD
Already up-to-date.
> 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.

packed-ref pointer seems to also relate to the strace output around the point of message:

[pid 12843] open(".git/packed-refs", O_RDONLY) = 3 [pid 12843] fstat(3, {st_mode=S_IFREG|0644, st_size=5042, ...}) = 0 [pid 12843] fstat(3, {st_mode=S_IFREG|0644, st_size=5042, ...}) = 0 [pid 12843] brk(0x2b5704317000) = 0x2b5704276000 [pid 12843] mmap(NULL, 1048576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2b570451d000 [pid 12843] read(3, "# pack-refs with: peeled fully-p"..., 524288) = 5042 [pid 12843] read(3, "", 524288) = 0 [pid 12843] fstat(2, {st_mode=S_IFIFO|0600, st_size=0, ...}) = 0 [pid 12843] write(2, "fatal: Out of memory, getdelim f"..., 38fatal: Out of memory, getdelim failed ) = 38 [pid 12843] lseek(0, -41, SEEK_CUR) = -1 ESPIPE (Illegal seek) [pid 12843] exit_group(128) = ?

I verified that content of that packed-refs didn't change between good and bad runs.

NB is there a diff which could be given regexes within a line to ignore in diffs in so we could still retain original lines, i.e. answer to https://stackoverflow.com/questions/15841223/diff-while-ignoring-patterns-within-a-line-but-not-the-entire-line ?

FWIW -- here is a diff (from good to bad run) of strace (with pid/address info changed to stay the same for comparisons):

