Atropos fails on macOS with ANTs 2.5.0

[devDonnn]

Hi,

I've been running ANTs Atropos using the downloaded GitHub release binary ants-2.5.0-macos-12-X64-clang.zip for my Mac Studio, Apple M1 Max, macOS 14.1.1:

noglob Atropos -d 3 -x brainmask.nii.gz \
-c [ 200,0.0005 ] \
-a diff.nii.gz \
-i kmeans[ 2 ] \
-s 1x2 \
-k HistogramParzenWindows[ 1,32 ] \
-m [ 0.1,1x1x1 ] \
-o [ tmpSegmentation.nii.gz,posteriors%d.nii.gz ] \
-r 1 -p Socrates[ 0 ]

However, it crashes with the following terminal output:

Atropos(6030,0x30f7b5000) malloc: *** error for object 0x600002380f00: pointer being freed was not allocated
Atropos(6030,0x30f7b5000) malloc: *** set a breakpoint in malloc_error_break to debug
zsh: abort noglob Atropos -d 3 -x VISIT01/T1_brainmask.nii.gz -c [ 200,0.0005 ] -a -i

On the other hand, I had no problems with the ANTs 2.4.2 version (also downloaded GitHub release binary).

[cookpa]

Hi @devDonnn , sorry for the delay in getting to this. I don't have an arm64 machine so I didn't investigate right away.

I can reproduce this though on Intel Mac and Linux. It goes away if I replace the likelihood model 'HistogramParzenWindows' with 'Gaussian'

Reproduced with

Atropos -d 3 -x tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz \
-c [ 200,0.0005 ] \
-a tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz \
-i kmeans[ 2 ] \
-k HistogramParzenWindows[ 1, 32 ] \
-m [ 0.1,1x1x1 ] \
-o [ tmpSegmentation.nii.gz,posteriors%d.nii.gz ] \
-r 1 -p Socrates[ 0 ] \
--verbose

[cookpa]

Many ANTs compilations later, I have isolated the commit:

0ac02f6f4475ce3d83f871d3437d512184b51cde is the first bad commit
commit 0ac02f6f4475ce3d83f871d3437d512184b51cde
Author: Christian P. V. Christoffersen <88783438+br-cpvc@users.noreply.github.com>
Date:   Tue Dec 6 13:12:39 2022 +0000

    accelerating antsAtroposSegmentationImageFilter.hxx function GetPosteriorProbabilityImage using ITK ParallelizeImageRegion

 ImageSegmentation/antsAtroposSegmentationImageFilter.hxx | 11 +++++++++--

[cookpa]

OK so to gather the information,

this fails if multi-threaded, starting at commit 0ac02f6 by @br-cpvc

Atropos -d 3 -x tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz \
-c [ 200,0.0005 ] \
-a tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz \
-i kmeans[ 2 ] \
-k HistogramParzenWindows[ 1, 32 ] \
-m [ 0.1,1x1x1 ] \
-o [ tmpSegmentation.nii.gz,posteriors%d.nii.gz ] \
-r 1 -p Socrates[ 0 ] \
--verbose

It works if I use a single thread, or if I change the likelihood to Gaussian. But it fails if using HistogramParzenWindows and multiple threads.

[cookpa]

(lldb) run -d 3 -x tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -c [ 200,0.0005 ] -a tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz -i kmeans[ 2 ] -k HistogramParzenWindows[ 1, 32 ] -m [ 0.1,1x1x1 ] -o [ tmpSegmentation.nii.gz,posteriors%d.nii.gz ] -r 1 -p Socrates[ 0 ] --verbose
Process 77613 launched: '/Users/pcook/tmp/NOT_BACKED_UP/antsAtroposMalloc/install/bin/Atropos' (x86_64)

Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 200): posterior probability = 0 (annealing temperature = 1)
Atropos(77613,0x70000d846000) malloc: *** error for object 0x600001708640: pointer being freed was not allocated
Atropos(77613,0x70000d846000) malloc: *** set a breakpoint in malloc_error_break to debug
Process 77613 stopped
* thread #2, stop reason = breakpoint 1.1
    frame #0: 0x00007ff8130345bc libsystem_malloc.dylib`malloc_error_break
libsystem_malloc.dylib`malloc_error_break:
->  0x7ff8130345bc <+0>: pushq  %rbp
    0x7ff8130345bd <+1>: movq   %rsp, %rbp
    0x7ff8130345c0 <+4>: nop    
    0x7ff8130345c1 <+5>: nopl   (%rax)
Target 0: (Atropos) stopped.
(lldb) thread backtrace
* thread #2, stop reason = breakpoint 1.1
  * frame #0: 0x00007ff8130345bc libsystem_malloc.dylib`malloc_error_break
    frame #1: 0x00007ff8130262eb libsystem_malloc.dylib`malloc_vreport + 443
    frame #2: 0x00007ff81302952b libsystem_malloc.dylib`malloc_report + 151
    frame #3: 0x00000001010edfd5 Atropos`void std::__1::__libcpp_operator_delete<void*>(__args=0x0000600001708640) at new:245:3
    frame #4: 0x00000001010edf89 Atropos`void std::__1::__do_deallocate_handle_size<>(__ptr=0x0000600001708640, __size=64) at new:269:10
    frame #5: 0x00000001010edf15 Atropos`std::__1::__libcpp_deallocate(__ptr=0x0000600001708640, __size=64, __align=8) at new:285:14
    frame #6: 0x00000001010eff8a Atropos`std::__1::allocator<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, void*> >::deallocate(this=0x0000000106304768, __p=0x0000600001708640, __n=1) at allocator.h:117:13
    frame #7: 0x00000001010efeb5 Atropos`std::__1::allocator_traits<std::__1::allocator<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, void*> > >::deallocate(__a=0x0000000106304768, __p=0x0000600001708640, __n=1) at allocator_traits.h:282:13
    frame #8: 0x00000001010efde3 Atropos`std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool> > >::destroy(this=0x0000000106304760, __nd=0x0000600001708640) at __tree:1804:9
    frame #9: 0x00000001010f86f5 Atropos`std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool> > >::clear(this=0x0000000106304760) at __tree:1840:5
    frame #10: 0x00000001010ed315 Atropos`std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, bool> > >::clear(this=0x0000000106304760 size=0) at map:1336:37
    frame #11: 0x00000001010ed45f Atropos`itk::ProcessObject::RestoreInputReleaseDataFlags(this=0x00000001063046b0) at itkProcessObject.cxx:1780:33
    frame #12: 0x00000001010ed1aa Atropos`itk::ProcessObject::UpdateOutputData(this=0x00000001063046b0, (null)=0x0000000106304830) at itkProcessObject.cxx:1739:9
    frame #13: 0x0000000101123a4a Atropos`itk::DataObject::UpdateOutputData(this=0x0000000106304830) at itkDataObject.cxx:388:17
    frame #14: 0x000000010018d917 Atropos`itk::ImageBase<1u>::UpdateOutputData(this=0x0000000106304830) at itkImageBase.hxx:265:23
    frame #15: 0x0000000101123757 Atropos`itk::DataObject::Update(this=0x0000000106304830) at itkDataObject.cxx:319:9
    frame #16: 0x00000001010ebe51 Atropos`itk::ProcessObject::Update(this=0x00000001063046b0) at itkProcessObject.cxx:1286:20
    frame #17: 0x000000010017e79f Atropos`itk::BSplineInterpolateImageFunction<itk::Image<float, 1u>, double, double>::SetInputImage(this=0x0000000106304550, inputData=0x0000000103e04720) at itkBSplineInterpolateImageFunction.hxx:124:26
    frame #18: 0x000000010017c280 Atropos`itk::ants::Statistics::HistogramParzenWindowsListSampleFunction<itk::Statistics::ListSample<itk::Array<float> >, float, float>::Evaluate(this=0x000060000330c000, measurement=0x000070000d845598) const at antsHistogramParzenWindowsListSampleFunction.hxx:205:29
    frame #19: 0x000000010030e7d6 Atropos`itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(this=0x00007ff7bfefa830, outputRegionForThread=0x000070000d845af0)::'lambda'(itk::ImageRegion<3u> const&)::operator()(itk::ImageRegion<3u> const&) const at antsAtroposSegmentationImageFilter.hxx:2090:70
