Re: [ZODB-Dev] Problem with RelStorage zodbpack

2011-03-30 Thread Shane Hathaway 
On 03/29/2011 09:16 PM, Erik Dahl wrote:
 Ok looked a little deeper.  I think solution 2 is the way to go (ie clear the 
 object_ref table from references that are in my range of non-packed 
 transactions.  Does that sound right?  Statement would be:

 delete from object_ref where tid  255908476364112230;

 I think once this is done the code will refill the table and go on its way. 
 Thoughts?

I haven't read the whole thread, but I will say this: it is quite safe 
to remove rows from object_ref as long as you *also* remove the 
corresponding rows from object_refs_added.  To be 100% safe, you could 
just clear both object_refs_added and object_ref before packing.

IOW, the object_ref table serves as a cache between pack operations and 
the object_refs_added table indicates how much of the object_ref cache 
is filled.

Shane
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Re: [ZODB-Dev] Problem with RelStorage zodbpack

2011-03-30 Thread Shane Hathaway 
On 03/29/2011 07:39 PM, Erik Dahl wrote:
 I was running a pack and canceled so that I could reboot my box.  After it 
 came back up I tried to restart the pack and got this:
[...]
File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 397, in _add_refs_for_tid
  self.runner.run_many(cursor, stmt, add_rows)
[...]
 IntegrityError: (1062, Duplicate entry '255911127406517196-2714-893440' for 
 key 'PRIMARY')

Ah, I recognize this now.  This is a minor bug that I believe has been 
fixed for 1.5.0.  It only affects packing; it has zero impact on your 
application.

The bug occurs when filling the object_ref table for packing.  If you 
interrupt the pack operation while the object_ref table is being filled, 
the corresponding entry in object_refs_added will not be created and the 
next attempt to pack will try again and stumble in exactly this way. 
The bug has been solved by replacing entries in object_ref rather than 
just inserting them.  The object_ref and object_refs_added tables are 
only used during packing.

Perhaps the quickest thing to do is remove only the offending entries:

delete from object_refs_added where tid = 255911127406517196;
delete from object_ref where tid = 255911127406517196;

A bit of trivia: that error message says that object 2714 in transaction 
255911127406517196 has at least one direct reference to object 893440.

Shane
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Re: [ZODB-Dev] Problem with RelStorage zodbpack

2011-03-30 Thread Erik Dahl 
Shane,

Thanks for the quick response and the great tool!  I brought the app back up 
last night when I realized that this was primarily related to packing.  I'll 
give this a shot tonight when the app is quiet and I can run a pack.

-EAD



On Mar 30, 2011, at 12:34 PM, Shane Hathaway wrote:

 On 03/29/2011 07:39 PM, Erik Dahl wrote:
 I was running a pack and canceled so that I could reboot my box.  After it 
 came back up I tried to restart the pack and got this:
 [...]
   File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 397, in _add_refs_for_tid
 self.runner.run_many(cursor, stmt, add_rows)
 [...]
 IntegrityError: (1062, Duplicate entry '255911127406517196-2714-893440' for 
 key 'PRIMARY')
 
 Ah, I recognize this now.  This is a minor bug that I believe has been fixed 
 for 1.5.0.  It only affects packing; it has zero impact on your application.
 
 The bug occurs when filling the object_ref table for packing.  If you 
 interrupt the pack operation while the object_ref table is being filled, the 
 corresponding entry in object_refs_added will not be created and the next 
 attempt to pack will try again and stumble in exactly this way. The bug has 
 been solved by replacing entries in object_ref rather than just inserting 
 them.  The object_ref and object_refs_added tables are only used during 
 packing.
 
 Perhaps the quickest thing to do is remove only the offending entries:
 
 delete from object_refs_added where tid = 255911127406517196;
 delete from object_ref where tid = 255911127406517196;
 
 A bit of trivia: that error message says that object 2714 in transaction 
 255911127406517196 has at least one direct reference to object 893440.
 
 Shane

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Re: [ZODB-Dev] Problem with RelStorage zodbpack

2011-03-29 Thread Erik Dahl 
Ok I'm starting to understand things a little better.  The transaction 
255911127406517196 was the last transaction who's references were added to the 
object_ref table.  But (I'm guessing because I interrupted the pack) it didn't 
get marked in the transaction table as packed.  In fact there are 11088 
transactions in this state.  Below are the details.  I haven't fully understood 
the code yet (and its getting too late for productive thinking :) ) but I see 
to potential solutions: 

1. Mark the transactions that have been moved to object_ref as packed but I'm 
guessing though that this isn't a good idea because there is other stuff that 
needs to happen during the pack.

