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ntds.dit databse 49GB in size after windows update

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Hello All,

After installing some updates (12th December) we noticed that one of our AD servers was running out of storage space and RAM utilisation had reached 90% - on investigation we found that the NTDS database was 49GB in size!

Environment:
- 2x Windows Server 2008 R2 running as Virtual Machines; only two domain/DNS servers in the architecture
- Each has 12GB RAM and 8 cores
- 200 AD users, nothing special...
- Tombstone lifetime 180 Day default

So Far:
I have cloned the VMWare servers into an isolated network to play with - I have now spent 6 days on it to no avail (well; I got it down to 16GB with some serious hacks...). Here are some of the key things I have tried in many combinations:
- When the server reboots the RAM utilisation slowly creeps back up to 90% utilisation for lsass.exe
- I have tried offline defrag; this actually makes the database bigger by 2GB...
- Tried 'Semantic Database Analysis' which outputs the following (from this it looks like there are a lot of objects which are deleted but not removed):

Summary:
Active Objects: 5930
Phantoms: 4580
Security descriptor summary:
SD count: 181
Total SD size before single-instancing: 20715440 Kb
Total SD size after single-instancing: 182 Kb

- Tried lowering the 'tombstone lifetime' to 2 days; obviously didn’t change the size after online defrag - after offline defrag the file size reduced to 16GB (on one occasion) and 30GB (on another occasion). So there are definitely a lot of dead objects...

- Running 'esentutl /ms c:\windows\ntds\ntds.dit' reveals:

------------------------------------------------------------------------------------------------
C:\Users\Administrator.server>esentutl /ms c:\Windows\NTDS\ntds.dit

Extensible Storage Engine Utilities for Microsoft(R) Windows(R)
Version 6.1
Copyright (C) Microsoft Corporation. All Rights Reserved.

Initiating FILE DUMP mode...
         Database: c:\Windows\NTDS\ntds.dit

******************************** MSysDefrag DUMP ***********************************
            ObjidFDP: 2
           OLDStatus: NULL
   PassStartDateTime: 05/01/2013 01:19 (0x1cdeae2b91886e3)
  PassElapsedSeconds: 3324
     PassInvocations: 1
    PassPagesVisited: 3986066
      PassPagesFreed: 372
   PassPartialMerges: 90
         TotalPasses: 1204
 TotalElapsedSeconds: 7387
    TotalInvocations: 1210
     TotalDefragDays: 1204
   TotalPagesVisited: 199486704
     TotalPagesFreed: 2774
  TotalPartialMerges: 38345

******************************** SPACE DUMP *****************************************
Name                    Type    Owned(MB)     %OfDb  %OfTable    Avail(MB) Avail
%Tbl
=====================================================================================
c:\Windows\NTDS\ntds.di  Db     47998.876   100.00%              16405.461


  datatable              Pri    31589.336    65.81%   100.00%      348.227     1.10%
    Ancestors_index      Idx      790.329     1.65%     2.50%        0.180     0.00%
    DRA_USN_CREATED_ind  Idx      386.055     0.80%     1.22%        0.711     0.00%
    INDEX_00000000       Idx      475.383     0.99%     1.50%        1.376     0.00%
    INDEX_00020013       Idx      259.149     0.54%     0.82%       11.899     0.04%
    INDEX_00020078       Idx      256.446     0.53%     0.81%        4.110     0.01%
    INDEX_00090001       Idx     3057.274     6.37%     9.68%        1.422     0.00%
    INDEX_00090002       Idx     1092.477     2.28%     3.46%       85.141     0.27%
    nc_guid_Index        Idx     1097.086     2.29%     3.47%        4.469     0.01%
    PDNT_index           Idx     3059.055     6.37%     9.68%        1.329     0.00%
Note: Some small tables/indices were not printed (use /v option to see those smaller than 0.5% of the database).
-------------------------------------------------------------------------------------

    Enumerated 12 Tables ( 108 Internal Trees, 2 Long Value Trees, 156 Secondary Indices )

    Pages 6143856 ( 3981829 Used (64.8%), 2162027 Available (35.2%) )

    Note: This database is over 20% empty, an offline defragmentation can be used to shrink the file.


Operation completed successfully in 1.498 seconds.

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Although a production system; I am happy to try anything on a cloned VM - if successful I am willing to schedule downtime to fix.

Any help would be greatly appreciated

Thanks

Matthew


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