grue
Vista SP 2, 64 bit OS, 4 GB memory
PB 5.5.2.4
J-1.6_20

When I try to merge a 45 thought brain into a 1700 thought brain, the status bar displays halfway, then hangs. PB CPU activity is zero to minimal (1-2%). The same thing happens if I do a copy selected thoughts in one brain and try to copy them into another. I was able to make a "smaller" copy work from another brain to the same target. I cancel the PB process after half hour to hour wait. Any thoughts? I haven't spent the time (yet) testing out other merges and copies. 

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mcaton
Gary,

I've seen this happen with larger Brains in version 5.5.  The problem has been fixed in the latest PB6.0 beta with its augmented database.  Could you try upgrading to the Beta version to see if this resolves the merge issue for you?

Thank you,
Matt
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keenable
Matt or whoever's monitoring:

I upgraded to v6 yesterday and have the same problem.  I'm trying to merge a 12,000-thought brain into a 9,000-thought brain.  The "hang" is almost a dead stop, but there is some slight response still.  I can't "see" any of the material from the brain I'm attempting to merge, only the destination brain.

Could it be I need to wait a day or so before the merge completes?  I've waited about 12 hours so far.

Minutes after I wrote this PB failed, perhaps because it had a queue of keystrokes waiting to be executed.  When I reopened it the destination database had about 1300 of the 12000 thoughts it was due to receive viewable only as orphans.  I had zipped this brain, so I just got rid of the spoiled copy.

This happened before.  The last time, I thought the merge was over because nothing indicated it was still running, and when I closed the database there was a working bar, so I figured I interrupted the process unintentionally.  When I opened the brain again, it showed a problem message about thoughts.

How do I merge these two large brains?  Perhaps I should output Brain XML from the one brain and input it into the other?  If I do so, I should probably do a global replace to put a "!" in front of all the guids on the extremely remote chance that a guid in the one PB is already in use by the other.

It's a couple hours later and I'm importing Brain XML into the 9000-thought brain om the 12,000-thought brain.  It appears to be hung on record 981.  However, unlike merge, import is not using all available memory so I'm hoping it's making progress.

I'll continue to edit this, will make it a support ticket if the process fails again.  In the meantime, any reply appreciated.

Thanks.





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mcaton
Bernard,

Yes, these sound like some very large brain files, so it may take some time. Please be sure to make and send a copy of your Output.log file if the merge/import is not successful.  This could help us determine if the problem is in the Brain file or if it is a memory issue. 

Thank you,
Matt
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keenable
Thanks, Matt:

Merge apparently does not show it's working unless I do something like type the output log.  It's still processing after 16 hours.  Is that reasonale?  In the log I see progress, different selects being executed.  I also see the following error from time to time:

Exception in thread “AWT-EventQueue-1” Java.lang.OutOfMemoryError: Java heap space

 

Does this mean that the merge is spoiled?  I don't want to run it for days and learn it failed today.  I don't like that I can move around in PB while the merge is still processing--I did so before I realized that was the case, and "parked" back at the thought that's where the merge is supposedly occuring.  Unless it's a feature that allows me to contune to use PB while the merge is in progress without ill effect.

 

Please advise, thanks,

 

Bernard

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Moe
Bernard, Thank You for posting. That means that Java ran out of memory while executing the merge. Can you try increasing the amount of available memory using the instructions below to see if it helps.

By default, PB uses a maximum of 192 MB. This is usually enough but for some operations there may be an issue with running out of heap space. 

The example below raised the max to 320 MB, but the number can be higher if needed.

1. Close PB

2. Create a text file and put the following content into it:

-Xmx320m

Make sure there is a linefeed (Enter) at the of the text. Save this file and name it PersonalBrain.vmoptions in the PB program folder.

To access the PB program folder, go into Program Files\PersonalBrain on Windows. On Mac OS, Ctrl-Click on the PersonalBrain icon and select Show Package Contents then navigate to Contents > Resources > app. (The PersonalBrain.vmoptions file must be in the same location as the file PersonalBrain.jar)

3. Restart PB.

Thanks,

Moe

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keenable
Thanks, Moe!  It worked... 

...but I had to use a far larger max MB value.  I can only say for sure that 512 was not enough, 1286 worked.  Which is fortunate, because my 2 Gig memory would not allow the heap to be 1536 (1.5 Gig).

My brain has "only" 18,468 thoughts.  10,281 have Notes, a very few are rather large.  But the 12,000+ I added to (merged into) the brain are very flat--not a lot of complicated links, and no other frills, no attachments, except they each are labelled. 

I have two questions:

1.  Should I just leave the heap as is, or clock it back?  Seems to me I should leave it, to help my brain function.  Will it affect performance for other apps if PB is running?

2.  Do you anticipate me having problems with this size brain?  Seems fine now, but my main purpose in merging it is in establishing lots of useful additional links.  I also intend on expanding the brain further, though nothing like this time.  I expect it will top-out at 20,000 thoughts.  Can I run such a beast on a Vista Ultimate 2 Gig memory machine?

Finally, although this took your help and me days to sort out, I think it's a pretty straightforward matter.  I'm going to suggest you create an advanced user guide for the more tekkie among us, and will post this recommendation on the appropriate board.

Thanks so much for your help!
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zenrain
I've added this information to the PersonalBrain User Knowledgebase WebBrain.
Windows 7
J-1.6.0_22
--
OSX 10.6.3
Java SE 6
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keenable
Thanks for letting me know about WebBrain, zenrain!  I'm still wondering what's a good vmoption size for my 20,000 thought brain.  Does that parameter affect the overall efficiency of PB?  Was thinking of setting it to 1024 on my 2 Gig machine.  Or perhaps this parameter does not affect the speed of navigating around my brain?
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zenrain
No problem, glad you've found it useful.

I'm not associated with TheBrain (just used it a while), so hopefully someone will correct me if I'm mistaken, but I think that is just used for modifying the memory limit for particularly intensive tasks (such as copying or merging a very large brain). 

I think PB has been optimized to run on it's normal memory allocation, so you shouldn't need to up the memory in normal use. Unless you see improved performance during normal usage, I'd rename the .vmoptions file so you still have it when needed. 
If you do see a performance boost using that file, I'd probably experiment a bit, lowering the amount of memory until you lose the performance increase, and then raising it back to where it was just before you lost that increase.
Windows 7
J-1.6.0_22
--
OSX 10.6.3
Java SE 6
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