2. Remove the unpacked transactions from the object_ref table. (this seems very 
scary to me).

I will continue looking at the code tomorrow.  In the mean time is there an 
issue with continuing to use the database?  Will the orphaned object_ref 
records cause a problem.  (doesn't seem like they would).

Here are the details:

mysql select tid from transaction where tid =  255911127406517196 and 
packed=true order by tid desc limit 1;
++
| tid|
++
| 255908476364112230 | -- the last transaction marked as packed
++


mysql select count(*) from transaction where tid = 255908476364112230 and tid 
 255911127406517196 order by tid desc;
+--+
| count(*) |
+--+
|11088 | -- this is the number of transactions that seem to have been 
packed without being marked as packed.
+--+

mysql select count(*) from transaction where tid  255911127406517196;
+--+
| count(*) |
+--+
|   178909 | -- number of transactions that haven't made it into the object_ref 
table
+--+

mysql select count(*) from object_ref where tid  255911127406517196;
+--+
| count(*) |
+--+
|0 | -- confirmation that the transactions after 255911127406517196 
have not made it into the object_ref table
+--+
1 row in set (0.00 sec)

mysql select count(*) from object_ref where tid = 255911127406517196;
+--+
| count(*) |
+--+
| 3907 | -- confirmation again
+--+
1 row in set (0.00 sec)

mysql select count(*) from object_ref where tid = 255911127406517196;
+--+
| count(*) |
+--+
| 3907 | -- and again
+--+
1 row in set (0.00 sec)



-EAD



On Mar 29, 2011, at 9:39 PM, Erik Dahl wrote:

 I was running a pack and canceled so that I could reboot my box.  After it 
 came back up I tried to restart the pack and got this:
 
 2011-03-29 20:53:07,259 [zodbpack] INFO Opening storage (RelStorageFactory)...
 2011-03-29 20:53:07,457 [zodbpack] INFO Packing storage (RelStorageFactory).
 2011-03-29 20:53:07,464 [relstorage] INFO pack: analyzing transactions 
 committed Tue Mar 29 20:49:48 2011 or before
 2011-03-29 20:53:07,465 [relstorage.adapters.packundo] INFO pre_pack: start 
 with gc enabled
 2011-03-29 20:53:08,846 [relstorage.adapters.packundo] INFO discovering 
 references from objects in 178910 transaction(s)
 2011-03-29 20:53:10,808 [relstorage.adapters.packundo] ERROR pre_pack: failed
 Traceback (most recent call last):
  File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 431, in pre_pack
conn, cursor, pack_tid, get_references)
  File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 525, in _pre_pack_with_gc
self.fill_object_refs(conn, cursor, get_references)
  File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 347, in fill_object_refs
added += self._add_refs_for_tid(cursor, tid, get_references)
  File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 397, in _add_refs_for_tid
self.runner.run_many(cursor, stmt, add_rows)
  File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/scriptrunner.py,
  line 90, in run_many
cursor.executemany(stmt, items)
  File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 206, in 
 executemany
r = r + self.execute(query, a)
  File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 174, in execute
self.errorhandler(self, exc, value)
  File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 36, in 
 defaulterrorhandler
raise errorclass, errorvalue
 IntegrityError: (1062, Duplicate entry '255911127406517196-2714-893440' for 
 key 'PRIMARY')
 Traceback (most recent call last):
  File /opt/zenoss/bin/zodbpack, line 8, in module
load_entry_point('RelStorage==1.4.2', 'console_scripts', 'zodbpack')()
 
 
 I'm in process of running mysqlcheck against the database and I have the 
 application off line.  I've looked at the code but I'm not 100% what it's 
 trying to do.  Thoughts?  Is my database hosed? or just my packing process.

Re: [ZODB-Dev] Problem with RelStorage zodbpack

2011-03-29 Thread Erik Dahl 
Ok looked a little deeper.  I think solution 2 is the way to go (ie clear the 
object_ref table from references that are in my range of non-packed 
transactions.  Does that sound right?  Statement would be:

delete from object_ref where tid  255908476364112230;

I think once this is done the code will refill the table and go on its way. 
Thoughts?  