    frame #20: 0x000000010030dced Atropos`void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(this=0x0000600006d6c098, index=0x00006000008d4100, size=0x00006000008d4120)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)::operator()(long const*, unsigned long const*) const at itkMultiThreaderBase.h:352:9
    frame #21: 0x000000010030dc1b Atropos`decltype(__f=0x0000600006d6c098, __args=0x000070000d845ca0, __args=0x000070000d845c98)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)&>(fp)(static_cast<long const*>(fp0), static_cast<unsigned long const*>(fp0))) std::__1::__invoke<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)&, long const*, unsigned long const*>(void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)&, long const*&&, unsigned long const*&&) at type_traits:3918:1
    frame #22: 0x000000010030dbc7 Atropos`void std::__1::__invoke_void_return_wrapper<void, true>::__call<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(__args=0x0000600006d6c098, __args=0x000070000d845ca0, __args=0x000070000d845c98)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)&, long const*, unsigned long const*>(void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)&, long const*&&, unsigned long const*&&) at invoke.h:61:9
    frame #23: 0x000000010030db77 Atropos`std::__1::__function::__alloc_func<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*), std::__1::allocator<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)>, void (long const*, unsigned long const*)>::operator(this=0x0000600006d6c098, __arg=0x000070000d845ca0, __arg=0x000070000d845c98)(long const*&&, unsigned long const*&&) at function.h:178:16
    frame #24: 0x000000010030c8b6 Atropos`std::__1::__function::__func<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*), std::__1::allocator<void itk::MultiThreaderBase::ParallelizeImageRegion<3u, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&)>(itk::ImageRegion<3u> const&, itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >::GetPosteriorProbabilityImage(unsigned int)::'lambda'(itk::ImageRegion<3u> const&), itk::ProcessObject*)::'lambda'(long const*, unsigned long const*)>, void (long const*, unsigned long const*)>::operator(this=0x0000600006d6c090, __arg=0x000070000d845ca0, __arg=0x000070000d845c98)(long const*&&, unsigned long const*&&) at function.h:352:12
    frame #25: 0x000000010110845f Atropos`std::__1::__function::__value_func<void (long const*, unsigned long const*)>::operator(this=0x0000600006d6c090, __args=0x000070000d845ca0, __args=0x000070000d845c98)(long const*&&, unsigned long const*&&) const at function.h:505:16
    frame #26: 0x00000001011029c2 Atropos`std::__1::function<void (long const*, unsigned long const*)>::operator(this=0x0000600006d6c090, __arg=0x00006000008d4100, __arg=0x00006000008d4120)(long const*, unsigned long const*) const at function.h:1182:12
    frame #27: 0x0000000101184ac6 Atropos`itk::PoolMultiThreader::ParallelizeImageRegion(this=0x0000600006d6c090)>, itk::ProcessObject*)::$_5::operator()() const at itkPoolMultiThreader.cxx:271:13
    frame #28: 0x0000000101184a65 Atropos`std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(this=0x0000600006d6c090)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda'()::operator()() const at itkThreadPool.h:92:58
    frame #29: 0x0000000101184a45 Atropos`decltype(__f=0x0000600006d6c090)>, itk::ProcessObject*)::$_5>(fp)()) std::__1::__invoke<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda'()&>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&) at type_traits:3918:1
    frame #30: 0x00000001011843a1 Atropos`std::__1::__packaged_task_func<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda'(), std::__1::allocator<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda'()>, void* ()>::operator(this=0x0000600006d6c080)() at future:1687:12
    frame #31: 0x000000010117ed0a Atropos`std::__1::__packaged_task_function<void* ()>::operator(this=0x0000600002610680)() const at future:1869:12
