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[Seg3D] Re: Re: Internal error in Database


Chronological Thread 
  • From: Sergio Vera <sergio.vera@alma3d.com>
  • To: seg3d@sci.utah.edu, ayla@sci.utah.edu
  • Subject: [Seg3D] Re: Re: Internal error in Database
  • Date: Tue, 20 Aug 2013 11:21:55 +0200
Dear Ayla, 
thanks for your reply.

I tried to save the project on another new project to no avail (the new copy also refused to save properly the data)... at the end i just reloaded the  source images on a completely new project and continued from there. At some point I will need to merge the mask layers from both projects... but... one step at a time.
The log file does not add many information: 

[2013-Aug-20 11:06:02|ActionLoadProject.cc|160] SUCCESS: Successfully loaded project '/mnt/rd_data/Data/EU-HEAR-EU/Segs/Manual/coclea29LR.seg3dproj/coclea29LR.s3d'.
[2013-Aug-20 11:06:36|Isosurface.cc|1682] MESSAGE: Isosurface Batch 0: 167353 vertices, 333832 triangles. Total memory: 8022456
[2013-Aug-20 11:06:36|Isosurface.cc|1682] MESSAGE: Isosurface Batch 1: 169511 vertices, 336114 triangles. Total memory: 8101632
[2013-Aug-20 11:06:36|Isosurface.cc|1682] MESSAGE: Isosurface Batch 2: 169812 vertices, 336106 triangles. Total memory: 8108760
[2013-Aug-20 11:06:36|Isosurface.cc|1682] MESSAGE: Isosurface Batch 3: 168518 vertices, 334452 triangles. Total memory: 8057856
[2013-Aug-20 11:06:36|Isosurface.cc|1682] MESSAGE: Isosurface Batch 4: 86109 vertices, 171232 triangles. Total memory: 4121400
[2013-Aug-20 11:06:36|Isosurface.cc|1686] MESSAGE: Total memory required for the isosurface: 36412104
[2013-Aug-20 11:06:43|Isosurface.cc|1682] MESSAGE: Isosurface Batch 0: 166485 vertices, 333846 triangles. Total memory: 8001792
[2013-Aug-20 11:06:43|Isosurface.cc|1682] MESSAGE: Isosurface Batch 1: 163690 vertices, 329498 triangles. Total memory: 7882536
[2013-Aug-20 11:06:43|Isosurface.cc|1686] MESSAGE: Total memory required for the isosurface: 15884328
[2013-Aug-20 11:10:31|Project.cc|504] ERROR: Internal error in database.
[2013-Aug-20 11:10:31|ActionSaveSession.cc|86] SUCCESS: Successfully saved session for project: 'coclea29LR'.

I've attached the session, log and db files for further checks.

Many thanks

Sergio


On Sat, Aug 17, 2013 at 12:49 AM, Ayla Khan <ayla@sci.utah.edu> wrote:
Hi Sergio,

The log files corresponding to the sessions where you ran into problems may be helpful. You can find them under ~/.Seg3D - the files are data and time stamped.
It's possible that the session information and database files are getting corrupted when Seg3D fails to save your sessions. It may also be useful to send the sessions and database files from the project that is failing to save. If you look in the directory in which your projects are being saved, you'll see directories with the naming pattern *.seg3dproj. It should be laid out as follows:

yukon:bin.debug ayla$ ll ~/test.seg3dproj/
total 8
drwxr-xr-x@   7 ayla  sci   238 Oct  8  2012 .
drwxr-xr-x+ 140 ayla  sci  4760 Aug 16 15:27 ..
drwxr-xr-x    4 ayla  sci   136 Oct 10  2012 data
drwxr-xr-x    5 ayla  sci   170 Oct 10  2012 database
drwxr-xr-x   17 ayla  sci   578 Jan 10  2013 inputfiles
drwxr-xr-x    4 ayla  sci   136 Oct 10  2012 sessions
-rw-r--r--    1 ayla  sci  1065 Oct 10  2012 test.s3d

You can find the session and database files under database and sessions:

yukon:bin.debug ayla$ ll ~/test.seg3dproj/database/
total 80
drwxr-xr-x  5 ayla  sci    170 Oct 10  2012 .
drwxr-xr-x@ 7 ayla  sci    238 Oct  8  2012 ..
-rw-r--r--  1 ayla  sci   4096 Oct 10  2012 notes.sqlite
-rw-r--r--  1 ayla  sci  25600 Oct 10  2012 provenance.sqlite
-rw-r--r--  1 ayla  sci   8192 Oct 10  2012 sessions.sqlite
yukon:bin.debug ayla$ ll ~/test.seg3dproj/sessions/
total 56
drwxr-xr-x  4 ayla  sci    136 Oct 10  2012 .
drwxr-xr-x@ 7 ayla  sci    238 Oct  8  2012 ..
-rw-r--r--  1 ayla  sci   9211 Oct  8  2012 1.xml
-rw-r--r--  1 ayla  sci  13844 Oct 10  2012 2.xml

In the meanwhile, have you tried saving your work in a new project (using File -> Save Project As)?

Ayla


On Aug 16, 2013, at 4:01 AM, Sergio Vera wrote:

Hello
I'm using Seg2D2 2.1.5 (compiled from source code in linux) to handle some rather big segmentations (data is about 15-20 Gb). At some point, Seg3D refuses to keep saving my sessions
with the message "Internal error in database".
I cannot modify the segmentations nor add new layers because the information is not saved when I close the program.


Is there any workaround or further check that I might perform?

many thanks

--
Sergio Vera

 Alma IT Systems
 C/ Vilana, 4B, 4º 1ª
 08022 Barcelona
 T. (+34) 932 380 592
 www.alma3d.com




--
Sergio Vera

 Alma IT Systems
 C/ Vilana, 4B, 4º 1ª
 08022 Barcelona
 T. (+34) 932 380 592
 www.alma3d.com

Attachment: database.zip
Description: Zip archive

Attachment: sessions.zip
Description: Zip archive

Attachment: Seg3D_2.1.5_20130820T110318_22693.log
Description: Binary data


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