-EAD



On Mar 29, 2011, at 11:00 PM, Erik Dahl wrote:

 Ok I'm starting to understand things a little better.  The transaction 
 255911127406517196 was the last transaction who's references were added to 
 the object_ref table.  But (I'm guessing because I interrupted the pack) it 
 didn't get marked in the transaction table as packed.  In fact there are 
 11088 transactions in this state.  Below are the details.  I haven't fully 
 understood the code yet (and its getting too late for productive thinking :) 
 ) but I see to potential solutions: 
 
 1. Mark the transactions that have been moved to object_ref as packed but I'm 
 guessing though that this isn't a good idea because there is other stuff that 
 needs to happen during the pack.
 
 2. Remove the unpacked transactions from the object_ref table. (this seems 
 very scary to me).
 
 I will continue looking at the code tomorrow.  In the mean time is there an 
 issue with continuing to use the database?  Will the orphaned object_ref 
 records cause a problem.  (doesn't seem like they would).
 
 Here are the details:
 
 mysql select tid from transaction where tid =  255911127406517196 and 
 packed=true order by tid desc limit 1;
 ++
 | tid|
 ++
 | 255908476364112230 | -- the last transaction marked as packed
 ++
 
 
 mysql select count(*) from transaction where tid = 255908476364112230 and 
 tid  255911127406517196 order by tid desc;
 +--+
 | count(*) |
 +--+
 |11088 | -- this is the number of transactions that seem to have been 
 packed without being marked as packed.
 +--+
 
 mysql select count(*) from transaction where tid  255911127406517196;
 +--+
 | count(*) |
 +--+
 |   178909 | -- number of transactions that haven't made it into the 
 object_ref table
 +--+
 
 mysql select count(*) from object_ref where tid  255911127406517196;
 +--+
 | count(*) |
 +--+
 |0 | -- confirmation that the transactions after 255911127406517196 
 have not made it into the object_ref table
 +--+
 1 row in set (0.00 sec)
 
 mysql select count(*) from object_ref where tid = 255911127406517196;
 +--+
 | count(*) |
 +--+
 | 3907 | -- confirmation again
 +--+
 1 row in set (0.00 sec)
 
 mysql select count(*) from object_ref where tid = 255911127406517196;
 +--+
 | count(*) |
 +--+
 | 3907 | -- and again
 +--+
 1 row in set (0.00 sec)
 
 
 
 -EAD
 
 
 
 On Mar 29, 2011, at 9:39 PM, Erik Dahl wrote:
 
 I was running a pack and canceled so that I could reboot my box.  After it 
 came back up I tried to restart the pack and got this:
 
 2011-03-29 20:53:07,259 [zodbpack] INFO Opening storage 
 (RelStorageFactory)...
 2011-03-29 20:53:07,457 [zodbpack] INFO Packing storage (RelStorageFactory).
 2011-03-29 20:53:07,464 [relstorage] INFO pack: analyzing transactions 
 committed Tue Mar 29 20:49:48 2011 or before
 2011-03-29 20:53:07,465 [relstorage.adapters.packundo] INFO pre_pack: start 
 with gc enabled
 2011-03-29 20:53:08,846 [relstorage.adapters.packundo] INFO discovering 
 references from objects in 178910 transaction(s)
 2011-03-29 20:53:10,808 [relstorage.adapters.packundo] ERROR pre_pack: failed
 Traceback (most recent call last):
 File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 431, in pre_pack
   conn, cursor, pack_tid, get_references)
 File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 525, in _pre_pack_with_gc
   self.fill_object_refs(conn, cursor, get_references)
 File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 347, in fill_object_refs
   added += self._add_refs_for_tid(cursor, tid, get_references)
 File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/packundo.py,
  line 397, in _add_refs_for_tid
   self.runner.run_many(cursor, stmt, add_rows)
 File 
 /opt/zenoss/lib/python2.6/site-packages/RelStorage-1.4.2-py2.6.egg/relstorage/adapters/scriptrunner.py,
  line 90, in run_many
   cursor.executemany(stmt, items)
 File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 206, in 
 executemany
   r = r + self.execute(query, a)
 File build/bdist.linux-x86_64/egg/MySQLdb/cursors.py, line 174, in execute
   self.errorhandler(self, exc, value)
 File build/bdist.linux-x86_64/egg/MySQLdb/connections.py, line 36, in 
 defaulterrorhandler
   raise errorclass, errorvalue
 IntegrityError: