[SERVER-37419] Suddenly could not start - Failed with result 'core-dump' Created: 02/Oct/18  Updated: 04/Oct/18  Resolved: 03/Oct/18

Status: Closed
Project: Core Server
Component/s: None
Affects Version/s: 4.0.2
Fix Version/s: None

Type: Bug Priority: Major - P3
Reporter: Dong Nguyen Assignee: Nick Brewer
Resolution: Done Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Attachments: PNG File mongo fail at starting.png     PNG File system info.png    
Operating System: ALL
Participants:

 Description   

Today when I start my computer, MongoDB does't not start any more. Manually runing its related systemd service (I would describe later), the error logs said:

sudo systemctl status mongo.service 
● mongo.service - MongoDB
   Loaded: loaded (/etc/systemd/system/mongo.service; enabled; vendor preset: enabled)
   Active: failed (Result: core-dump) since Tue 2018-10-02 09:49:41 +07; 424ms ago
  Process: 6022 ExecStart=/storage/mongodb/bin/mongod --dbpath /storage/mongodb/data (code=dumped, signal=SEGV)
 Main PID: 6022 (code=dumped, signal=SEGV)Oct 02 09:49:41 u1804d mongod[6022]:  mongod(+0xAB80BD) [0x5568f56e30bd]
Oct 02 09:49:41 u1804d mongod[6022]:  mongod(_ZN5mongo23initializeStorageEngineEPNS_14ServiceContextENS_22StorageEngineInitFlagsE+0xBF5) [0x5568f5d2d0b5]
Oct 02 09:49:41 u1804d mongod[6022]:  mongod(+0x988F56) [0x5568f55b3f56]
Oct 02 09:49:41 u1804d mongod[6022]:  mongod(_ZN5mongo11mongoDbMainEiPPcS1_+0x873) [0x5568f5699f73]
Oct 02 09:49:41 u1804d mongod[6022]:  mongod(main+0x9) [0x5568f5630f99]
Oct 02 09:49:41 u1804d mongod[6022]:  libc.so.6(__libc_start_main+0xE7) [0x7f6ac0835b97]
Oct 02 09:49:41 u1804d mongod[6022]:  mongod(_start+0x2A) [0x5568f5698a2a]
Oct 02 09:49:41 u1804d mongod[6022]: -----  END BACKTRACE  -----
Oct 02 09:49:41 u1804d systemd[1]: mongo.service: Main process exited, code=dumped, status=11/SEGV
Oct 02 09:49:41 u1804d systemd[1]: mongo.service: Failed with result 'core-dump'.

If I try to run it directy, it says:

