Failed to compute results. Command 'elastix' died with <Signals.SIGABRT: 6>. about slicerelastix

[lassoan]

@jcfr could you have a look? Maybe there are still some packaging errors on mac? We saw a similar problem yesterday on a SlicerMorph workshop participant's xomouter: ModelToModelDistance was failing with this error on an M2 (Slicer-5.4 with latest extension).

[jcfr]

Maybe there are still some packaging errors on mac?

Indeed, I didn't have a chance to fix this issue:

• #43

[jcfr]

won't work on new MacBook anymore?

Once the issue referenced above is fixed, it will be available again.

[lassoan]

@jcfr Could you have a look at this? We need to use Elastix in the SlicerHeart project but most of the research assistants use macOS, so they cannot. It fails with the same <Signals.SIGABRT: 6> error on both the latest Slicer Stable Release and latest Slicer Preview Release.

[Ox1deL]

Does that mean Elastix won't work on new MacBook anymore?

[aabrown100-git]

Thank you for this tool! Just wondering if there is a fix for this issue yet?

[lassoan]

Please try again with the latest Slicer Stable Release (currenty 5.6.1) and latest Slicer Preview Release and let us know if you still experience any problem.

[aabrown100-git]

Thanks for your response. I still get the error on both the latest Slicer Stable Release and Preview Release.

[lassoan]

Thanks for testing. I guess @jcfr will get back to us here soon (probably after the holidays).

[lassoan]

It seems that the issue is that OpenMP is not found: https://discourse.slicer.org/t/command-elastix-died-with-signals-sigabrt-6/32970/9?u=lassoan

@jcfr so you think we an bundle OpenMP or we should disable OpenMP on macOS?

[che85]

@DevLaurence Do you know anyone from our group encountering this issue when using propagation with my modified module?

[sulentica]

DevLaurence Do you know anyone from our group encountering this issue when using propagation with my modified module?

@che85 I encountered this issue when meeting with @lassoan this morning.

[che85]

I just ran it in a Slicer 5.7.0 preview release and indeed getting the same error. In the meantime, as a workaround, one could use the elastix binary of the Slicer 5.2.2 stable release which works fine.

When using the elastix binary of 5.4.0 release getting the same error:

Command 'elastix' died with <Signals.SIGABRT: 6>.
Traceback (most recent call last):
  File "/Applications/Slicer-5.7.0_preview.app/Contents/Extensions-32651/SequenceRegistration/lib/Slicer-5.7/qt-scripted-modules/SequenceRegistration.py", line 439, in onApplyButton
    self.logic.registerVolumeSequence(self.inputSelector.currentNode(),
  File "/Applications/Slicer-5.7.0_preview.app/Contents/Extensions-32651/SequenceRegistration/lib/Slicer-5.7/qt-scripted-modules/SequenceRegistration.py", line 561, in registerVolumeSequence
    self.elastixLogic.registerVolumes(
  File "/Applications/Slicer-5.7.0_preview.app/Contents/Extensions-32651/SlicerElastix/lib/Slicer-5.7/qt-scripted-modules/Elastix.py", line 564, in registerVolumes
    self.logProcessOutput(elastixProcess)
  File "/Applications/Slicer-5.7.0_preview.app/Contents/Extensions-32651/SlicerElastix/lib/Slicer-5.7/qt-scripted-modules/Elastix.py", line 499, in logProcessOutput
    raise subprocess.CalledProcessError(return_code, "elastix")
subprocess.CalledProcessError: Command 'elastix' died with <Signals.SIGABRT: 6>.

[che85]

Same error with Slicer 5.3.0 on M2 Max. So I am assuming that it must have been a change between 5.2.0 and 5.3.0

@jcfr Hope that helps to narrow it down

Traceback (most recent call last):
  File "/Applications/Slicer-5.3.0_stable.app/Contents/Extensions-31913/SequenceRegistration/lib/Slicer-5.3/qt-scripted-modules/SequenceRegistration.py", line 439, in onApplyButton
    self.logic.registerVolumeSequence(self.inputSelector.currentNode(),
  File "/Applications/Slicer-5.3.0_stable.app/Contents/Extensions-31913/SequenceRegistration/lib/Slicer-5.3/qt-scripted-modules/SequenceRegistration.py", line 561, in registerVolumeSequence
    self.elastixLogic.registerVolumes(
  File "/Applications/Slicer-5.3.0_stable.app/Contents/Extensions-31913/SlicerElastix/lib/Slicer-5.3/qt-scripted-modules/Elastix.py", line 564, in registerVolumes
    self.logProcessOutput(elastixProcess)
  File "/Applications/Slicer-5.3.0_stable.app/Contents/Extensions-31913/SlicerElastix/lib/Slicer-5.3/qt-scripted-modules/Elastix.py", line 499, in logProcessOutput
    raise subprocess.CalledProcessError(return_code, "elastix")
subprocess.CalledProcessError: Command 'elastix' died with <Signals.SIGABRT: 6>.

[che85]

I just built Slicer and SlicerElastix locally on my M2 and everything seems to be working just fine.

[jcfr]

I will have a look this afternoon, could you provide me with the steps (and data) leading to the issue ?

[che85]

1. Download SampleData MRBrainTumor1 and MRBrainTumor2
2. Open General Registration (Elastix)
3. Set Fixed and Moving volume
4. Create output transform
5. Run

[lassoan]

@che85 got this error when trying to execute Elastix on the console:

(base) herzc@K4YF7L70NQ Slicer-5.4 % ./elastix
dyld[26616]: Library not loaded: @rpath/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib
  Referenced from: <B727E4F5-7E1A-3E0A-92BE-2389498D5492> /Applications/Slicer-5.4.0_stable.app/Contents/Extensions-31938/SlicerElastix/lib/Slicer-5.4/elastix
  Reason: tried: '/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/usr/local/lib:/Users/svc-dashboard/D/S/A/ITK-build/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib:/Users/svc-dashboard/D/S/A/ITK-build/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/svc-dashboard/D/Support/clang+llvm-14.0.6-x86_64-apple-darwin/lib/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/usr/local/lib:/Users/svc-dashboard/D/S/A/ITK-build/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib:/Users/svc-dashboard/D/S/A/ITK-build/Extensions-31938/SlicerElastix/lib/Slicer-5.4/libomp.dylib' (no such file), '/usr/local/lib/libomp.dylib' (no such file), '/usr/lib/libomp.dylib' (no such file, not in dyld cache)
zsh: abort      ./elastix

It seems that OpenMP (libomp.dylib) is used during building the extension but it is not included in the package. As a quick workaround, I've disabled OpenMP in Elastix (we'll see tomorrow if it fixes the issue).

It would be nicer if it could be enabled. @jcfr how libomp.dylib could be added to the package? Could adding it to the package cause any problems for other components (Slicer modules, extensions, Python packages, ...) that use also OpenMP, but perhaps a different version?

[che85]

@jcfr @lassoan The changes you made to SlicerElastix fixed the issue. I just tested with the update SlicerElastix version on macOS and it works.

[jcfr]

We can now close the corresponding issue were we suggested disabling openmp:

• #43

[lassoan]

Thank you @che85 for testing!