E STORAGE [WTCheckpointThread] WiredTiger error (5)

Hello Everyone,

I get some error as below and due to this mongod instance was crashed.

2022-05-21T05:31:35.557+0000 E STORAGE [WTCheckpointThread] WiredTiger error (5) [1653111095:442272][11024:0x7f0c7bbe5700], file:index-35–2958543832295789442.wt, WT_SESSION.checkpoint: __posix_sync, 99: /var/lib/mongo/index-35–2958543832295789442.wt: handle-sync: fdatasync: Input/output error Raw: [1653111095:442272][11024:0x7f0c7bbe5700], file:index-35–2958543832295789442.wt, WT_SESSION.checkpoint: __posix_sync, 99: /var/lib/mongo/index-35–2958543832295789442.wt: handle-sync: fdatasync: Input/output error

2022-05-21T05:31:35.562+0000 E STORAGE [WTCheckpointThread] WiredTiger error (-31804) [1653111095:562169][11024:0x7f0c7bbe5700], file:index-35–2958543832295789442.wt, WT_SESSION.checkpoint: __wt_panic, 494: the process must exit and restart: WT_PANIC: WiredTiger library panic Raw: [1653111095:562169][11024:0x7f0c7bbe5700], file:index-35–2958543832295789442.wt, WT_SESSION.checkpoint: __wt_panic, 494: the process must exit and restart: WT_PANIC: WiredTiger library panic
2022-05-21T05:31:35.563+0000 F - [WTCheckpointThread] Fatal Assertion 50853 at src/mongo/db/storage/wiredtiger/wiredtiger_util.cpp 420
2022-05-21T05:31:35.563+0000 F - [WTCheckpointThread]

***aborting after fassert() failure

2022-05-21T05:31:35.605+0000 F - [WTCheckpointThread] Got signal: 6 (Aborted).
0x55e23ede6c21 0x55e23ede5e39 0x55e23ede631d 0x7f0c87524600 0x7f0c8717d3b7 0x7f0c8717eaa8 0x55e23d39f28b 0x55e23d4a2c76 0x55e23d50d741 0x55e23d325ed1 0x55e23d3262eb 0x55e23d4e0243 0x55e23d5de894 0x55e23d520559 0x55e23d52147b 0x55e23d5069ba 0x55e23d4800d6 0x55e23e831c31 0x55e23eef6630 0x7f0c8751ce75 0x7f0c872459bd
----- BEGIN BACKTRACE -----
{“backtrace”:[{“b”:“55E23C975000”,“o”:“2471C21”,“s”:"_ZN5mongo15printStackTraceERSo"},{“b”:“55E23C975000”,“o”:“2470E39”},{“b”:“55E23C975000”,“o”:“247131D”},{“b”:“7F0C87515000”,“o”:“F600”},{“b”:“7F0C87147000”,“o”:“363B7”,“s”:“gsignal”},{“b”:“7F0C87147000”,“o”:“37AA8”,“s”:“abort”},{“b”:“55E23C975000”,“o”:“A2A28B”,“s”:"_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj"},{“b”:“55E23C975000”,“o”:“B2DC76”},{“b”:“55E23C975000”,“o”:“B98741”},{“b”:“55E23C975000”,“o”:“9B0ED1”,“s”:"__wt_err_func"},{“b”:“55E23C975000”,“o”:“9B12EB”,“s”:"__wt_panic"},{“b”:“55E23C975000”,“o”:“B6B243”},{“b”:“55E23C975000”,“o”:“C69894”},{“b”:“55E23C975000”,“o”:“BAB559”},{“b”:“55E23C975000”,“o”:“BAC47B”,“s”:"__wt_txn_checkpoint"},{“b”:“55E23C975000”,“o”:“B919BA”},{“b”:“55E23C975000”,“o”:“B0B0D6”,“s”:"_ZN5mongo18WiredTigerKVEngine26WiredTigerCheckpointThread3runEv"},{“b”:“55E23C975000”,“o”:“1EBCC31”,“s”:"_ZN5mongo13BackgroundJob7jobBodyEv"},{“b”:“55E23C975000”,“o”:“2581630”},{“b”:“7F0C87515000”,“o”:“7E75”},{“b”:“7F0C87147000”,“o”:“FE9BD”,“s”:“clone”}],“processInfo”:{ “mongodbVersion” : “4.0.16”, “gitVersion” : “2a5433168a53044cb6b4fa8083e4cfd7ba142221”, “compiledModules” : [], “uname” : { “sysname” : “Linux”, “release” : “4.9.51-10.52.amzn1.x86_64”, “version” : “#1 SMP Fri Sep 29 01:16:19 UTC 2017”, “machine” : “x86_64” }, “somap” : [ { “b” : “55E23C975000”, “elfType” : 3, “buildId” : “5DD743B8BBEB16201177D6D09046399B64F5E029” }, { “b” : “7FFDC0775000”, “elfType” : 3, “buildId” : “E1FD0678C5C561D462A1DAA29BD08CC5361EF117” }, { “b” : “7F0C8893F000”, “path” : “/usr/lib64/libcurl.so.4”, “elfType” : 3, “buildId” : “9E7C58F4A4EE9752AF068429BA3DB14397639056” }, { “b” : “7F0C88725000”, “path” : “/lib64/libresolv.so.2”, “elfType” : 3, “buildId” : “AE1FDB1B0712ABF27B24A3F0E983619A30981750” }, { “b” : “7F0C882C6000”, “path” : “/lib64/libcrypto.so.10”, “elfType” : 3, “buildId” : “3270D2720328EEC2846C4B0D993582A0F657F54B” }, { “b” : “7F0C88055000”, “path” : “/lib64/libssl.so.10”, “elfType” : 3, “buildId” : “183215EA0DA6EE9C80A1E3A3319EC2905D1BF6E0” }, { “b” : “7F0C87E51000”, “path” : “/lib64/libdl.so.2”, “elfType” : 3, “buildId” : “D8859C267836C8AF28BBB238819141B6BF34F8D9” }, { “b” : “7F0C87C49000”, “path” : “/lib64/librt.so.1”, “elfType” : 3, “buildId” : “DB30FAB7C82FF7E06EE4913B0D3AB02C51DC0530” }, { “b” : “7F0C87947000”, “path” : “/lib64/libm.so.6”, “elfType” : 3, “buildId” : “19CC4E1B82AD44838E8DFD1FF893CA0CDAB7A5F5” }, { “b” : “7F0C87731000”, “path” : “/lib64/libgcc_s.so.1”, “elfType” : 3, “buildId” : “AC58019512A5359B077D2610DEA4AD6CF14CAC53” }, { “b” : “7F0C87515000”, “path” : “/lib64/libpthread.so.0”, “elfType” : 3, “buildId” : “E45DFDE9B88CABE002BE746AD486F620DE2B3E54” }, { “b” : “7F0C87147000”, “path” : “/lib64/libc.so.6”, “elfType” : 3, “buildId” : “75FE5BEDAD7802FF4A0268752CB4B4FFB293D1DC” }, { “b” : “7F0C88BC6000”, “path” : “/lib64/ld-linux-x86-64.so.2”, “elfType” : 3, “buildId” : “FD30DCC79F68A409A7C742A6943C16AE02E52986” }, { “b” : “7F0C86F21000”, “path” : “/usr/lib64/libnghttp2.so.14”, “elfType” : 3, “buildId” : “903C20D899C962C2E93B006E3BB7172C83D8ACF4” }, { “b” : “7F0C86D00000”, “path” : “/usr/lib64/libidn2.so.0”, “elfType” : 3, “buildId” : “5235BD50D3FB450683328735B730532020DEE4BF” }, { “b” : “7F0C86AD8000”, “path” : “/usr/lib64/libssh2.so.1”, “elfType” : 3, “buildId” : “E03CF776B39054AC3B2EA2AB15B161A858B5732C” }, { “b” : “7F0C86863000”, “path” : “/usr/lib64/libpsl.so.0”, “elfType” : 3, “buildId” : “09BFE69665CFEEC18F81D8C4A971DCA29310186C” }, { “b” : “7F0C86615000”, “path” : “/usr/lib64/libgssapi_krb5.so.2”, “elfType” : 3, “buildId” : “1BE9E6309ED365E35806E13FA9E23350D71F2513” }, { “b” : “7F0C8632E000”, “path” : “/usr/lib64/libkrb5.so.3”, “elfType” : 3, “buildId” : “9EE23694485D684651195C7B51766E47D0CB95E3” }, { “b” : “7F0C860FC000”, “path” : “/usr/lib64/libk5crypto.so.3”, “elfType” : 3, “buildId” : “FD5974E4861D56DFFFFC8BF5DB35E74B1C20ABD5” }, { “b” : “7F0C85EF9000”, “path” : “/usr/lib64/libcom_err.so.2”, “elfType” : 3, “buildId” : “5C01209C5AE1B1714F19B07EB58F2A1274B69DC8” }, { “b” : “7F0C85CA7000”, “path” : “/lib64/libldap-2.4.so.2”, “elfType” : 3, “buildId” : “97F36EE026428345EEB18EE7F9EFB048ADB415A7” }, { “b” : “7F0C85A98000”, “path” : “/lib64/liblber-2.4.so.2”, “elfType” : 3, “buildId” : “BBE520FB0B4F67D5F708D233C31E7047B759068D” }, { “b” : “7F0C85882000”, “path” : “/lib64/libz.so.1”, “elfType” : 3, “buildId” : “89C6AF118B6B4FB6A73AE1813E2C8BDD722956D1” }, { “b” : “7F0C8556C000”, “path” : “/usr/lib64/libunistring.so.0”, “elfType” : 3, “buildId” : “2B090A6860553944846E3C227B6AD12F279B304F” }, { “b” : “7F0C851F6000”, “path” : “/usr/lib64/libicuuc.so.50”, “elfType” : 3, “buildId” : “06AB750458E6948B6F40F05E705996DB44ADDF9B” }, { “b” : “7F0C84FE7000”, “path” : “/usr/lib64/libkrb5support.so.0”, “elfType” : 3, “buildId” : “1B55330B231D45AF433F7D9DCA507C5FB0609780” }, { “b” : “7F0C84DE4000”, “path” : “/lib64/libkeyutils.so.1”, “elfType” : 3, “buildId” : “37A58210FA50C91E09387765408A92909468D25B” }, { “b” : “7F0C84BC9000”, “path” : “/usr/lib64/libsasl2.so.2”, “elfType” : 3, “buildId” : “354560FFC93703E5A80EEC8C66DF9E59DA335001” }, { “b” : “7F0C8496D000”, “path” : “/usr/lib64/libssl3.so”, “elfType” : 3, “buildId” : “D6B37F82A6D0A2DC428F305A2F5D9D78DB60D488” }, { “b” : “7F0C84746000”, “path” : “/usr/lib64/libsmime3.so”, “elfType” : 3, “buildId” : “2FF9EB779ACEAB03691997491A29D7275013D770” }, { “b” : “7F0C84419000”, “path” : “/usr/lib64/libnss3.so”, “elfType” : 3, “buildId” : “19D59FF9A54C790463BCD0349B0D78A4B8E1304E” }, { “b” : “7F0C841E9000”, “path” : “/usr/lib64/libnssutil3.so”, “elfType” : 3, “buildId” : “353A34D6411C8F45DB54E122B06E97EF6AEFD4F9” }, { “b” : “7F0C83FE5000”, “path” : “/lib64/libplds4.so”, “elfType” : 3, “buildId” : “D835EB19EC07E13AECBE3E80652846DAB04553CE” }, { “b” : “7F0C83DE0000”, “path” : “/lib64/libplc4.so”, “elfType” : 3, “buildId” : “668B5E4DEDFB2CABFEE75B097CC04CBBF8EC231D” }, { “b” : “7F0C83BA2000”, “path” : “/lib64/libnspr4.so”, “elfType” : 3, “buildId” : “8C8278A9557AA5D7942C94992BE85C2E73EA358B” }, { “b” : “7F0C825CF000”, “path” : “/usr/lib64/libicudata.so.50”, “elfType” : 3, “buildId” : “291EDB545286F945CDE3AF6F5CF24FA2F53FDDDA” }, { “b” : “7F0C8224C000”, “path” : “/usr/lib64/libstdc++.so.6”, “elfType” : 3, “buildId” : “699868CB2BF35D0936C954AF8AD53A001D6690EE” }, { “b” : “7F0C8202B000”, “path” : “/usr/lib64/libselinux.so.1”, “elfType” : 3, “buildId” : “F5054DC94443326819FBF3065CFDF5E4726F57EE” }, { “b” : “7F0C81DF4000”, “path” : “/lib64/libcrypt.so.1”, “elfType” : 3, “buildId” : “CA95D3723C3A72A75EAA6448328B06470DE7D1CC” }, { “b” : “7F0C81BF2000”, “path” : “/lib64/libfreebl3.so”, “elfType” : 3, “buildId” : “6C6DA5F0ECDD84E81C6A44036EBACD7AA77707EB” } ] }}
mongod(_ZN5mongo15printStackTraceERSo+0x41) [0x55e23ede6c21]
mongod(+0x2470E39) [0x55e23ede5e39]
mongod(+0x247131D) [0x55e23ede631d]
libpthread.so.0(+0xF600) [0x7f0c87524600]
libc.so.6(gsignal+0x37) [0x7f0c8717d3b7]
libc.so.6(abort+0x148) [0x7f0c8717eaa8]
mongod(_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj+0x0) [0x55e23d39f28b]
mongod(+0xB2DC76) [0x55e23d4a2c76]
mongod(+0xB98741) [0x55e23d50d741]
mongod(__wt_err_func+0x90) [0x55e23d325ed1]
mongod(__wt_panic+0x39) [0x55e23d3262eb]
mongod(+0xB6B243) [0x55e23d4e0243]
mongod(+0xC69894) [0x55e23d5de894]
mongod(+0xBAB559) [0x55e23d520559]
mongod(__wt_txn_checkpoint+0x1DB) [0x55e23d52147b]
mongod(+0xB919BA) [0x55e23d5069ba]
mongod(_ZN5mongo18WiredTigerKVEngine26WiredTigerCheckpointThread3runEv+0x356) [0x55e23d4800d6]
mongod(_ZN5mongo13BackgroundJob7jobBodyEv+0x131) [0x55e23e831c31]
mongod(+0x2581630) [0x55e23eef6630]
libpthread.so.0(+0x7E75) [0x7f0c8751ce75]
libc.so.6(clone+0x6D) [0x7f0c872459bd]
----- END BACKTRACE -----

Hi @Aditya_Sharma3 and welcome in the MongoDB Community :muscle: !

https://jira.mongodb.org/browse/SERVER-49317

You should try a repair operation from what I’m reading in this ticket.

Hi @MaBeuLux88,

Thanks for your reply, If I go for the repair option, what will be the impact of that on the production server, However after restart the mongo instance is running fine.

Do we still need to go for the repair option?

If it’s running fine now then don’t do a repair.
Repair only tries to restores corrupted data. If it’s running now, it means you don’t have any corrupted data in your cluster at the moment.
The impact would be that it could save your production env if it was completely stopped and couldn’t be restarted at all because of some corrupted data due to an incorrect stop.