Paraview 5.9 stopped working

massisenergy · March 19, 2021, 6:23pm

Recently, paraview suddenly stopped working (till 5.8 it was working fine) after updating. When I try to launch the guiGUI, it doesn’t open at all. In the console, with paraview launch command, it gives the following error:

Loguru caught a signal: SIGABRT
Stack trace:
39      0x55f944a5f88e paraview(+0x788e) [0x55f944a5f88e]
38      0x7fa9f84f9b25 __libc_start_main + 213
37      0x55f944a5f562 paraview(+0x7562) [0x55f944a5f562]
36      0x55f944a648ce paraview(+0xc8ce) [0x55f944a648ce]
35      0x55f944a60767 paraview(+0x8767) [0x55f944a60767]
34      0x7fa9f837aaaa pqParaViewBehaviors::pqParaViewBehaviors(QMainWindow*, QObject*) + 1114
33      0x7fa9f82ecaac pqAlwaysConnectedBehavior::pqAlwaysConnectedBehavior(QObject*) + 332
32      0x7fa9f76655aa pqObjectBuilder::createServer(pqServerResource const&, int) + 410
31      0x7fa9f66da706 vtkSMSession::ConnectToSelf(int) + 134
30      0x7fa9f5e7b37c vtkProcessModule::RegisterSession(vtkSession*) + 172
29      0x7fa9f3dfe942 /usr/bin/../lib/libvtkCommonCore-pv5.9.so.1(+0x42c942) [0x7fa9f3dfe942]
28      0x7fa9f3c57629 vtkCallbackCommand::Execute(vtkObject*, unsigned long, void*) + 25
27      0x7fa9f67d72de /usr/bin/../lib/libvtkGUISupportQt-pv5.9.so.1(+0x262de) [0x7fa9f67d72de]
26      0x7fa9f6b7fdc0 /usr/bin/../lib/libQt5Core.so.5(+0x2ecdc0) [0x7fa9f6b7fdc0]
25      0x7fa9f75f87f3 pqServerManagerObserver::connectionCreated(long long) + 67
24      0x7fa9f6b7fdc0 /usr/bin/../lib/libQt5Core.so.5(+0x2ecdc0) [0x7fa9f6b7fdc0]
23      0x7fa9f76b37dd pqServerManagerModel::onConnectionCreated(long long) + 893
22      0x7fa9f75f5353 pqServerManagerModel::serverAdded(pqServer*) + 67
21      0x7fa9f6b7fdc0 /usr/bin/../lib/libQt5Core.so.5(+0x2ecdc0) [0x7fa9f6b7fdc0]
20      0x7fa9f8342340 pqDefaultViewBehavior::onServerCreation(pqServer*) + 688
19      0x7fa9f766198b pqObjectBuilder::createView(QString const&, pqServer*) + 187
18      0x7fa9f66e8b67 vtkSMSessionProxyManager::NewProxy(char const*, char const*, char const*) + 183
17      0x7fa9f66e8770 vtkSMSessionProxyManager::NewProxy(vtkPVXMLElement*, char const*, char const*, char const*) + 736
16      0x7fa9f1d11884 vtkSMViewProxy::ReadXMLAttributes(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 20
15      0x7fa9f66afa71 vtkSMProxy::ReadXMLAttributes(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 1697
14      0x7fa9f66b1fc8 vtkSMProxy::CreateSubProxiesAndProperties(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 440
13      0x7fa9f66aecaf vtkSMProxy::NewProperty(char const*, vtkPVXMLElement*) + 607
12      0x7fa9f671c5b0 vtkSMStringVectorProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 48
11      0x7fa9f67272e8 vtkSMVectorProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 40
10      0x7fa9f6698dab vtkSMProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 5307
9       0x7fa9f1cd5c1d vtkSMRendererDomain::ReadXMLAttributes(vtkSMProperty*, vtkPVXMLElement*) + 29
8       0x7fa9f1cd589c vtkSMRendererDomain::Update(vtkSMProperty*) + 60
7       0x7fa9eee2c904 vtkOSPRayPass::IsBackendAvailable(char const*) + 36
6       0x7fa9eee0cac2 /usr/bin/../lib/libvtkRenderingRayTracing-pv5.9.so.1(+0x1eac2) [0x7fa9eee0cac2]
5       0x7fa9e89dd333 ospInit + 2611
4       0x7fa9b415489b ospray::api::ISPCDevice::commit() + 379
3       0x7fa9b41cadd0 ISPCDevice_programCount + 64
2       0x7fa9f84f8862 abort + 278
1       0x7fa9f850eef5 gsignal + 325
0       0x7fa9f850ef80 /usr/bin/../lib/libc.so.6(+0x3cf80) [0x7fa9f850ef80]
(   0.784s) [paraview        ]                       :0     FATL| Signal: SIGABRT
[1]    232050 abort (core dumped)  paraview

