Grouper Users - Open Discussion List

[David Langenberg <>]

Once you delete the data & MySQL has purged[1] MySQL will then re-use the 
available space freed up by your deletes.  So yes, in the end you still have 
the 40GB file, but it won't be growing further.


[1] https://dev.mysql.com/doc/refman/5.7/en/glossary.html#glos_purge


Dave

--
David Langenberg
Asst Director, Identity Management
The University of Chicago 
 
On 1/29/18, 3:23 PM, 
"
 on behalf of Rory Larson" 
<
 on behalf of 
>
 wrote:

    Well, there is a "created_on" and a "last_updated" field, which are 
apparently Unix-type dates.  That would make it possible to delete everything 
in the table prior to a chosen date.  There's also "server_user_name", which 
gives the account that ran the transaction, e.g., myself vs. the 
grouperLoader.  That would let us delete only the ones that were run 
regularly under the grouperLoader, and keep the changes made by individual 
users.  I'm not sure how worried we should be about keeping that information. 
 On a 40 GB table, how long would a selected DML delete take?  And if we do 
it that way, we are still left with a huge table, because MySQL only marks 
records for deletion without actually deleting them.  In fact, wouldn't it 
just make the table bigger by adding all the deletion transactions?
    
    Thanks,
    Rory
    
    
    -----Original Message-----
    From: Hyzer, Chris 
[mailto:]
 
    Sent: Monday, January 29, 2018 2:45 PM
    To: Rory Larson 
<>;
 Shilen Patel 
<>
    Cc: 

    Subject: RE: [grouper-users] Maintaining Grouper database size
    
    Is there a way to look at the data of the audit table and see which 
records to delete?   I think any loader jobs audits can be deleted 
(GrouperSystem is the entity?), but things users do through the UI for 
example should be kept so you know who did what.  Make sense?  Take a look 
and see if anything jumps out or we can look at our audit tables too...
    
    Thanks
    Chris
    
    -----Original Message-----
    From: Rory Larson 
[mailto:]
    Sent: Monday, January 29, 2018 3:42 PM
    To: Hyzer, Chris 
<>;
 Shilen Patel 
<>
    Cc: 

    Subject: RE: [grouper-users] Maintaining Grouper database size
    
    Thanks, all, for the suggestions.  I think I'm hearing that I don't want 
to purge data from large point-in-time tables manually through SQL.  Instead, 
I should run an edu.internet2.middleware.grouper... command under gsh, such 
as:
    
        
edu.internet2.middleware.grouper.pit.PITUtils.deleteInactiveRecords(new 
Date(), true); or
        
edu.internet2.middleware.grouper.pit.PITUtils.deleteInactiveObjectsInStem("my:stem",
 true);
    
    This will eliminate inactive records or objects only, meaning that if the 
people are still around, they will still be taking up space with 
point-in-time data going back perhaps for many years, correct?  And 
additionally, we would still have to perform an OPTIMIZE TABLE on each PIT 
table to (possibly) realize any gains?
    
    I will plan to do this, but I'm unsure of how much space, if any, I'm 
likely to recover.
    
    Another suggestion was made off-line, that I should perform a TRUNCATE on 
the grouper_audit_entry table.  In fact, this table has grown to about 40 GB, 
and is apparently the biggest source of our problem.  I understand that this 
is simply a transaction log table, and that nothing else depends on it.  
Truncation means that the table would essentially be dropped and then 
re-created, minus all the data.  That would be done in SQL.  Is there any 
reason not to do this?  If so, is there a better way to reduce its size?
    
    Thanks,
    Rory
    
    
    -----Original Message-----
    From: Hyzer, Chris 
[mailto:]
    Sent: Monday, January 29, 2018 1:03 PM
    To: Shilen Patel 
<>;
 Rory Larson 
<>
    Cc: 

    Subject: RE: [grouper-users] Maintaining Grouper database size
    
    Im worried about the future state of using direct SQL, maybe something 
else in future will be needed that we put in the GSH command... you should 
definitely use that.
    
    
    
    Thanks
    
    Chris
    
    
    
    -----Original Message-----
    
    From: 

 
[mailto:]
 On Behalf Of Shilen Patel
    
    Sent: Monday, January 29, 2018 1:34 PM
    
    To: Rory Larson 
<>
    
    Cc: 

    
    Subject: Re: [grouper-users] Maintaining Grouper database size
    
    
    
    If you’re going to trim the audit based on time, I’d suggest using the 
gsh command since it’ll delete the records from the tables in the right order 
(taking into account foreign keys).  But as long as you delete them in the 
right order via sql directly, that should be fine as well.  Also, recently, I 
documented how much space was being taken up at Duke (we use Oracle).  
https://urldefense.proofpoint.com/v2/url?u=https-3A__spaces.internet2.edu_display_Grouper_Duke-2BDisk-2BSpace-2BUsage&d=DwIGaQ&c=Cu5g146wZdoqVuKpTNsYHVKLgTZS09MUACeOXHWmTvE&r=8UxP4WgXNK7VFhDT-iCutw&m=i5pbjVCyOSrgzJa3qHir_ok5n_Zw8MCNGbVSHFXVgZs&s=1qaggpDGSz3DUP03rlkM40RUuYd4lBXJ6ylGMs76vQQ&e=
   I was surprised to see so much of the space being used by indexes.  We 
could possibly look at reducing the number of indexes to help.
    
    
    
    - Shilen
    
    
    
    On 1/29/18, 9:13 AM, 
"
 on behalf of Rory Larson" 
<
 on behalf of 
>
 wrote:
    
    
    
        Hello,
    
        
    
        We are encountering an issue of our Grouper database growing to a 
size that threatens to use up the entire hard drive space available.  The 
database server is a physical machine with no room to expand, running a 
MySQL-type database (5.5.56-MariaDB MariaDB Server).
    
        
    
        The problem is not so much the size of the group data itself, but 
with point-in-time tables that record what that data was back to the 
beginning of the Grouper installation.  Some of these have grown to huge 
sizes, on the order of 20 GB or so.  A suggestion has been made that we could 
delete a lot of this prior to some reasonable point in time, especially 
groups or memberships that no longer exist.  This would be fine, but I'm 
wondering if this can be done from the database command line on a per-table 
basis, or whether there are dependencies that require doing this through gsh 
function calls?
    
        
    
        Also, because this is a MySQL-type database, shrinking the database 
physical size after deletion of unnecessary data is not trivial.  OPTIMIZE 
TABLE ... might work, or it might make a table bigger.  ALTER TABLE ... ROW 
FORMAT=COMPRESSED is promising as tried on our test database, but takes about 
four times as long as OPTIMIZE TABLE.  In either case, updating has to be 
shut down while running them, and they may require duplicating the table 
during the operation.  We are at 90% now, and can't afford any more big 
tables.  The ultimate MySQL solution seems to be to dump the database, delete 
the whole thing, and reload it, which would mean complete downtime for 
Grouper.
    
        
    
        Does anyone else using a MySQL-type database have a system for 
handling this problem and maintaining a reasonable database size?
    
        
    
        Thanks,
    
        Rory

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