Hi Jonathan -- thank you very much for looking into it > > Subject: patched version needed to avoid fatal: Out of memory, getdelim > > failed crash > You could say that about all bugs. A patched version is needed to fix > the bug. :)
;) indeed... should have said "attached patch is needed to ..." ;-) > [...] > > For a while this issue was haunting us in various deployments, in > > particular > > - on NFS mounts > > - within standalone build of git-annex > > that many git commands could crash randomly at various points with > > fatal: Out of memory, getdelim failed > > message. Recently upstream tracked it down, and offered a perspective patch > > (see attached, cherry-picked from git upstream repository) -- it is a very > > simple patch. I have tested it on our deployments (as applied against > > 1:2.11.0-3 in stretch, but it is applicable to sid/experimental version as > > well) > > original report upstream and the thread with further discussion(s) on > > possible improvements to the patch: > > https://public-inbox.org/git/20170809173928.h2ylvg5tp2p5i...@hopa.kiewit.dartmouth.edu/ > > Please please consider adapting this patch for the official packages of git > > in > > Debian sid, and ideally to the version in stretch. This would be of great > > help > > to avoid those problems on the NFS-mounts and to generate fixed standalone > > builds of git-annex (CCing git-annex author, Joey) which many users rely > > upon > > on various (even non-Debian) systems. > Thanks for writing. Can you say more about the impact? devastation... pain ... suffering... really -- somehow it started to show up more for us recently and since no easy workaround -- I just had to provide a patched version to get around. In datalad we use git extensively so we run into higher chance to hit it because git is likely to be invoked multiple times per 1 datalad command. Just now, my previous email was to a student reporting the issue while trying to tame git. Also running it within singularity container also seems to make this bug more reproducible -- and we are switching to use Debian singularity container for many computations on our CentOS HPC... so although very basic, its impact is large and it greatly reduces our quality of life ;) > E.g. is there a > reproduction recipe I can use to experience this on stable? How often > do people experience this, and do they have a workaround? (un)fortunately so far I just had experienced it within stable debian singularity environment (such as our neurodebian one, e.g. this one (http://datasets.datalad.org/singularity/neurodebian-v2.2.img.tgz, it is huge etc), must be on a bind-mount of NFS-mounted partition (not sure if specific mount options are in play here as well). but because issue is kinda ill-messaged (has actually nothing to do with insufficient memory as far as I see it), I think it also misguides some folks: quick google lead to https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842586 which was closed since on the next run build succeeded... I do not think that there is a workaround besides a patch or rebuild (with HAVE_GETDELIM=) > The patch also appeared to still be under discussion upstream. Someone > investigating how the standard and various platforms handle errors from > getdelim would likely be appreciated there. yeah > One possibility in the Debian packaging would be for us to pass > HAVE_GETDELIM= in our build flags to avoid using getdelim altogether. > That way, we get correct behavior while waiting for the upstream > discussion to settle. whatever you think would be more appropriate is good with me, as long as we do not keep hitting this issue ;-) I just know that initial patch seems have resolved issue for me, and I haven't tried building without that functionality (i.e. with HAVE_GETDELIM=) so not sure if that one wouldn't have any side-effects if upstream largely builds/tests with it -- 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
