After running git-annex add
for a bunch of large files, I saw this memory usage report (per the qacct command on an SGE cluster):
maxvmem 86.683G
maxrss 40.617M
maxpss 30.359M
Is this memory usage expected? (I also saw another git-annex job killed for exceeding memory usage, and saw the top
command indicating high git-annex memory usage). The number of files in the repo is small, and I assume git-annex-add
doesn't need to read the whole file into memory, so what could explain the large maxvmem
usage?
git annex version
git-annex version: 10.20220127-gf616630
build flags: Assistant Webapp Pairing Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite S3 WebDAV
dependency versions: aws-0.22 bloomfilter-2.0.1.0 cryptonite-0.29 DAV-1.3.4 feed-1.3.2.0 ghc-8.10.7 http-client-0.7.9 persistent-sqlite-2.13.0.3 torrent-10000.1.1 uuid-1.3.15 yesod-1.6.1.2
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso borg hook external
operating system: linux x86_64
supported repository versions: 8 9 10
upgrade supported from repository versions: 0 1 2 3 4 5 6 7 8 9 10
local repository version: 8
(rnaseq-04-env) [shlyakhi@ctchpcpx190 11:36 lewis19_ra]$ git config -l --global
...
annex.supportunlocked=false
annex.gitaddtoannex=false
Is maxvmem what top would display as "VIRT"?
Sometimes a few years ago, ghc started just mapping the entire available memory range, which makes it appear in VIRT that it's using the entire size of the system memory. Of course, the actual RSS is much lower. It appears to have been 40 mb for you.
git-annex add can add files of arbitrary size without buffering them all in memory.