gerrit jgit gc caused mediawiki/core repo problems
Closed, ResolvedPublic

Description

reedy@deployment-tin:/srv/mediawiki-staging/php-master$ git pull -vvv
Server supports multi_ack_detailed
Server supports no-done
Server supports side-band-64k
Server supports ofs-delta
Server version is JGit/4.1.2.201602141800-r
Marking 8f3f831e7ccbc176702c3baac6732decd243479d as complete
want 64f7660b6dfd4433f3a5490c99bf1d55dbb3d83e (refs/heads/REL1_27)
want 0ddb8064b9ba4dab686454e78cb3b7fc4fede6de (refs/heads/REL1_28)
have 8f3f831e7ccbc176702c3baac6732decd243479d
have ab78081514f6a4f0170d54fc74001a01abb68b91
have d0ba633fc4a65dee84c849714898e6c1e8392539
have d7ed14407aa7be9a790778cae644c2b320bb7aa4
have 7e1dbe568ff0bf392271349e1bff740cb2ce5c30
have 79498f99e0783933637bc4aadd61ee2ddcd67b56
have 577a8b65bd49fd9ea3d947928bb1b2319666ad96
have cd6acfaf9065fe3561c1cf5d1fb19de73b4f5b7c
have 52c744e19d9882cf2912d48f037db967c2c4bbf9
have 1c0b4577daef10856e6e604ead8d46383b403ce6
have b3ba0a75ea7c6f757ab79f92a05a8d5a3bea85f1
have 95f479b6e3da75651b748880fe6deadfec6eb22b
have cf2e0df384711251249c8ff69851a5aaffac60bc
have 319ebe5d7b47e8e6d30f40464390715262c48bae
have 22a0e9d958f084044f7f280877fc73c5629c39ad
have 91b79ac288e6218407aa0a0fef99c5ca4ab7e78d
POST git-upload-pack (997 bytes)
got ack 3 8f3f831e7ccbc176702c3baac6732decd243479d
got ack 3 ab78081514f6a4f0170d54fc74001a01abb68b91
got ack 3 d0ba633fc4a65dee84c849714898e6c1e8392539
got ack 3 d7ed14407aa7be9a790778cae644c2b320bb7aa4
got ack 3 7e1dbe568ff0bf392271349e1bff740cb2ce5c30
got ack 3 79498f99e0783933637bc4aadd61ee2ddcd67b56
got ack 3 577a8b65bd49fd9ea3d947928bb1b2319666ad96
got ack 3 cd6acfaf9065fe3561c1cf5d1fb19de73b4f5b7c
got ack 3 52c744e19d9882cf2912d48f037db967c2c4bbf9
got ack 3 1c0b4577daef10856e6e604ead8d46383b403ce6
got ack 3 b3ba0a75ea7c6f757ab79f92a05a8d5a3bea85f1
got ack 3 95f479b6e3da75651b748880fe6deadfec6eb22b
got ack 3 cf2e0df384711251249c8ff69851a5aaffac60bc
got ack 3 319ebe5d7b47e8e6d30f40464390715262c48bae
got ack 3 22a0e9d958f084044f7f280877fc73c5629c39ad
got ack 3 91b79ac288e6218407aa0a0fef99c5ca4ab7e78d
got ack 4 91b79ac288e6218407aa0a0fef99c5ca4ab7e78d
done
got ack (1) 91b79ac288e6218407aa0a0fef99c5ca4ab7e78d
remote: internal server error
fatal: protocol error: bad pack header

and jenkins jobs also failing for the same reason

12:43:00 INFO:main:Starting updating tasks...
12:43:00 INFO:mwcore:cwd: /srv/mediawiki-staging/php-master
12:43:00 INFO:mwcore:running: git pull
12:43:03 remote: internal server error
12:43:03 fatal: protocol error: bad pack header
Reedy created this task.Nov 26 2016, 12:50 PM
Restricted Application added a subscriber: Aklapper. · View Herald TranscriptNov 26 2016, 12:50 PM
Reedy added a subscriber: demon.Nov 26 2016, 12:50 PM

Seems fine locally

Reedy updated the task description. (Show Details)Nov 26 2016, 12:54 PM
TTO triaged this task as Unbreak Now! priority.
TTO added subscribers: Nemo_bis, Ladsgroup, TerraCodes and 4 others.

copying UBN from other task

Reedy added a comment.Nov 26 2016, 1:24 PM

Clean clone of all of core over HTTPS is fine too

Paladox added a comment.EditedNov 26 2016, 1:30 PM

It is affecting my local pc too.

