Difference between revisions of "Documentation/Labs/BRAINS and ITKv4 issue"

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 +
This page documents the experiment done while trying to sort the issue causing BRAINS to crash when built within Slicer.
 +
 +
See this bug report: http://na-mic.org/Bug/view.php?id=3071
 +
 +
== Experiment Setup ==
 +
 +
Here is the VERY simple program that is failing:
 +
https://github.com/BRAINSia/BRAINSTools/blob/SlicerDebugBRAINSFitInstrumentation/BRAINSFit/DebugSlicerProg.cxx
 +
 +
In my slicer build tree:
 +
/scratch/johnsonhj/src/Slicer-DEBUG/BRAINSTools (SlicerDebugBRAINSFitInstrumentation)
 +
 +
With git remove –v:
 +
origin git://github.com/BRAINSia/BRAINSTools.git (push)
  
−
This page documents the experiment done while trying to sort the issue causing BRAINS to crash when built within Slicer.
+
And BRAINSTools hash  31beee592eba2d98655b864e6dc704ac9bf995e8
  
 
== Experiment results ==
 
== Experiment results ==
 +
 +
<pre>
 +
=======================
 +
[FAILED]
 +
Build Slicer:  Run Slicers version of Debug
 +
johnsonhj@neuron$ /scratch/johnsonhj/src/Slicer-DEBUG/Slicer-build/bin/DebugSlicerProg
 +
TESTING: STARTED
 +
PRE : 9945 Segmentation fault: 11
 +
 +
 +
=======================
 +
[PASSED]
 +
 +
Build Stand Alone version of BRAINSTools using the same source code:
 +
 +
johnsonhj@neuron$ /scratch/johnsonhj/src/Slicer-DEBUG/BT_DEBUG/bin/DebugSlicerProg
 +
TESTING: STARTED
 +
PRE : 9945 0
 +
POST: 9945 9945
 +
PRE : 9945 0
 +
POST: 9945 9945
 +
TESTING: STOPPED
 +
 +
========================================
 +
I have a separate build of Slicer available under a branch named "InstrumentForBRAINSFitFailures" at
 +
git@github.com:hjmjohnson/Slicer.git ( a version built on top of today's SlicerSVN)
 +
 +
This branch includes a version of BRAINSTools with a very small program that demonstrates the problem
 +
we are seeing in BRAINSFit.
 +
 +
I still think there is something that is overwriting the vtable of this object, and that is the root cause
 +
of our problems, but I don't know how to continue debugging that guess.
 +
 +
 +
This is mostly for my own note taking:
 +
There are the experiments that I have done to try to figure out what the heck is going on:
 +
 +
"StandAlone Shared library build of BRAINSTools"
 +
BSA_BASE=/scratch/johnsonhj/src/BT_FAILURED_SHARED/BT-DEBUG-SHARED/
 +
 +
"Slicer build of BRAINSTools"
 +
SLICER_BASE=/Volumes/scratch/johnsonhj/src/Slicer-DEBUG
 +
 +
TEST #1:  [PASS]
 +
===========================
 +
BIN=${BSA_BASE}/bin/BRAINSFit
 +
DYLD_LIBRARY_PATH=${BSA_BASE}/ITKv4-install/lib
 +
 +
TEST #2:  [PASS]
 +
===========================
 +
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
 +
DYLD_LIBRARY_PATH=${BSA_BASE}/ITKv4-install/lib
 +
 +
TEST #3:  [FAIL]
 +
===========================
 +
BIN=${BSA_BASE}/bin/BRAINSFit
 +
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib
 +
 +
TEST #4:  [FAIL]
 +
===========================
 +
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
 +
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib
 +
 +
TEST #5: [FAIL]
 +
================================
 +
Build with DICOM support turned off.
 +
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
 +
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib
 +
 +
TEST #6: [FAIL]
 +
================================
 +
Build minimum CLI based program to replicate the problem.
 +
 +
When debugging TEST #6 I put a break point at:
 +
/Volumes/scratch/johnsonhj/src/Slicer-DEBUG/BRAINSTools/BRAINSFit/DebugSlicerCLI.cxx  line 59
 +
59├>      std::cout << "PRE : " << LBFGSBoptimizer->GetUpperBound().size() << " " << upperBound.size() << std::endl;
 +
 +
 +
When stepping into the line, it reports segfault at line 209 of /Volumes/scratch/johnsonhj/src/Slicer-DEBUG/ITKv4/Modules/Numerics/Optimizers/src/itkLBFGSBOptimizer.cxx
 +
204│ void
 +
205│ LBFGSBOptimizer
 +
206│ ::SetUpperBound(
 +
207│  const BoundValueType & value)
 +
208│ {
 +
209├>  m_UpperBound = value;
 +
210│  if ( m_OptimizerInitialized )
 +
211│    {
 +
212│    m_VnlOptimizer->set_upper_bound(m_UpperBound);
 +
213│    }
 +
214│
 +
215│  this->Modified();
 +
216│ }
 +
 +
NOTE: NOTE: NOTE:  Line 59 of DebugSlicerCLI.cxx DOES NOT CALL "SetUpperBound" it calls "GetUpperBound",  and that is the same type of problem we are seeing in BRAINSFit.
 +
</pre>

Latest revision as of 12:48, 22 April 2013

Home < Documentation < Labs < BRAINS and ITKv4 issue

This page documents the experiment done while trying to sort the issue causing BRAINS to crash when built within Slicer.

