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