My local pc as in not wmf owned and running windows.

$ git pull
fatal: internal server error
remote: internal server error
fatal: protocol error: bad pack header

Adding Operations as this seems like this will require gerrit's server to be accessed to fix this.

I found this https://bugs.chromium.org/p/gerrit/issues/detail?id=1954 and seems to be the error as we are having.

the error should be in the logs.

/var/lib/gerrit2/review_site/logs/error_log

Re cloning worked for me.

Mentioned in SAL (#wikimedia-releng) [2016-11-26T14:14:11Z] <Reedy> moved old /srv/mediawiki-staging/php-master to /tmp/php-master, recloned MW Core, copied in LocalSettings, skins, vendor and extensions. T151676. scap sync-dir running

There seems to be a fix for gc in jgit 4.3.1 that looks like something that will fix our problem. Note I am not 100% correct but hopefully it will.

https://projects.eclipse.org/projects/technology.jgit/releases/4.3.1

Gerrit 2.13 uses jgit 4.4.1 so it includes the fix.

https://github.com/gerrit-review/gerrit/blob/stable-2.13/WORKSPACE#L85

https://git.eclipse.org/c/jgit/jgit.git/commit/?id=05fd01656ee295e4a8d3c1efff0ca3a6f48c1f4c

Reedy added a subscriber: Volans.Nov 26 2016, 2:48 PM

Quick workaround is:

cp .git/config .git/config.backup
git remote remove origin
mv .git/config.backup .git/config
git fetch

Thanks to @Volans on P4510

guess I should add the info from the logs here:

/var/lib/gerrit2/review_site/logs/error_log, the first relevant thing seems to be

[2016-11-26 00:44:01,534] WARN  com.google.gerrit.server.change.ChangeKindCacheImpl : Cannot check trivial rebase of new patch set 1ce5e88e4283cd1659c90d4024b53ed3339a0a66 in mediawiki/extensions/Lingo java.util.concurrent.ExecutionException: org.eclipse.jgit.errors.MissingObjectException: Missing unknown a602a8b2400730a8d9a0d20b79bfb55ec0de4d86

looking at the queue gave:

...
5464d3ef 13:49:52.519 13:48:52.518      (retry 3027) [7551df03] push git@github.com:wikimedia/mediawiki-services-trending-edits
7eaf2067 22:59:43.645 Nov-23 21:59      Log File Compressor
5eb25cd4 Dec-03 02:00 Nov-23 21:59      GC runner
Reedy lowered the priority of this task from Unbreak Now! to High.Nov 26 2016, 4:20 PM

Lowered slightly; beta and CI have been unbroken, still some gerrit related stuff to be done

@Reedy had to delete the local zuul clone for ci to unbreak it's self.

Clones will take longer for all mw extensions then usual.

Change 323655 had a related patch set uploaded (by Reedy):
Disable git gc as source of breakages

https://gerrit.wikimedia.org/r/323655

Reedy renamed this task from git pull on mw core broken on beta to gerrit jgit gc caused mediawiki/core repo problems.Nov 26 2016, 5:17 PM
demon claimed this task.Nov 26 2016, 7:06 PM
demon added a comment.Nov 26 2016, 8:52 PM

Ran git fsck --full --strict on all repos. Most were fine. A lot of these are probably fine too, but here's the results that are interesting.