See this bug report: http://na-mic.org/Bug/view.php?id=3071

Experiment Setup

Here is the VERY simple program that is failing: https://github.com/BRAINSia/BRAINSTools/blob/SlicerDebugBRAINSFitInstrumentation/BRAINSFit/DebugSlicerProg.cxx

In my slicer build tree: /scratch/johnsonhj/src/Slicer-DEBUG/BRAINSTools (SlicerDebugBRAINSFitInstrumentation)

With git remove –v: origin git://github.com/BRAINSia/BRAINSTools.git (push)

And BRAINSTools hash 31beee592eba2d98655b864e6dc704ac9bf995e8

Experiment results

=======================
[FAILED]
Build Slicer:  Run Slicers version of Debug
johnsonhj@neuron$ /scratch/johnsonhj/src/Slicer-DEBUG/Slicer-build/bin/DebugSlicerProg
TESTING: STARTED
PRE : 9945 Segmentation fault: 11


=======================
[PASSED]

Build Stand Alone version of BRAINSTools using the same source code:

johnsonhj@neuron$ /scratch/johnsonhj/src/Slicer-DEBUG/BT_DEBUG/bin/DebugSlicerProg 
TESTING: STARTED
PRE : 9945 0
POST: 9945 9945
PRE : 9945 0
POST: 9945 9945
TESTING: STOPPED

========================================
I have a separate build of Slicer available under a branch named "InstrumentForBRAINSFitFailures" at 
git@github.com:hjmjohnson/Slicer.git ( a version built on top of today's SlicerSVN)

This branch includes a version of BRAINSTools with a very small program that demonstrates the problem 
we are seeing in BRAINSFit.

I still think there is something that is overwriting the vtable of this object, and that is the root cause 
of our problems, but I don't know how to continue debugging that guess.


This is mostly for my own note taking:
There are the experiments that I have done to try to figure out what the heck is going on:

"StandAlone Shared library build of BRAINSTools"
BSA_BASE=/scratch/johnsonhj/src/BT_FAILURED_SHARED/BT-DEBUG-SHARED/

"Slicer build of BRAINSTools"
SLICER_BASE=/Volumes/scratch/johnsonhj/src/Slicer-DEBUG

TEST #1:  [PASS]
===========================
BIN=${BSA_BASE}/bin/BRAINSFit
DYLD_LIBRARY_PATH=${BSA_BASE}/ITKv4-install/lib

TEST #2:  [PASS]
===========================
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
DYLD_LIBRARY_PATH=${BSA_BASE}/ITKv4-install/lib

TEST #3:  [FAIL]
===========================
BIN=${BSA_BASE}/bin/BRAINSFit
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib

TEST #4:  [FAIL]
===========================
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib

TEST #5: [FAIL]
================================
Build with DICOM support turned off.
BIN=${SLICER_BASE}/Slicer-build/lib/Slicer-4.2/cli-modules/BRAINSFit
DYLD_LIBRARY_PATH=${SLICER_BASE}/ITKv4-build/lib

TEST #6: [FAIL]
================================
Build minimum CLI based program to replicate the problem. 

When debugging TEST #6 I put a break point at:
/Volumes/scratch/johnsonhj/src/Slicer-DEBUG/BRAINSTools/BRAINSFit/DebugSlicerCLI.cxx   line 59
59├>      std::cout << "PRE : " << LBFGSBoptimizer->GetUpperBound().size() << " " << upperBound.size() << std::endl;


When stepping into the line, it reports segfault at line 209 of /Volumes/scratch/johnsonhj/src/Slicer-DEBUG/ITKv4/Modules/Numerics/Optimizers/src/itkLBFGSBOptimizer.cxx 
204│ void
205│ LBFGSBOptimizer
206│ ::SetUpperBound(
207│   const BoundValueType & value)
208│ {
209├>  m_UpperBound = value;
210│   if ( m_OptimizerInitialized )
211│     {
212│     m_VnlOptimizer->set_upper_bound(m_UpperBound);
213│     }
214│
215│   this->Modified();
216│ } 

NOTE: NOTE: NOTE:  Line 59 of DebugSlicerCLI.cxx DOES NOT CALL "SetUpperBound" it calls "GetUpperBound",  and that is the same type of problem we are seeing in BRAINSFit.
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