I tried running paraview from a downloaded pre-complied binary. Which results in the same outcome. Can any one have any idea how can this be rectified? My system is : Archlinux with KDEPlasma.

wascott · March 19, 2021, 7:16pm

The root cause of the issue is almost definitely your configuration files. Please move them to the side, and if this fixes it, Cory may want to look at them.

Please close all versions of ParaView. Go to your home directory (I assume on Mac or Linux), and then cd to .config. Move (mv) the directory ParaView to ParaView-store.

Now try ParaView again.

@cory.quammen

massisenergy · March 19, 2021, 8:52pm

Nope. Sorry. That didn’t work, but I think of similar cause, since installed Paraview (version 5.9.0-1
, from aur: Arch User Repository) & packaged binary behaves in the same way…

Here I’m posting the error from the downloaded version (ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/Paraview). This might give some hint to you guys, but not in my forte:

(   1.277s) [paraview        ]      VisRTXBackend.cxx:42    WARN| VisRTX Error: Unsupported device
(   1.277s) [paraview        ]      VisRTXBackend.cxx:42    WARN| VisRTX Error: Unsupported device

Loguru caught a signal: SIGABRT
Stack trace:
42            0x407b2a /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/paraview-real() [0x407b2a]
41      0x7f7a17c21b25 __libc_start_main + 213
40            0x40776d /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/paraview-real() [0x40776d]
39            0x40c6d0 /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/paraview-real() [0x40c6d0]
38            0x408978 /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/paraview-real() [0x408978]
37      0x7f7a178a6a19 pqParaViewBehaviors::pqParaViewBehaviors(QMainWindow*, QObject*) + 1049
36      0x7f7a17819366 pqAlwaysConnectedBehavior::pqAlwaysConnectedBehavior(QObject*) + 310
35      0x7f7a178191ee pqAlwaysConnectedBehavior::serverCheck() + 174
34      0x7f7a1621375d pqObjectBuilder::createServer(pqServerResource const&, int) + 605
33      0x7f7a1447526a vtkSMSession::ConnectToSelf(int) + 106
32      0x7f7a13691388 vtkProcessModule::RegisterSession(vtkSession*) + 376
31      0x7f7a0e9ba102 /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/../lib/libvtkCommonCore-pv5.9.so.1(+0x3f3102) [0x7f7a0e9ba102]
30      0x7f7a0e841209 vtkCallbackCommand::Execute(vtkObject*, unsigned long, void*) + 25
29      0x7f7a1497df10 /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/../lib/libvtkGUISupportQt-pv5.9.so.1(+0x39f10) [0x7f7a1497df10]
28      0x7f7a1496a2ab /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/../lib/libvtkGUISupportQt-pv5.9.so.1(+0x262ab) [0x7f7a1496a2ab]
27      0x7f7a150c81ea QMetaObject::activate(QObject*, int, int, void**) + 1850
26      0x7f7a161a97b9 /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/../lib/libpqCore-pv5.9.so.1(+0x7a7b9) [0x7f7a161a97b9]
25      0x7f7a161a64f2 pqServerManagerObserver::connectionCreated(long long) + 50
24      0x7f7a150c81ea QMetaObject::activate(QObject*, int, int, void**) + 1850