/storage/mongodb/bin/mongod --dbpath /storage/mongodb/data
2018-10-02T09:53:15.992+0700 I CONTROL  [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] MongoDB starting : pid=6111 port=27017 dbpath=/storage/mongodb/data 64-bit host=u1804d
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] db version v4.0.2
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] git version: fc1573ba18aee42f97a3bb13b67af7d837826b47
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.1.0g  2 Nov 2017
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] allocator: tcmalloc
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] modules: none
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] build environment:
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten]     distmod: ubuntu1804
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten]     distarch: x86_64
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten]     target_arch: x86_64
2018-10-02T09:53:15.999+0700 I CONTROL  [initandlisten] options: { storage: { dbPath: "/storage/mongodb/data" } }
2018-10-02T09:53:15.999+0700 I STORAGE  [initandlisten] Detected data files in /storage/mongodb/data created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2018-10-02T09:53:15.999+0700 I STORAGE  [initandlisten] 
2018-10-02T09:53:15.999+0700 I STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2018-10-02T09:53:15.999+0700 I STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2018-10-02T09:53:15.999+0700 I STORAGE  [initandlisten] wiredtiger_open config: create,cache_size=3436M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),statistics_log=(wait=0),verbose=(recovery_progress),
2018-10-02T09:53:16.683+0700 I STORAGE  [initandlisten] WiredTiger message [1538448796:683576][6111:0x7f3b99134a00], txn-recover: Main recovery loop: starting at 487/256
2018-10-02T09:53:16.683+0700 I STORAGE  [initandlisten] WiredTiger message [1538448796:683829][6111:0x7f3b99134a00], txn-recover: Recovering log 487 through 488
2018-10-02T09:53:16.760+0700 I STORAGE  [initandlisten] WiredTiger message [1538448796:760168][6111:0x7f3b99134a00], txn-recover: Recovering log 488 through 488
2018-10-02T09:53:16.807+0700 I STORAGE  [initandlisten] WiredTiger message [1538448796:807688][6111:0x7f3b99134a00], txn-recover: Set global recovery timestamp: 0
2018-10-02T09:53:17.026+0700 I RECOVERY [initandlisten] WiredTiger recoveryTimestamp. Ts: Timestamp(0, 0)
2018-10-02T09:53:17.063+0700 E STORAGE  [initandlisten] WiredTiger error (2) [1538448797:63312][6111:0x7f3b99134a00], file:collection-30-2623056915678715117.wt, WT_SESSION.open_cursor: __posix_open_file, 711: /storage/mongodb/data/collection-30-2623056915678715117.wt: handle-open: open: No such file or directory Raw: [1538448797:63312][6111:0x7f3b99134a00], file:collection-30-2623056915678715117.wt, WT_SESSION.open_cursor: __posix_open_file, 711: /storage/mongodb/data/collection-30-2623056915678715117.wt: handle-open: open: No such file or directory
2018-10-02T09:53:17.063+0700 E STORAGE  [initandlisten] no cursor for uri: table:collection-30-2623056915678715117
2018-10-02T09:53:17.063+0700 F -        [initandlisten] Invalid access at address: 0x58
2018-10-02T09:53:17.072+0700 F -        [initandlisten] Got signal: 11 (Segmentation fault).
 0x55cb0a04fae1 0x55cb0a04ecf9 0x55cb0a04f366 0x7f3b977ef890 0x55cb08772418 0x55cb0877daad 0x55cb0876488c 0x55cb088e8108 0x55cb088e2885 0x55cb088e354d 0x55cb0874f0bd 0x55cb08d990b5 0x55cb0861ff56 0x55cb08705f73 0x55cb0869cf99 0x7f3b9740db97 0x55cb08704a2a