    frame #32: 0x000000010117ebd1 Atropos`std::__1::packaged_task<void* ()>::operator(this=0x0000600002610680)() at future:1960:24
    frame #33: 0x000000010118687d Atropos`std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(this=0x000070000d845ef8)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()::operator()() const at itkThreadPool.h:97:43
    frame #34: 0x0000000101186845 Atropos`decltype(__f=0x000070000d845ef8)>, itk::ProcessObject*)::$_5>(fp)()) std::__1::__invoke<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()&>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&) at type_traits:3918:1
    frame #35: 0x00000001011867fd Atropos`void std::__1::__invoke_void_return_wrapper<void, true>::__call<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(__args=0x000070000d845ef8)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()&>(std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()&) at invoke.h:61:9
    frame #36: 0x00000001011867cd Atropos`std::__1::__function::__alloc_func<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'(), std::__1::allocator<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()>, void ()>::operator(this=0x000070000d845ef8)() at function.h:178:16
    frame #37: 0x00000001011853b9 Atropos`std::__1::__function::__func<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'(), std::__1::allocator<std::__1::future<std::__1::invoke_result<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>::type> itk::ThreadPool::AddWork<itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5>(itk::PoolMultiThreader::ParallelizeImageRegion(unsigned int, long const*, unsigned long const*, std::__1::function<void (long const*, unsigned long const*)>, itk::ProcessObject*)::$_5&&)::'lambda0'()>, void ()>::operator(this=0x000070000d845ef0)() at function.h:352:12
    frame #38: 0x0000000101155542 Atropos`std::__1::__function::__value_func<void ()>::operator(this=0x000070000d845ef0)() const at function.h:505:16
    frame #39: 0x0000000101151a15 Atropos`std::__1::function<void ()>::operator(this=0x000070000d845ef0)() const at function.h:1182:12
    frame #40: 0x000000010118747a Atropos`itk::ThreadPool::ThreadExecute() at itkThreadPool.cxx:211:5
    frame #41: 0x000000010118cf12 Atropos`decltype(__f=0x0000600000018048)()) std::__1::__invoke<void (*)()>(void (*&&)()) at type_traits:3918:1
    frame #42: 0x000000010118ceb5 Atropos`void std::__1::__thread_execute<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct> >, void (*)()>(__t=size=2, (null)=__tuple_indices<> @ 0x000070000d845f68)()>&, std::__1::__tuple_indices<>) at thread:287:5
    frame #43: 0x000000010118c732 Atropos`void* std::__1::__thread_proxy<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct> >, void (*)()> >(__vp=0x0000600000018040) at thread:298:5
    frame #44: 0x00007ff8131fe4e1 libsystem_pthread.dylib`_pthread_start + 125
    frame #45: 0x00007ff8131f9f6b libsystem_pthread.dylib`thread_start + 15

Debug stack trace from lldb. Looking at frame #18. Can't do much more for now but will look again later

[cookpa]

Looks like the problem is here

ANTs/ImageSegmentation/antsHistogramParzenWindowsListSampleFunction.hxx

Line 205 in b1dc295

this->m_Interpolator->SetInputImage(this->m_HistogramImages[d]);

Multiple threads are using the same m_Interpolator object simultaneously. Using a local interpolator (as is done in antsJointHistogramParzenWindowsListSampleFunction.hxx) fixes the malloc error but makes the overall process much slower than it was when single-threaded.

I'm not sure of the best way to proceed here, @ntustison would you mind taking a look when you have some time? Thanks

[ntustison]

Will do. Thanks for tracking this down @cookpa

[cookpa]

Thanks! FYI ManifoldParzenWindows also seg faults, but I haven't used that one much.

[cookpa]

@devDonnn I believe this is fixed now with #1663

[cookpa]

Results look good and consistent with v2.4.0