Fragmented clustered primary key (sequential GUID) index after processing - SQL Server I'm in the process of evaluating a schema change on the primary keys of several of our biggest tables in our software.
Till now we used varchar(36) for all of our PKs and FKs and Hibernate generated the random GUIDs in insert operations.
Moreover SQL server just makes all those columns clustered indexes also, so I'm worried now (after researching about) for the index fragmentation that all those inserts (and we have a lot of inserts and deletes and updates) will cause to the indexes.
A query made on the tables showed that almost all indexes are heavily fragmented.

So I decided to change the column type for several of our biggest tables (between 3 million and 1 million, so not that big) from varchar(36) to unique identifier with the DEFAULT option newsequentialid().

I did a test yesterday on a much smaller db: after changing those PKs and after a big processing (about 20k inserts and I think the same amount of deletes) it shows an index fragmentation for the clustered keys (id) from 30% to 40%.

How is this possible?

Of course I rebuilt the indexes before the processing.

These are the fragmentation data of ax example table (46528 rows) -> 42% fragmentation:

Schema  Table   Index   avg_fragmentation_in_percent    page_count  fragment_count
dbo e2_per_out_presenze PK_e2_per_out_presenze_id   42,91   3714    1704
dbo e2_per_out_presenze FK_e2_per_out_presenze_2    1,78    448       36
dbo e2_per_out_presenze FK_e2_per_out_presenze_3    0       194       11
dbo e2_per_out_presenze FK_e2_per_out_presenze_4    0       444       12
dbo e2_per_out_presenze FK_e2_per_out_presenze_6    0       161       16
dbo e2_per_out_presenze FK_e2_per_out_presenze_7    0       166       14
dbo e2_per_out_presenze Index_8                     0       466       28 


Now I'm worried that this schema change won't help that much.

EDIT: I think it's important to note that the fill factor on the tables is set to 80 and that after the insert it's very possible that the row gets also updated.

For the sake of the test I also include the fragmentation data of the table after the same test but without the sequential GUID (it shows anyway a big improvement in fragmentation, but I wonder how will it perform on bigger tables)

Schema  Table               Index                       avg_fragmentation_in_percent    page_count  fragment_count
dbo     e2_per_out_presenze FK_e2_per_out_presenze_7    95,03676471                     544         524
dbo     e2_per_out_presenze FK_e2_per_out_presenze_3    94,43413729                     539         515
dbo     e2_per_out_presenze FK_e2_per_out_presenze_6    93,56060606                     528         501
dbo     e2_per_out_presenze FK_e2_per_out_presenze_2    92,22343921                     913         854
dbo     e2_per_out_presenze PK_e2_per_out_presenze_id   86,9864487                      4649        4102
dbo     e2_per_out_presenze FK_e2_per_out_presenze_4    68,6827957                      744         522
dbo     e2_per_out_presenze Index_8                     0                               501         21
Now I'm worried that this schema change won't help that much.


Changing the column from a varchar(36) to a uniqueidentifier will greatly reduce storage requirements from 36 bytes per row to 16 bytes per row; for each 100,000 row table, that equates to a savings of 2MB.  2MB may not sound like much by itself, but since the column is the primary key, that 2MB applies to each non-clustered index on the table.  If any other tables are using foreign keys to ensure relational integrity, the space savings applies to those tables as well.  Realize also that this space savings doesn't only apply to on-disk storage, it also applies equally, and one might argue, more importantly, to rows contained in the buffer-pool.  

It appears from a cursory glance at your sample table above that the average row size is somewhere around 600 bytes.  Converting the varchar(36) to a uniqueidentifier will immediately offer a 3.3% space savings for the clustered index, and more than that for each non-clustered index.

As a bonus, once you convert the column from a varchar(36) to a uniqueidentifier, it will no longer be possible to insert this is a bad key into the column, as is currently possible.  This will result in much better data integrity, and will potentially save you a lot of work down the road.