----- BEGIN BACKTRACE -----
{"backtrace":[{"b":"55CB07C97000","o":"23B8AE1","s":"_ZN5mongo15printStackTraceERSo"},{"b":"55CB07C97000","o":"23B7CF9"},{"b":"55CB07C97000","o":"23B8366"},{"b":"7F3B977DD000","o":"12890"},{"b":"55CB07C97000","o":"ADB418","s":"_ZN5mongo31WiredTigerRecordStoreCursorBase4nextEv"},{"b":"55CB07C97000","o":"AE6AAD","s":"_ZN5mongo21WiredTigerRecordStore19postConstructorInitEPNS_16OperationContextE"},{"b":"55CB07C97000","o":"ACD88C","s":"_ZN5mongo18WiredTigerKVEngine21getGroupedRecordStoreEPNS_16OperationContextENS_10StringDataES3_RKNS_17CollectionOptionsENS_8KVPrefixE"},{"b":"55CB07C97000","o":"C51108","s":"_ZN5mongo26KVDatabaseCatalogEntryBase14initCollectionEPNS_16OperationContextERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb"},{"b":"55CB07C97000","o":"C4B885","s":"_ZN5mongo15KVStorageEngine11loadCatalogEPNS_16OperationContextE"},{"b":"55CB07C97000","o":"C4C54D","s":"_ZN5mongo15KVStorageEngineC2EPNS_8KVEngineERKNS_22KVStorageEngineOptionsESt8functionIFSt10unique_ptrINS_26KVDatabaseCatalogEntryBaseESt14default_deleteIS8_EENS_10StringDataEPS0_EE"},{"b":"55CB07C97000","o":"AB80BD"},{"b":"55CB07C97000","o":"11020B5","s":"_ZN5mongo23initializeStorageEngineEPNS_14ServiceContextENS_22StorageEngineInitFlagsE"},{"b":"55CB07C97000","o":"988F56"},{"b":"55CB07C97000","o":"A6EF73","s":"_ZN5mongo11mongoDbMainEiPPcS1_"},{"b":"55CB07C97000","o":"A05F99","s":"main"},{"b":"7F3B973EC000","o":"21B97","s":"__libc_start_main"},{"b":"55CB07C97000","o":"A6DA2A","s":"_start"}],"processInfo":{ "mongodbVersion" : "4.0.2", "gitVersion" : "fc1573ba18aee42f97a3bb13b67af7d837826b47", "compiledModules" : [], "uname" : { "sysname" : "Linux", "release" : "4.15.0-33-generic", "version" : "#36-Ubuntu SMP Wed Aug 15 16:00:05 UTC 2018", "machine" : "x86_64" }, "somap" : [ { "b" : "55CB07C97000", "elfType" : 3, "buildId" : "8F771DD94C444FE18EFA84CA664CE8A0E6100804" }, { "b" : "7FFEC19E6000", "path" : "linux-vdso.so.1", "elfType" : 3, "buildId" : "FFC34FD287857F2EB9923E5FF16B73F3BF3F7B39" }, { "b" : "7F3B98CBB000", "path" : "/usr/lib/x86_64-linux-gnu/libcurl.so.4", "elfType" : 3, "buildId" : "33F6C90EE440B440A9ADBD0124BDCAE2FFE7C47B" }, { "b" : "7F3B98AA0000", "path" : "/lib/x86_64-linux-gnu/libresolv.so.2", "elfType" : 3, "buildId" : "390E9CC4C215314B6D8ADE6D6E28F8518418039C" }, { "b" : "7F3B98628000", "path" : "/usr/lib/x86_64-linux-gnu/libcrypto.so.1.1", "elfType" : 3, "buildId" : "DA6345B41E06A9001B5C51DEAF0784BE9D49810D" }, { "b" : "7F3B983BE000", "path" : 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"/usr/lib/x86_64-linux-gnu/libgmp.so.10", "elfType" : 3, "buildId" : "D40EA9B5EC5BC46799E4A412319617BD38BE9341" }, { "b" : "7F3B95214000", "path" : "/usr/lib/x86_64-linux-gnu/libkrb5.so.3", "elfType" : 3, "buildId" : "AFF9A2A2B6ACB066BF450CC4A0772B9DC04299CB" }, { "b" : "7F3B94FE2000", "path" : "/usr/lib/x86_64-linux-gnu/libk5crypto.so.3", "elfType" : 3, "buildId" : "04AADCB371B97A570756D69A0D5B3B0E6737E349" }, { "b" : "7F3B94DDE000", "path" : "/lib/x86_64-linux-gnu/libcom_err.so.2", "elfType" : 3, "buildId" : "9E885FB7F54DA464A3D2A978C71C1178A6EC7512" }, { "b" : "7F3B94BD3000", "path" : "/usr/lib/x86_64-linux-gnu/libkrb5support.so.0", "elfType" : 3, "buildId" : "27A5983855C50A37EFA526BB12EA48CDAE3B5FCA" }, { "b" : "7F3B949B8000", "path" : "/usr/lib/x86_64-linux-gnu/libsasl2.so.2", "elfType" : 3, "buildId" : "ABB7E3F40302E6509DAD1F91DFB1F04B6A5FD072" }, { "b" : "7F3B94777000", "path" : "/usr/lib/x86_64-linux-gnu/libgssapi.so.3", "elfType" : 