Dear Git gurus,
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...?
any recommendations on how to pin point the "offender"? ;) Here is the
trailer of one of the straced calls:
...
[pid 19713] getcwd("/ihome/yhalchen/datalad", 129) = 24
[pid 19713] stat(".git", {st_mode=S_IFDIR|0755, st_size=322, ...}) = 0
[pid 19713] lstat(".git/HEAD", {st_mode=S_IFREG|0644, st_size=41, ...}) = 0
[pid 19713] open(".git/HEAD", O_RDONLY) = 3
[pid 19713] read(3, "39f80454d31cfb691b006302b1f29dee"..., 255) = 41
[pid 19713] read(3, "", 214) = 0
[pid 19713] close(3) = 0
[pid 19713] lstat(".git/commondir", 0x7ffc1a571190) = -1 ENOENT (No such file
or directory)
[pid 19713] access(".git/objects", X_OK) = 0
[pid 19713] access(".git/refs", X_OK) = 0
[pid 19713] lstat(".git/commondir", 0x7ffc1a571120) = -1 ENOENT (No such file
or directory)
[pid 19713] open(".git/config", O_RDONLY) = 3
[pid 19713] fstat(3, {st_mode=S_IFREG|0644, st_size=257, ...}) = 0
[pid 19713] mmap(NULL, 528384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) = 0x2ba7894e7000
[pid 19713] read(3, "[core]\n\trepositoryformatversion "..., 524288) = 257
[pid 19713] read(3, "", 524288) = 0
[pid 19713] close(3) = 0
[pid 19713] munmap(0x2ba7894e7000, 528384) = 0
[pid 19713] stat(".", {st_mode=S_IFDIR|0755, st_size=907, ...}) = 0
[pid 19713] getcwd("/ihome/yhalchen/datalad", 129) = 24
[pid 19713] chdir(".") = 0
[pid 19713] getcwd("/ihome/yhalchen/datalad", 130) = 24
[pid 19713] lstat("/ihome/yhalchen/datalad", {st_mode=S_IFDIR|0755,
st_size=907, ...}) = 0
[pid 19713] chdir("/ihome/yhalchen/datalad") = 0
[pid 19713] stat(".git", {st_mode=S_IFDIR|0755, st_size=322, ...}) = 0
[pid 19713] lstat(".git/commondir", 0x7ffc1a571140) = -1 ENOENT (No such file
or directory)
[pid 19713] access("/etc/gitconfig", R_OK) = -1 ENOENT (No such file or
directory)
[pid 19713] access("/ihome/yhalchen/.config/git/config", R_OK) = -1 ENOENT (No
such file or directory)
[pid 19713] access("/ihome/yhalchen/.gitconfig", R_OK) = -1 ENOENT (No such
file or directory)
[pid 19713] access(".git/config", R_OK) = 0
[pid 19713] open(".git/config", O_RDONLY) = 3
[pid 19713] fstat(3, {st_mode=S_IFREG|0644, st_size=257, ...}) = 0
[pid 19713] brk(0x2ba78afea000) = 0x2ba78afea000
[pid 19713] read(3, "[core]\n\trepositoryformatversion "..., 524288) = 257
[pid 19713] read(3, "", 524288) = 0
[pid 19713] close(3) = 0
[pid 19713] access("/etc/gitconfig", R_OK) = -1 ENOENT (No such file or
directory)
[pid 19713] access("/ihome/yhalchen/.config/git/config", R_OK) = -1 ENOENT (No
such file or directory)
[pid 19713] access("/ihome/yhalchen/.gitconfig", R_OK) = -1 ENOENT (No such
file or directory)
[pid 19713] access(".git/config", R_OK) = 0
[pid 19713] open(".git/config", O_RDONLY) = 3
[pid 19713] fstat(3, {st_mode=S_IFREG|0644, st_size=257, ...}) = 0
[pid 19713] read(3, "[core]\n\trepositoryformatversion "..., 524288) = 257
[pid 19713] read(3, "", 524288) = 0
[pid 19713] close(3) = 0
[pid 19713] open(".git/objects/pack",
O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC) = 3
[pid 19713] fstat(3, {st_mode=S_IFDIR|0755, st_size=270, ...}) = 0
[pid 19713] getdents(3, /* 6 entries */, 524288) = 336
[pid 19713]
access(".git/objects/pack/pack-fd9e70075570d8ec41f12605852f54f1cb9771a8.keep",
F_OK) = -1 ENOENT (No such file or directory)
[pid 19713]
stat(".git/objects/pack/pack-fd9e70075570d8ec41f12605852f54f1cb9771a8.pack",
{st_mode=S_IFREG|0444, st_size=10019975, ...}) = 0
[pid 19713]
access(".git/objects/pack/pack-f1fc124e3aa1619d65a6ba56219f84871a762775.keep",
F_OK) = -1 ENOENT (No such file or directory)
[pid 19713]
stat(".git/objects/pack/pack-f1fc124e3aa1619d65a6ba56219f84871a762775.pack",
{st_mode=S_IFREG|0444, st_size=610330, ...}) = 0
[pid 19713] getdents(3, /* 0 entries */, 524288) = 0
[pid 19713] close(3) = 0
[pid 19713] getcwd("/ihome/yhalchen/datalad", 129) = 24
[pid 19713] open(".git/objects/info/alternates", O_RDONLY|O_NOATIME|O_CLOEXEC)
= -1 ENOENT (No such file or directory)
[pid 19713] open(".git/objects/17", O_RDONLY|O_NONBLOCK|O_DIRECTORY|O_CLOEXEC)
= -1 ENOENT (No such file or directory)
[pid 19713] fstat(1, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 17), ...}) = 0
[pid 19713] close(1) = 0
[pid 19713] exit_group(0) = ?
[pid 19713] +++ exited with 0 +++
[pid 19710] <... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0,
NULL) = 19713
[pid 19710] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=19713,
si_uid=14076, si_status=0, si_utime=0, si_stime=0} ---
[pid 19710] exit_group(1) = ?
[pid 19710] +++ exited with 1 +++
<... wait4 resumed> [{WIFEXITED(s) && WEXITSTATUS(s) == 1}], 0, NULL) = 19710
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=19710, si_uid=14076,
si_status=1, si_utime=0, si_stime=2} ---
exit_group(1) = ?
+++ exited with 1 +++
PS please CC me in replies! Thanks in advance
[1] http://datasets.datalad.org/singularity/neurodebian-v2.1.img.tgz
it is a tarball to extract/run with , I promise I did no evil in there ;)
--
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