Having said that, I decided to try to recreate the problems you're seeing with index fragmentation.  I created a test table with the varchar(36) primary key column with 100,000 rows.  I then converted the column to a uniqueidentifier and was unable to see a drastic increase in index fragmentation.  My test bed code is:

USE tempdb;

/* create our test table, with a VARCHAR primary key */
IF OBJECT_ID('dbo.guid_insert') IS NOT NULL
DROP TABLE dbo.guid_insert;
CREATE TABLE dbo.guid_insert
(
    PK VARCHAR(36) NOT NULL
        CONSTRAINT PK_guid_insert
        PRIMARY KEY CLUSTERED
        WITH (
            DATA_COMPRESSION = NONE
            , PAD_INDEX = OFF
            , ALLOW_ROW_LOCKS = ON
            , ALLOW_PAGE_LOCKS = ON
            , FILLFACTOR = 80
            )
    , SomeData VARCHAR(600)
    , CreatedDate DATETIME
        CONSTRAINT DF_quid_insert_CreatedDate
        DEFAULT (GETDATE())
) ON [PRIMARY];

/* insert 100,000 rows into the test table */
INSERT INTO dbo.guid_insert (PK, SomeData)
SELECT NEWID(), REPLICATE('.', 600)
FROM (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v1(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v2(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v3(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v4(num);

/* show the fragmentation details */
SELECT ObjectName = QUOTENAME(s.name) + '.' + QUOTENAME(o.name)
    , IndexName = QUOTENAME(i.name)
    , [FillFactor] = 'FILLFACTOR = ' + CONVERT(VARCHAR(50), CASE WHEN i.fill_factor = 0 THEN '100' ELSE i.fill_factor END)
    , CompressOption = 'DATA_COMPRESSION = ' + p.data_compression_desc
    , NumberOfFragments = ips.fragment_count
    , NumberOfPages = ips.page_count
    , AvgFragmentSizeInPages = ips.avg_fragment_size_in_pages
    , AvgFragmentationInPercent = ips.avg_fragmentation_in_percent
    , IndexType = i.type_desc
    , IsUnique = i.is_unique
    , IsPrimary = i.is_primary_key
    , IsPartitioned = CASE WHEN ps.data_space_id IS NULL THEN 0 ELSE 1 END
    , IsClustered = CASE WHEN i.type = 1 THEN 1 ELSE 0 END
FROM sys.indexes i WITH (NOLOCK)
    INNER JOIN sys.objects o WITH (NOLOCK) ON i.object_id = o.object_id
    INNER JOIN sys.schemas s WITH (NOLOCK) ON o.schema_id = s.schema_id
    INNER JOIN sys.data_spaces ds WITH (NOLOCK) ON i.data_space_id = ds.data_space_id
    INNER JOIN sys.partitions p WITH (NOLOCK) ON o.object_id = p.object_id
                                    AND i.index_id = p.index_id
    LEFT JOIN sys.partition_schemes ps WITH (NOLOCK) ON ds.data_space_id = ps.data_space_id
CROSS APPLY sys.dm_db_index_physical_stats(DB_ID(), o.object_id, i.index_id, p.partition_number, 'DETAILED') ips
WHERE o.is_ms_shipped = 0
    AND NOT (
        o.type = 'TF' -- table valued function
        OR o.type = 'TT' -- table type
        OR o.type = 'SO' -- sequence object
        )
    AND i.index_id &gt; 0
    AND i.is_disabled = 0
    AND i.is_hypothetical = 0
    AND (
        ds.type = 'FG' -- filegroup
        OR ds.type = 'PS' -- partition stream
        ) 
    AND i.type_desc IN 
        ( --we only support rebuilding/reorganizing these index types:
            'CLUSTERED'
            , 'NONCLUSTERED'
            , 'XML'
        )
    AND ips.index_level = 0 -- leaf-levels only
    AND ips.fragment_count &gt; 1
ORDER BY ips.fragment_count * ips.avg_fragmentation_in_percent DESC; 


The fragmentation query results:



/* rebuild the index to remove fragmentation */
ALTER INDEX PK_guid_insert ON dbo.guid_insert REBUILD;

/* drop the primary key, since we can't modify the PK column when it is a primary key */
ALTER TABLE dbo.guid_insert
DROP CONSTRAINT PK_guid_insert;