1​/srv/gerrit/git/rcstream.git
2​dangling commit 534c2363ba7f5b22010b60cbca39e21dbe0e502a
3​---
4​/srv/gerrit/git/wikipedia/gadgets/ProveIt.git
5​dangling commit 6f18195326fa30d764b672949fffe564038ff9d1
6​---
7​/srv/gerrit/git/maps/kartotherian/deploy.git
8​dangling commit 042ed449244ee3d1d3d0414bbde7d96dbd6a2ffd
9​dangling blob 3743863d2b11fc8522174293b5829609713d732a
10​dangling blob 1a73ce5960f631faa6869b2838b4c96e67a8d10b
11​dangling commit 909cfae4531e9d8813d6d1fdea1ec805a750ca60
12​dangling blob 66b6d2d2ac9df801d3ffe62abe50f47d49c4e2e2
13​dangling commit c7466f6e3a917ce8155eb6650592e4d67a8d7b6a
14​dangling commit 768a8b3198058b79b2653b14f8a6827564667ff5
15​---
16​/srv/gerrit/git/maps/kartotherian.git
17​dangling commit 9bab6024a356c14bff6a6014fb2caa1c6c025b74
18​dangling commit 350e3eb72799a510f56c7d7929963a7ea5116b15
19​dangling commit e0f0ce49b1f94635ddde13106b2c4b4c5a44df5c
20​dangling commit 649d54f73c11bd6f0e60d2be952926ce2506b6e6
21​---
22​/srv/gerrit/git/phabricator/phabricator.git
23​dangling blob 645d304446679d92528bea317b5202069d436c36
24​dangling commit a6abead442b24931c1fea24c6023b6d54c6d5e57
25​dangling blob a2b10a73c0c72bf5e25ae1b39e0c55fdb7c272cf
26​dangling commit 2826235c62b2fd689027e9424e4314017c7c0219
27​dangling commit 6a75fc3e7ca1950549376b57a3b1aee49c849886
28​dangling blob 3966bf13abba281ce748739bd38cc841ddadf25a
29​dangling blob 7f836763b2de7613b19a35931f78ca86ae81224c
30​---
31​/srv/gerrit/git/phabricator/tools.git
32​dangling commit 4e5a2057a46ef34ab8cfe5e65adee09302eb297f
33​dangling commit 5f8c870c5f239be0205b2eef4b7b11158119c193
34​dangling commit 4135cb64dbbdaecd01deec6beaa358cbac3eb69c
35​dangling commit bff619d75ffcb64d5370ba3e456d8e7673ebd9ae
36​dangling commit 0d17977fe33328759bd4b0568d097e5a28f1b231
37​dangling commit 4bc73313659d9e58a106f556cd9f1bdb1fd6f8b0
38​---
39​/srv/gerrit/git/phabricator/deployment.git
40​dangling commit 67021671deeef0de57aa597c51eb4dacde669cab
41​---
42​/srv/gerrit/git/phabricator/extensions/Sprint.git
43​dangling commit cecd542cdcc131418c92486111c82a1bb642640a
44​dangling commit 9497cb1c468bcf76bb64e915e379f35ba2a2e715
45​---
46​/srv/gerrit/git/phabricator/extensions.git
47​dangling commit 2f01073c50363f0891cf32257d86751bc407cc91
48​dangling commit 3323f6b5fb04286a03ec2362ccd5dd1c5a720fae
49​dangling commit 60159fc32e82b96d29422599ec4d5a6bffc883f4
50​---
51​/srv/gerrit/git/phabricator/test.git
52​dangling commit fc672b5630b2f210d951d7543e10d00dba94f4c4
53​---
54​/srv/gerrit/git/wikimedia/bots/jouncebot.git
55​dangling commit eb158a43cac489cc9ed9eaeb1a0416b9d1ead87c
56​dangling commit 6daf8767a28ccce0013169cd164aafa0aa1f1d2d
57​---
58​/srv/gerrit/git/wikimedia/portals.git
59​dangling blob 9c9b4d803946de7e442d45c8b95eccf50cf2a69e
60​dangling blob d3c280451171b0d09fb8306004b782bd520f0e46
61​dangling commit 17457dc1cdbc58ac9853784c8913a0f6d0122983
62​dangling blob 6ccc685c635022c87a1b7607827d630514737fce
63​dangling blob 8ad8247bf7b8da8b98105a53789081f826b1d9d7
64​dangling commit 9759ad4feebac775de96b5161c97a7d8c5d30c96
65​dangling blob 205f4de11c9589e2e41e16ee2c99a571d2f909ee
66​dangling blob 19e6328773c93eff62fd240a099b7af26db5d7a1
67​---
68​/srv/gerrit/git/wikimedia/TransparencyReport-private.git
69​dangling commit d3d235f24e6c0948c1c3207dd6c46fd6cd7723e8
70​dangling commit 27131330068753884e1108b0f35fa86184613b17
71​---
72​/srv/gerrit/git/wikimedia/fundraising/tools.git
73​dangling commit f92084c720520ba83c500c24cc5ac91a5c6dfde3
74​dangling blob 26a8b36fb0285439648022c87297cb5482fd72ff
