segfault importing vtkhdf files

Development
1

Hi there,

I’m experiencing a segfault importing vtkhdf files with paraview 5.13, 6.0.0, and 6.0.1

This only seems to happen on fedora, I do not get a segfault on debian 13

Any ideas?

application called MPI_Abort(MPI_COMM_WORLD, 738811141) - process 0
[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=738811141 message=application called MPI_Abort(MPI_COMM_WORLD, 738811141) - process 0
:
system msg for write_line failure : Bad file descriptor
[fedora:11744:0:11744] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace (tid:  11744) ====
 0  /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7f74cffb2df4]
 1  /lib64/libucs.so.0(+0x17aed) [0x7f74cffb4aed]
 2  /lib64/libucs.so.0(+0x17cbd) [0x7f74cffb4cbd]
 3  /lib64/libc.so.6(+0x1a070) [0x7f74ec828070]
 4  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libQt6Core.so.6(_ZNK18QThreadStorageData3getEv+0x34) [0x7f74f4f3ea24]
 5  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libQt6Gui.so.6(_ZN21QOpenGLContextPrivate17setCurrentContextEP14QOpenGLContext+0x46) [0x7f74f59af976]
 6  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libQt6Gui.so.6(_ZN14QOpenGLContext11makeCurrentEP8QSurface+0xd5) [0x7f74f59b0f15]
 7  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkGUISupportQt-pv6.0.so.1(+0x3b9ec) [0x7f74f62c19ec]
 8  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkCommonCore-pv6.0.so.1(+0x18065ed) [0x7f74ee6065ed]
 9  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRenderingCore-pv6.0.so.1(_ZN11vtkViewport14RemoveViewPropEP7vtkProp+0xa5) [0x7f74f2942965]
10  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkInteractionWidgets-pv6.0.so.1(_ZN17vtkAbstractWidgetD1Ev+0x3b) [0x7f74f3e3f55b]
11  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkInteractionWidgets-pv6.0.so.1(_ZN26vtkCameraOrientationWidgetD0Ev+0x9) [0x7f74f3e94339]
12  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingViews-pv6.0.so.1(_ZN15vtkPVRenderViewD2Ev+0x37e) [0x7f74eaa147be]
13  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingViews-pv6.0.so.1(_ZN15vtkPVRenderViewD0Ev+0x9) [0x7f74eaa14839]
14  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkCommonCore-pv6.0.so.1(_ZN19vtkSmartPointerBaseD1Ev+0x1e) [0x7f74ee6a064e]
15  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkCommonCore-pv6.0.so.1(_ZN19vtkSmartPointerBaseaSEP13vtkObjectBase+0x2f) [0x7f74ee6a06ef]
16  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN10vtkSIProxy16DeleteVTKObjectsEv+0x2b) [0x7f74f490c84b]
17  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN10vtkSIProxyD1Ev+0x20) [0x7f74f490d540]
18  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN10vtkSIProxyD0Ev+0x9) [0x7f74f490d729]
19  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN16vtkPVSessionCoreD2Ev+0x175) [0x7f74f48ed155]
20  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN16vtkPVSessionCoreD0Ev+0x9) [0x7f74f48ed269]
21  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN16vtkPVSessionBaseD1Ev+0x38) [0x7f74f48e9848]
22  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingServerManager-pv6.0.so.1(_ZN12vtkSMSessionD0Ev+0x9) [0x7f74f4a12669]
23  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkCommonCore-pv6.0.so.1(_ZN19vtkSmartPointerBaseD1Ev+0x1e) [0x7f74ee6a064e]
24  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingCore-pv6.0.so.1(+0x4c064) [0x7f74f3b23064]
25  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingCore-pv6.0.so.1(_ZN16vtkProcessModuleD1Ev+0x82) [0x7f74f3b232d2]
26  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingCore-pv6.0.so.1(_ZN16vtkProcessModuleD0Ev+0x9) [0x7f74f3b23359]
27  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkCommonCore-pv6.0.so.1(_ZN19vtkSmartPointerBaseD1Ev+0x1e) [0x7f74ee6a064e]
28  /lib64/libc.so.6(__cxa_finalize+0x1fc) [0x7f74ec82a27c]
29  /app/ParaView-6.0.1-MPI-Linux-Python3.12-x86_64/bin/../lib/libvtkRemotingCore-pv6.0.so.1(+0x41127) [0x7f74f3b18127]
=================================
error: exception occurred: Segmentation fault

thanks

2

Please share your data.

1 Like
3

Mathieu, thanks for the repsonse, I can tell you that the files imported and working elsewhere, but maybe the issue is due to wayland vs x11?

ions_pop_protons_density.vtkhdf (2.9 MB)

4

That doesnt sound related at all

In any case, I’m able to open your file using ParaView 6.0.1 binary release on Linux, but it opens as empty, no points, no cells.

5

I’m not positive my issue is even vtkhdf related, the stack trace says mpi abort

6

A release stack trace doesnt hold much truth.

Anyway, do you have segfaults only with this file ?

7

I have several vtkhdf files with mesh data, and they all segfault

I have no reason at the moment to work with another format, but I am open to testing something if you have a suggestion

8

Does the following work:

Source → Wavelet → Apply

?

9

it does, it seems the importing file dialog is where the trigger is, so

I’ve tried importing this mentioned here

and this does work, but perhaps it’s too simple compared to vtkhdf

10

As I’m unable to reproduce locally its hard for me to say what is hapenning.
You may want to try on another computer or OS to figure out what is causing this.

11

I’m building from source so we’ll see if it shows me a better stack

1 Like
12

building locally from source does not have any segfault

this uses qt6 libs on the host rather than those shipped with paraview, so not sure if it matters

I’ll probably just recompile in release and use that