3, "buildId" : "A1A98DB481968073636BBAECB561A3EA8ED198AE" }, { "b" : "7F3B94448000", "path" : "/usr/lib/x86_64-linux-gnu/libp11-kit.so.0", "elfType" : 3, "buildId" : "8DBD451EA5651283905E16FA7DFA9908688893A3" }, { "b" : "7F3B94235000", "path" : "/usr/lib/x86_64-linux-gnu/libtasn1.so.6", "elfType" : 3, "buildId" : "6036B89A3BB671B32E01464C0C82BFA016186352" }, { "b" : "7F3B94031000", "path" : "/lib/x86_64-linux-gnu/libkeyutils.so.1", "elfType" : 3, "buildId" : "F463E107B099910463BC32E837C73D341A52C27B" }, { "b" : "7F3B93E28000", "path" : "/usr/lib/x86_64-linux-gnu/libheimntlm.so.0", "elfType" : 3, "buildId" : "C2376C5B831991591F1A67B976758185F86896D8" }, { "b" : "7F3B93B9B000", "path" : "/usr/lib/x86_64-linux-gnu/libkrb5.so.26", "elfType" : 3, "buildId" : "69BDEE5FA0FEEDF317308BE850F78761861D520A" }, { "b" : "7F3B938F9000", "path" : "/usr/lib/x86_64-linux-gnu/libasn1.so.8", "elfType" : 3, "buildId" : "315D74995AAA32DE4D15BA25F335066988B1B230" }, { "b" : "7F3B936C3000", "path" : "/usr/lib/x86_64-linux-gnu/libhcrypto.so.4", "elfType" : 3, "buildId" : "6673972A1C24A89EBAFBAE696188A4CB26C6DDEB" }, { "b" : "7F3B934AD000", "path" : "/usr/lib/x86_64-linux-gnu/libroken.so.18", "elfType" : 3, "buildId" : "430827C33259C12248CF44B91A9A9821114376F5" }, { "b" : "7F3B932A5000", "path" : "/usr/lib/x86_64-linux-gnu/libffi.so.6", "elfType" : 3, "buildId" : "3555B5F599C9787DFDDBF9E8DF6F706B9044D985" }, { "b" : "7F3B9307C000", "path" : "/usr/lib/x86_64-linux-gnu/libwind.so.0", "elfType" : 3, "buildId" : "93A0931B1C2818F0EA224CE6FE5E31E84A9B55BB" }, { "b" : "7F3B92E6D000", "path" : "/usr/lib/x86_64-linux-gnu/libheimbase.so.1", "elfType" : 3, "buildId" : "669D4CCE42FA4382796EFFCF0C16F459F4382C4C" }, { "b" : "7F3B92C23000", "path" : "/usr/lib/x86_64-linux-gnu/libhx509.so.5", "elfType" : 3, "buildId" : "4B80C543356EE0AF9039EFE7C9EA1CC1F74C426A" }, { "b" : "7F3B9291A000", "path" : "/usr/lib/x86_64-linux-gnu/libsqlite3.so.0", "elfType" : 3, "buildId" : "9FD7B69263297314C83BB205234E182BD4D8B86A" }, { "b" : "7F3B926E2000", "path" : "/lib/x86_64-linux-gnu/libcrypt.so.1", "elfType" : 3, "buildId" : "810686AF0D5FD350A4FB1CC4B5AFF44A05C102CB" } ] }}
 mongod(_ZN5mongo15printStackTraceERSo+0x41) [0x55cb0a04fae1]
 mongod(+0x23B7CF9) [0x55cb0a04ecf9]
 mongod(+0x23B8366) [0x55cb0a04f366]
 libpthread.so.0(+0x12890) [0x7f3b977ef890]
 mongod(_ZN5mongo31WiredTigerRecordStoreCursorBase4nextEv+0x228) [0x55cb08772418]
 mongod(_ZN5mongo21WiredTigerRecordStore19postConstructorInitEPNS_16OperationContextE+0xCD) [0x55cb0877daad]
 mongod(_ZN5mongo18WiredTigerKVEngine21getGroupedRecordStoreEPNS_16OperationContextENS_10StringDataES3_RKNS_17CollectionOptionsENS_8KVPrefixE+0x27C) [0x55cb0876488c]
 mongod(_ZN5mongo26KVDatabaseCatalogEntryBase14initCollectionEPNS_16OperationContextERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0x568) [0x55cb088e8108]
 mongod(_ZN5mongo15KVStorageEngine11loadCatalogEPNS_16OperationContextE+0xA95) [0x55cb088e2885]
 mongod(_ZN5mongo15KVStorageEngineC2EPNS_8KVEngineERKNS_22KVStorageEngineOptionsESt8functionIFSt10unique_ptrINS_26KVDatabaseCatalogEntryBaseESt14default_deleteIS8_EENS_10StringDataEPS0_EE+0x22D) [0x55cb088e354d]
 mongod(+0xAB80BD) [0x55cb0874f0bd]
 mongod(_ZN5mongo23initializeStorageEngineEPNS_14ServiceContextENS_22StorageEngineInitFlagsE+0xBF5) [0x55cb08d990b5]
 mongod(+0x988F56) [0x55cb0861ff56]
 mongod(_ZN5mongo11mongoDbMainEiPPcS1_+0x873) [0x55cb08705f73]
 mongod(main+0x9) [0x55cb0869cf99]
 libc.so.6(__libc_start_main+0xE7) [0x7f3b9740db97]
 mongod(_start+0x2A) [0x55cb08704a2a]
-----  END BACKTRACE  -----
Segmentation fault (core dumped)

