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  1. Core Server
  2. SERVER-42208

Permission Denied Error, cannot start DB

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    • Resolution: Done
    • Icon: Minor - P4 Minor - P4
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    • Machine: NVIDIA DGX-1
      Kernel: 4.15.0-54-generic
      OS: Ubuntu 18.04.2 LTS


    Description

      Dear MongoDB community,

       

      I have the following error messages after running my usual startup command:

       

      numactl --interleave=all mongod

      ###############################

      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] MongoDB starting : pid=12762 port=27017 dbpath=/data/db 64-bit host=dgx-server
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] db version v3.6.3
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] git version: 9586e557d54ef70f9ca4b43c26892cd55257e1a5
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] allocator: tcmalloc
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] modules: none
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] build environment:
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] distarch: x86_64
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] target_arch: x86_64
      2019-07-12T17:15:42.293+0200 I CONTROL [initandlisten] options: {}
      2019-07-12T17:15:42.293+0200 I - [initandlisten] Detected data files in /data/db created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
      2019-07-12T17:15:42.293+0200 I STORAGE [initandlisten]
      2019-07-12T17:15:42.293+0200 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
      2019-07-12T17:15:42.293+0200 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
      2019-07-12T17:15:42.293+0200 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=257429M,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),
      2019-07-12T17:15:42.809+0200 E STORAGE [initandlisten] WiredTiger error (13) [1562944542:809396][12762:0x7f4fd45dc0c0], file:WiredTiger.wt, connection: /data/db/WiredTiger.turtle: handle-open: open: Permission denied
      2019-07-12T17:15:42.810+0200 E - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 413
      2019-07-12T17:15:42.810+0200 I STORAGE [initandlisten] exception in initAndListen: Location28595: 13: Permission denied, terminating
      2019-07-12T17:15:42.810+0200 I NETWORK [initandlisten] shutdown: going to close listening sockets...
      2019-07-12T17:15:42.810+0200 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-27017.sock
      2019-07-12T17:15:42.810+0200 I CONTROL [initandlisten] now exiting
      2019-07-12T17:15:42.810+0200 I CONTROL [initandlisten] shutting down with code:100

       

      Since this is a Permission Denied error, I tried sudoing

      sudo numactl --interleave=all mongod

      #############################################

       

      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] MongoDB starting : pid=12772 port=27017 dbpath=/data/db 64-bit host=dgx-server
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] db version v3.6.3
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] git version: 9586e557d54ef70f9ca4b43c26892cd55257e1a5
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.1.1 11 Sep 2018
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] allocator: tcmalloc
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] modules: none
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] build environment:
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] distarch: x86_64
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] target_arch: x86_64
      2019-07-12T17:23:23.845+0200 I CONTROL [initandlisten] options: {}
      2019-07-12T17:23:23.845+0200 I - [initandlisten] Detected data files in /data/db created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
      2019-07-12T17:23:23.845+0200 I STORAGE [initandlisten]
      2019-07-12T17:23:23.845+0200 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
      2019-07-12T17:23:23.845+0200 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
      2019-07-12T17:23:23.845+0200 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=257429M,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),
      2019-07-12T17:23:24.363+0200 E STORAGE [initandlisten] WiredTiger error (-31802) [1562945004:363175][12772:0x7fd8389b30c0], txn-recover: unsupported WiredTiger file version: this build only supports versions up to 2, and the file is version 3: WT_ERROR: non-specific WiredTiger error
      2019-07-12T17:23:24.363+0200 E STORAGE [initandlisten] WiredTiger error (0) [1562945004:363199][12772:0x7fd8389b30c0], txn-recover: WiredTiger is unable to read the recovery log.
      2019-07-12T17:23:24.363+0200 E STORAGE [initandlisten] WiredTiger error (0) [1562945004:363206][12772:0x7fd8389b30c0], txn-recover: This may be due to the log files being encrypted, being from an older version or due to corruption on disk
      2019-07-12T17:23:24.363+0200 E STORAGE [initandlisten] WiredTiger error (0) [1562945004:363211][12772:0x7fd8389b30c0], txn-recover: You should confirm that you have opened the database with the correct options including all encryption and compression options
      2019-07-12T17:23:24.363+0200 E STORAGE [initandlisten] WiredTiger error (-31802) [1562945004:363218][12772:0x7fd8389b30c0], txn-recover: Recovery failed: WT_ERROR: non-specific WiredTiger error
      2019-07-12T17:23:24.364+0200 E - [initandlisten] Assertion: 28595:-31802: WT_ERROR: non-specific WiredTiger error src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 413
      2019-07-12T17:23:24.364+0200 I STORAGE [initandlisten] exception in initAndListen: Location28595: -31802: WT_ERROR: non-specific WiredTiger error, terminating
      2019-07-12T17:23:24.364+0200 I NETWORK [initandlisten] shutdown: going to close listening sockets...
      2019-07-12T17:23:24.364+0200 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-27017.sock
      2019-07-12T17:23:24.364+0200 I CONTROL [initandlisten] now exiting
      2019-07-12T17:23:24.364+0200 I CONTROL [initandlisten] shutting down with code:100

       

      I am sorry but I have no clue what causes this issue since it has been starting up perfectly fine in the past. Perhaps there was a crash on the server that I am co-working with others. Do you know what I can do to resolve this?

      Kind regards

       

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            daniel.hatcher@mongodb.com Danny Hatcher (Inactive)
            tobias.eichinger@tu-berlin.de Tobias Eichinger
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