75​dangling blob cdaa76b76e30aed27b11651fff34c0c297b22c81
76​dangling commit acf3d40aa9f6be92e8df5966af8104b881973eb5
77​dangling commit 6cb58a1b352ad237cd6dfff1bd21621df9d2fa82
78​---
79​/srv/gerrit/git/wikimedia/fundraising/civicrm-buildkit/vendor/totten/amp.git
80​dangling commit 8e527410c1daf0315858b01eb5faa03ea717307a
81​---
82​/srv/gerrit/git/wikimedia/fundraising/crm/civicrm.git
83​dangling commit 9a07380368bcc7373cb7eab790ef4ca8990d1547
84​dangling commit f607a0ba12be9da7f73c5337c3f1536d8ef2e410
85​dangling commit 5f0c983142110d979bf7733b819be932a6805cac
86​dangling commit 251364bd0f49d9daffd3b8f8c1407f96e7e6f4e6
87​dangling commit cd1d64595e3a1281f7e2d1233814d332135d4110
88​dangling commit 8124d01de4618398574c71e7d797080231ae637f
89​dangling commit ee2a9c921b012e673bc2f635689cd7aa0d17887c
90​dangling commit 3c2c9a630e9eb5f9015120aaf066ff5b746ac233
91​dangling commit 202f920cb742d1cd5e7706ccc1dea8abc902dbf0
92​dangling commit ab314ec6c761fa996e5b43530dadcd1e1b6def51
93​dangling commit d631988a1311d3708dd911c64888f7141d81182d
94​dangling commit 8b33e0aad3b293be297180b8de3ab4a8afd3e25e
95​dangling commit af41a0b8419fe0987236e352ac4300f8e95990e8
96​dangling commit 8f4aa0c7d2d93ece2945f8146804ab2421306ef2
97​dangling commit 1e69f4efbff2c3aa94f3df8a465af21cb01ba9ea
98​dangling commit c16fe0c197dc874a63d8253c931b0ae1447781cf
99​dangling commit 527ab6adf2650ec69a1a43725314635246529153
100​dangling commit 4e82461d1db17f9b3dda76c7bf5256f9f1817453
101​dangling commit f2824463ae9207dc4d2369cae55df5c8b32e340b
102​dangling commit 0c83182336e0c7e56a31885c07b3fdaea4bcc185
103​dangling commit 8ca0160d4dec522639a0dc9efea2c3f08839fdc8
104​dangling commit a4a2503a7f42220e73df74c856ed5d2cb7f8560f
105​dangling commit 9fa508eca46446bbb638b70f0e29c5119674d0d8
106​dangling commit d7a5e48cc67b527d9bc3eb60f4ef7a73084a61e4
107​dangling commit 0eaa26f0e3269ea58267414473947b49decb59f4
108​dangling commit 71d4ae9a2ae8fe5717d9567bf5fd31b882b5e949
109​dangling commit 77d6209f186b2dd2754340216023749b5cca3f76
110​dangling commit 41db10c26616b6c08a4d530c81497928ee02acb2
111​dangling commit e1defe026154e1425e26c4a8a6db5d06e7227086
112​dangling commit 5cdf780eff80e3cd0fd22d218319a0c067886eae
113​dangling commit 51e108db5b11dcdcd19e0c006dc5adfeafe5f963
114​dangling commit 58e9009f5173e316f546fb017111e175b270f1a8
115​dangling commit 350795ab882c4a4886e6629942998a10712ecf76
116​dangling commit 750bd14265af41adc8ceb177b12f3cda0739dd2d
117​dangling commit 7b15759dd4913907ec88d9b6b1dc09f197f6fc78
118​dangling commit 3326fb2f0b645a1e2b5dbcccc06dbd69b47ea14c
119​dangling commit 7a2829d8df76bf7bce1d056cd0600c5beabad62e
120​dangling commit 322b612dde342d019ce7db633dda931315225d49
121​dangling commit a13911e7b330816174ff9e306f8fd7d42db8f5be
122​dangling commit 454c7f1b0691a0ed9ac8daadc071745d58cfde4e
123​dangling commit 1852ed1689ad7438736a46d073e3c978180fc285
124​dangling commit 46574d90f5461e912c7f4239897c3848e6fadf2b
125​dangling commit 156001c9b90cb145900cacb3a6c58d41402d2d07
126​dangling commit bf7449126c5d7a687756dab8822ab1a4493cf3f4
127​dangling commit f27eff8a8b1acb545f0f005b1894b886f1763ae4
128​dangling commit 028013b76efc5252375a7f603db3f5a914454d26
129​dangling commit fb81d5abaf5ae246c6b300c8c8b0a3aa41a93108
130​dangling commit 409a2dde36b3d9d64b1ceae7305f89d459f20974
131​dangling commit 9c9f3be1b5fe564b6155c960fb21255ba27ec4db
132​dangling commit 31c61fb3c3e016ae14a46db9c5bf489ab5fc0137
133​dangling commit b5cec3dfb7ffcf4734c18ddf114ff74dd034fbf7