@@ -3121,6 +3118,7 @@
 [pid YYYYY] close(3)                    = 0
 [pid YYYYY] brk(NULL)                   = 0xXXXXX
 [pid YYYYY] brk(0xXXXXX)         = 0xXXXXX
+[pid YYYYY] mmap(NULL, 1048576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xXXXXX
 [pid YYYYY] open("/usr/lib/locale/locale-archive", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
 [pid YYYYY] open("/usr/share/locale/locale.alias", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
 [pid YYYYY] open("/usr/lib/locale/en_US/LC_MESSAGES", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
@@ -3144,11 +3142,9 @@
 [pid YYYYY] lstat(".git/commondir", 0xXXXXX) = -1 ENOENT (No such file or directory)
 [pid YYYYY] open(".git/config", O_RDONLY) = 3
 [pid YYYYY] fstat(3, {st_mode=S_IFREG|0644, st_size=257, ...}) = 0
-[pid YYYYY] mmap(NULL, 528384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xXXXXX
 [pid YYYYY] read(3, "[core]\n\trepositoryformatversion "..., 524288) = 257
 [pid YYYYY] read(3, "", 524288)         = 0
 [pid YYYYY] close(3)                    = 0
-[pid YYYYY] munmap(0xXXXXX, 528384) = 0
 [pid YYYYY] stat(".", {st_mode=S_IFDIR|0755, st_size=907, ...}) = 0
 [pid YYYYY] getcwd("/mnt/scratch/yoh/datalad", 129) = 25
 [pid YYYYY] chdir(".")                  = 0
@@ -3163,7 +3159,6 @@
 [pid YYYYY] access(".git/config", R_OK) = 0
 [pid YYYYY] open(".git/config", O_RDONLY) = 3
 [pid YYYYY] fstat(3, {st_mode=S_IFREG|0644, st_size=257, ...}) = 0
-[pid YYYYY] brk(0xXXXXX)         = 0xXXXXX
 [pid YYYYY] read(3, "[core]\n\trepositoryformatversion "..., 524288) = 257
 [pid YYYYY] read(3, "", 524288)         = 0
 [pid YYYYY] close(3)                    = 0
@@ -3180,245 +3175,48 @@
 [pid YYYYY] read(0, "1f90ef474ee200befea19ba77242fa44"..., 4096) = 82
 [pid YYYYY] open(".git/refs/", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3
 [pid YYYYY] fstat(3, {st_mode=S_IFDIR|0755, st_size=70, ...}) = 0
-[pid YYYYY] brk(0xXXXXX)         = 0xXXXXX
+[pid YYYYY] mmap(NULL, 528384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xXXXXX
 [pid YYYYY] getdents(3, /* 5 entries */, 524288) = 136
 [pid YYYYY] stat(".git/refs/heads", {st_mode=S_IFDIR|0755, st_size=24, ...}) = 0
 [pid YYYYY] stat(".git/refs/remotes", {st_mode=S_IFDIR|0755, st_size=24, ...}) = 0
 [pid YYYYY] stat(".git/refs/tags", {st_mode=S_IFDIR|0755, st_size=47, ...}) = 0
 [pid YYYYY] getdents(3, /* 0 entries */, 524288) = 0
+[pid YYYYY] munmap(0xXXXXX, 528384) = 0
 [pid YYYYY] close(3)                    = 0
 [pid YYYYY] open(".git/refs/bisect", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
 [pid YYYYY] open(".git/packed-refs", O_RDONLY) = 3
 [pid YYYYY] fstat(3, {st_mode=S_IFREG|0644, st_size=5042, ...}) = 0
 [pid YYYYY] fstat(3, {st_mode=S_IFREG|0644, st_size=5042, ...}) = 0
-[pid YYYYY] read(3, "# pack-refs with: peeled fully-p"..., 524288) = 5042
-[pid YYYYY] read(3, "", 524288)         = 0
-[pid YYYYY] close(3)                    = 0
-[pid YYYYY] open(".git/objects/pack", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3
-[pid YYYYY] fstat(3, {st_mode=S_IFDIR|0755, st_size=405, ...}) = 0
-[pid YYYYY] getdents(3, /* 8 entries */, 524288) = 480
-[pid YYYYY] access(".git/objects/pack/pack-a5ed9c83e2a39b21a2ab12dc351d2a7513d76e48.keep", F_OK) = -1 ENOENT (No such file or directory)
-[pid YYYYY] stat(".git/objects/pack/pack-a5ed9c83e2a39b21a2ab12dc351d2a7513d76e48.pack", {st_mode=S_IFREG|0444, st_size=124835, ...}) = 0
-[pid YYYYY] access(".git/objects/pack/pack-fd9e70075570d8ec41f12605852f54f1cb9771a8.keep", F_OK) = -1 ENOENT (No such file or directory)
-[pid YYYYY] stat(".git/objects/pack/pack-fd9e70075570d8ec41f12605852f54f1cb9771a8.pack", {st_mode=S_IFREG|0444, st_size=10019975, ...}) = 0
-[pid YYYYY] access(".git/objects/pack/pack-f1fc124e3aa1619d65a6ba56219f84871a762775.keep", F_OK) = -1 ENOENT (No such file or directory)
-[pid YYYYY] stat(".git/objects/pack/pack-f1fc124e3aa1619d65a6ba56219f84871a762775.pack", {st_mode=S_IFREG|0444, st_size=610330, ...}) = 0

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
Previous: René ScharfeNext: René Scharfe
Message 3 of 21 in “fatal: Out of memory, getdelim failed under NFS mounts”
  1. Yaroslav HalchenkoAug 9, 2017
  2. René ScharfeAug 10, 2017
  3. Yaroslav HalchenkoAug 10, 2017
  4. René ScharfeAug 10, 2017
  5. Junio C HamanoAug 10, 2017
  6. Yaroslav HalchenkoAug 10, 2017
  7. René ScharfeAug 10, 2017
  8. Jeff KingAug 10, 2017
  9. Yaroslav HalchenkoAug 10, 2017
  10. strbuf: clear errno before calling getdelim(3)René Scharfe, Aug 10, 2017
  11. Jeff KingAug 10, 2017
  12. Yaroslav HalchenkoAug 10, 2017
  13. Junio C HamanoAug 10, 2017
  14. Simon RuderichAug 11, 2017
  15. René ScharfeAug 11, 2017
  16. Simon RuderichAug 12, 2017
  17. René ScharfeAug 12, 2017
  18. René ScharfeAug 12, 2017
  19. Jeff KingAug 13, 2017
  20. René ScharfeAug 13, 2017
  21. Jeff KingAug 13, 2017

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