/* convert the VARCHAR PK column into a UNIQUEIDENTIFIER column */
ALTER TABLE dbo.guid_insert
ALTER COLUMN PK UNIQUEIDENTIFIER NOT NULL;

/* recreate the primary key */
ALTER TABLE dbo.guid_insert
ADD CONSTRAINT PK_guid_insert
PRIMARY KEY CLUSTERED (PK);

/* add a DEFAULT constraint to create sequential keys */
ALTER TABLE dbo.guid_insert
ADD CONSTRAINT DF_guid_insert_PK
DEFAULT (NEWSEQUENTIALID())
FOR PK;

/* delete 10,000 random rows */
;WITH src AS
(
SELECT rn = ROW_NUMBER() OVER (ORDER BY NEWID()), *
FROM dbo.guid_insert
)
DELETE 
FROM src 
WHERE rn &lt; 10000;

/* insert 100,000 more rows */
INSERT INTO dbo.guid_insert (SomeData)
SELECT REPLICATE('.', 600)
FROM (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v1(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v2(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v3(num)
CROSS APPLY (VALUES (0), (1), (2), (3), (4), (5), (6), (7), (8), (9)) v4(num);

/* show the fragmentation details */
SELECT ObjectName = QUOTENAME(s.name) + '.' + QUOTENAME(o.name)
    , IndexName = QUOTENAME(i.name)
    , [FillFactor] = 'FILLFACTOR = ' + CONVERT(VARCHAR(50), CASE WHEN i.fill_factor = 0 THEN '100' ELSE i.fill_factor END)
    , CompressOption = 'DATA_COMPRESSION = ' + p.data_compression_desc
    , NumberOfFragments = ips.fragment_count
    , NumberOfPages = ips.page_count
    , AvgFragmentSizeInPages = ips.avg_fragment_size_in_pages
    , AvgFragmentationInPercent = ips.avg_fragmentation_in_percent
    , IndexType = i.type_desc
    , IsUnique = i.is_unique
    , IsPrimary = i.is_primary_key
    , IsPartitioned = CASE WHEN ps.data_space_id IS NULL THEN 0 ELSE 1 END
    , IsClustered = CASE WHEN i.type = 1 THEN 1 ELSE 0 END
FROM sys.indexes i WITH (NOLOCK)
    INNER JOIN sys.objects o WITH (NOLOCK) ON i.object_id = o.object_id
    INNER JOIN sys.schemas s WITH (NOLOCK) ON o.schema_id = s.schema_id
    INNER JOIN sys.data_spaces ds WITH (NOLOCK) ON i.data_space_id = ds.data_space_id
    INNER JOIN sys.partitions p WITH (NOLOCK) ON o.object_id = p.object_id
                                    AND i.index_id = p.index_id
    LEFT JOIN sys.partition_schemes ps WITH (NOLOCK) ON ds.data_space_id = ps.data_space_id
CROSS APPLY sys.dm_db_index_physical_stats(DB_ID(), o.object_id, i.index_id, p.partition_number, 'DETAILED') ips
WHERE o.is_ms_shipped = 0
    AND NOT (
        o.type = 'TF' -- table valued function
        OR o.type = 'TT' -- table type
        OR o.type = 'SO' -- sequence object
        )
    AND i.index_id &gt; 0
    AND i.is_disabled = 0
    AND i.is_hypothetical = 0
    AND (
        ds.type = 'FG' -- filegroup
        OR ds.type = 'PS' -- partition stream
        ) 
    AND i.type_desc IN 
        ( --we only support rebuilding/reorganizing these index types:
            'CLUSTERED'
            , 'NONCLUSTERED'
            , 'XML'
        )
    AND ips.index_level = 0 -- leaf-levels only
    AND ips.fragment_count &gt; 1
ORDER BY ips.fragment_count * ips.avg_fragmentation_in_percent DESC; --start with the most fragmented indexes first


The fragmentation details after the conversion, with deleting and inserting rows:



As you can see, after the conversion, and deleting 10,000 rows, then inserting 100,000 rows, index fragmentation for the primary key index (the table itself) is just 0.41%; hardly a concern.

If you need further help with this problem (I realize your question is a year old), you need to show the DDL for the table, its indexes, and the code you used for the conversion test.