134​dangling commit 08f1a391811a4ff3053e8e1f804818fbf252a528
135​dangling commit f7f631c0231513e2e0e8e63fb84b7a42ed9e533b
136​---
137​/srv/gerrit/git/wikimedia/fundraising/crm/drupal.git
138​dangling commit 29b438bf39b6704ab58f560fc4803041b597fddb
139​---
140​/srv/gerrit/git/wikimedia/fundraising/SmashPig.git
141​dangling commit 1f903bdd065a647070ae112bfab4edac23ec241a
142​dangling blob 94b9c57055c4ba790833e5c59bd8ea9d634842db
143​dangling blob 0d638874d86dbd68ab8192ab7d4084dd915c9132
144​dangling blob a9e826699538d758f025c094b859727ae474df1b
145​dangling blob 4070687689acab4997f2d55c90a4647848835ce8
146​---
147​/srv/gerrit/git/wikimedia/fundraising/crm.git
148​dangling commit 34079230f6279d45b2129bce5b120d79e1475dc8
149​dangling commit b21caa18e08cd2e2853153ab7404bfc2a31e2f19
150​dangling commit d3289e9c84aae5453f3a903177818e873dba9fd1
151​dangling blob ac34f2da506bd719f321ecce4916b5990ebde6c2
152​dangling commit e33ab0a6b045a61677a11fb7e2301d4692b0215b
153​dangling commit 4646243563b52473c7a973416364539f870a7a01
154​dangling commit d547a0b68209469e7650cabd3346cee54991a4c8
155​dangling commit d2739c700a3d3e90657c99e814bce583b4001c4c
156​dangling blob 857f383cd5f315483e48015039c8faf36921ea54
157​dangling commit 8289a4f4564ce6c9c0a3c49cc22931d5a2c3d0e2
158​dangling blob 91a202e2876050df32dc49d828b8698193854999
159​dangling blob cba7eede6119058aeff4b2e913737cce11074562
160​dangling commit 46a948b80b258055f5db0c38e1501b66d7b755ba
161​dangling commit 2ab5c022f1c47054c3be26c31efc2d1a8bd45e06
162​dangling commit eab514f255b78ec0c34d9e924d9f6bba3495ff62
163​dangling commit 8bbd3c529aa91256bf2a4ef4259dfd1e716a5da2
164​dangling commit 19c61ae250bfed0eeceb72a912590129e4518958
165​dangling commit 1acee6cb8c569cfc7052981a800deb2aabb0f28d
166​dangling commit 64e926c429f72f3e50ba5a01cec807238c085797
167​dangling commit fae9880058091ff2029c5204e5045b6433ec5b29
168​dangling commit 00f840529335946b0cd078293f3262440ab00fd7
169​dangling blob 0ffa9adfe1e015fc3d7e4d1634b28b826f746680
170​dangling commit d901398ed0cf3262fdb2efcbfdc6b040efc32b82
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173​dangling commit 7260239008c935975d3339f71a999308d6001da1
174​dangling commit cc64cf6c81e013da032d34ba49dbc8243a76e993
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183​dangling commit 10fb5d995d9fcbe7cbfba1cec7b578738a46048f
184​---
185​/srv/gerrit/git/mediawiki/skins/DeepSea.git
186​dangling commit d219478b6dd578199fb668dc47f1fb4452160d99
187​---
188​/srv/gerrit/git/mediawiki/skins/CustomPage.git
189​dangling commit 1ce276d1e92121f4eec2925f2cd8e4ac6ba840fb
190​---
191​/srv/gerrit/git/mediawiki/skins/WoOgLeShades.git
192​dangling commit e986dc38ae0d25304f6b04c0be31c05468c2a20a
193​---
194​/srv/gerrit/git/mediawiki/skins/apex.git
195​dangling commit 0dc3a5eae54b51d8859efce57c7a82afb294adba
196​---
197​/srv/gerrit/git/mediawiki/skins/Refreshed.git
198​dangling commit 5971f610e92c0c9a9a46e393cdfa85d5e57c8eb3
199​---
200​/srv/gerrit/git/mediawiki/skins/Nostalgia.git
201​dangling commit a6413b3a20cb68f11cebe6ecc68c018ab7110a27
202​---
203​/srv/gerrit/git/mediawiki/skins/HasSomeColours.git
204​dangling commit 11230d26a533076a2cbba2dcccfe172cee5917f7
205​---
206​/srv/gerrit/git/mediawiki/vagrant.git
207​dangling blob c00e626afe8580d0f71b527a01d0d5a14a704b8a
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Mentioned in SAL (#wikimedia-operations) [2016-11-28T02:05:03Z] <Reedy> fixed localisationupdate clone of mw core on tin due to T151676