Sorry for the very long stack trace inserted, I hope they make some sense.

For setting up MongoDB, I often do the same steps as below:

  • Create a location for database engine/storage
  • Download .tgz file, extract into its location
  • Create systemd service file to run it as service

I work on Ubuntu 18.04, minimal version with XFCE DE, gcc/g++ v7.3.0

Here is my installation script for MongoDB 4.0.2 that is occurring issue:

export MONGO_VERSION=4.0.2
export MONGO_DOWNLOAD_URL=https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu1804-$MONGO_VERSION.tgz
export MONGO_DIR=/storage/mongodb
sudo apt install libcurl3 openssl
sudo mkdir -p $MONGO_DIR/data
sudo chown ${USER} -R $MONGO_DIR
wget "$MONGO_DOWNLOAD_URL" -O mongo.tar.tgz
tar -zxvf mongo.tar.tgz -C $MONGO_DIR --strip-components=1

And mongo.service in /etc/systemd/system

[Unit]
Description=MongoDB
After=network.target[Service]
User=ndaidong
WorkingDirectory=/storage/mongodb
ExecStart=/storage/mongodb/bin/mongod --dbpath /storage/mongodb/data
Restart=always
RestartSec=500ms
StartLimitInterval=0[Install]
WantedBy=multi-user.target

It works like as charm until today. Nothing special changes in my system.

What's wrong with my configuration? And how to get it works again?

Thank you for any advice.



 Comments   
Comment by Dong Nguyen [ 04/Oct/18 ]

@nick.brewer  it's ok. Thank you so much for taking time on my issue. 

Best Regards,

Dong

Comment by Nick Brewer [ 03/Oct/18 ]

ndaidongGlad to hear you got it working - I'll close this ticket for you. If you want to re-open it later you can comment here.

-Nick

Comment by Dong Nguyen [ 03/Oct/18 ]

@Nick Brewer  No, I didn't phisically remove anything inside that location. However, you might have reason. Yesterday afternoon I've removed the whole folder /storage/mongodb/data, then __ created a new empty one instead, and restarted the service. Lastly it has been working without problem.
So it looks like there was something wrong with one of data files.
Anw, it works for me now. Should I change this issue status?

Comment by Nick Brewer [ 02/Oct/18 ]

ndaidong Have any files been deleted (manually or otherwise) from the dbpath, or any of its subdirectories?

-Nick

Comment by Dong Nguyen [ 02/Oct/18 ]

Hi Nick, thank you for your quick reply. Here is my confirmation:

  • Yes, dbpath is located at another disk. I have a SSD 120GB for OS system, and 1 HDD 500GB that has been splitted to 2 partitions: workspace and storage. All of them are ext4 filesystem.
  • This is my desktop at company, I often shutdown it before leaving office, then start it in the next morning.
  • It's completely native hardware because the resource is quite limit.

Regards,
Dong

Comment by Nick Brewer [ 02/Oct/18 ]

ndaidong Thanks for your report. There's a few initial details we'd like to confirm:

  • Is the dbpath kept on a separate disk? If so, the filesystem / hardware details would be useful.
  • Was this machine restarted or powered off unexpectedly?
  • What is the underlying platform (virtual machine, container, native hardware, etc)?

Thanks,
-Nick

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