Mentioned in SAL (#wikimedia-operations) [2016-11-28T15:13:04Z] <addshore> fixed /srv/mediawiki-staging/php-1.29.0-wmf.3 clone of mw core on tin due to T151676

A git pull on tin for ​operations/dumps.git worked just fine. Maybe knock that off the list?

demon lowered the priority of this task from High to Normal.Nov 29 2016, 4:12 AM

So, pretty sure this only affects core and maybe extensions that get wmf branches. Best we can tell, the missing sha1s are for objects that only existed in old wmf.N branches that were later deleted. I'm also pretty sure this only happens for auto-submodule-update commits.

The official workaround is git remote prune origin (repeat for "gerrit" remote, if you have one).

This is a "new" issue because we've only been doing auto gc for a couple of weeks since we updated to 2.12 from 2.8.

I'm not worried about losing objects from intact branches (master, REL1_xx). The upgrade to the new jgit should avoid this from happening again, I think.

Change 323655 merged by Dzahn:
gerrit: Disable git gc as source of breakages

https://gerrit.wikimedia.org/r/323655

hashar added a subscriber: hashar.

T152801 is the same issue for mediawiki/vagrant.git which has bunch of deleted wmf/* branches still referencing somehow missing commits.

Actually this looks like it is fixed in jgit 4.6 which gerrit 2.14 should be using when upstream realease gerrit 2.14.

https://github.com/eclipse/jgit/commit/4ddd4a3d1b38ecf908978d596531ac9cdc7544dd

Paladox moved this task from Backlog to Patch merged upstream on the Upstream board.

This should hopefully be fixed in gerrit 2.14. Though I doint know if there will be permenant damage. We have switch gc off so this problem won't happen again.

@hashar hi this task T153079 has nothing to do with the task here as the problem there was that the branch was deleted and then recreated with different commits and + the submodule repo needed updating which was the cause of the porblem.

This https://github.com/eclipse/jgit/commit/4ddd4a3d1 looks like a fix for this. Fixed in gerrit 2.13.7+.

This may have been caused by a jgit cache issue rather then gc, see https://groups.google.com/forum/m/#!topic/repo-discuss/N5bIo4VlPGU (I described us having a similar problem which we found it was gc. Looks like it is not gc)

This jgit cache issue should be fixed in gerrit 2.13.7 release.

Change 356824 had a related patch set (by Paladox) published:
[operations/puppet@production] Gerrit: Set gc.auto and gc.autopacklimit to 0 in ~/.gitconfig

https://gerrit.wikimedia.org/r/356824

Change 356824 merged by Dzahn:
[operations/puppet@production] Gerrit: Set gc.auto and gc.autopacklimit to 0 in ~/.gitconfig

https://gerrit.wikimedia.org/r/356824

demon closed this task as Resolved.Jun 6 2017, 10:04 PM

This shouldn't actually be a problem anymore.

Paladox removed a subscriber: gerritbot.