23      0x7f7a1626042e pqServerManagerModel::onConnectionCreated(long long) + 670
22      0x7f7a161a50a2 pqServerManagerModel::serverAdded(pqServer*) + 50
21      0x7f7a150c81ea QMetaObject::activate(QObject*, int, int, void**) + 1850
20      0x7f7a1786ce0a pqDefaultViewBehavior::onServerCreation(pqServer*) + 666
19      0x7f7a1620f3c1 pqObjectBuilder::createView(QString const&, pqServer*) + 161
18      0x7f7a1448197b vtkSMSessionProxyManager::NewProxy(char const*, char const*, char const*) + 203
17      0x7f7a144816d1 vtkSMSessionProxyManager::NewProxy(vtkPVXMLElement*, char const*, char const*, char const*) + 369
16      0x7f7a0b17f315 vtkSMViewProxy::ReadXMLAttributes(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 21
15      0x7f7a1444239a vtkSMProxy::ReadXMLAttributes(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 666
14      0x7f7a14443e77 vtkSMProxy::CreateSubProxiesAndProperties(vtkSMSessionProxyManager*, vtkPVXMLElement*) + 343
13      0x7f7a14441b2e vtkSMProxy::NewProperty(char const*, vtkPVXMLElement*) + 462
12      0x7f7a144b4409 vtkSMStringVectorProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 25
11      0x7f7a144bf497 vtkSMVectorProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 23
10      0x7f7a1442c8e4 vtkSMProperty::ReadXMLAttributes(vtkSMProxy*, vtkPVXMLElement*) + 6708
9       0x7f7a0b13c0ae vtkSMRendererDomain::ReadXMLAttributes(vtkSMProperty*, vtkPVXMLElement*) + 30
8       0x7f7a0b13bc4b vtkSMRendererDomain::Update(vtkSMProperty*) + 43
7       0x7f7a09cf3948 vtkOSPRayPass::IsBackendAvailable(char const*) + 24
6       0x7f7a09cc297f /home/massisenergy/Downloads/ParaView-5.9.0-MPI-Linux-Python3.8-64bit/bin/../lib/libvtkRenderingRayTracing-pv5.9.so.1(+0x2097f) [0x7f7a09cc297f]
5       0x7f7a098221e3 ospInit + 4067
4       0x7f79db21dcf1 ospray::api::ISPCDevice::commit() + 145
3       0x7f79dad32864 ISPCDevice_programCount + 52
2       0x7f7a17c20862 abort + 278
1       0x7f7a17c36ef5 gsignal + 325
0       0x7f7a17c36f80 /usr/lib/libc.so.6(+0x3cf80) [0x7f7a17c36f80]
(   1.286s) [paraview        ]                       :0     FATL| Signal: SIGABRT
error: exception occurred: Child aborted

mwestphal · March 22, 2021, 1:21pm

Using Arch here and no issues at all.

Could you try building ParaView yourself ?

massisenergy · April 2, 2021, 8:25pm

I tried building from source today, using the guideline here: https://gitlab.kitware.com/paraview/paraview/blob/master/Documentation/dev/build.md#archlinux

But facing the issue mentioned here: https://discourse.paraview.org/t/build-problem-vtkm-tbb-notfound/6659/3 and here: https://gitlab.kitware.com/paraview/paraview/-/issues/20557

mwestphal · April 2, 2021, 10:07pm

Just disable VTKm

massisenergy · April 3, 2021, 9:31am

Sorry for the noob questions, but this is my first try.

Just disable VTKm

Can you elaborate a bit on that? How to do it? Editing something?

mwestphal · April 3, 2021, 10:23am

set the cmake option: PARAVIEW_USE_VTKM=OFF

massisenergy · April 3, 2021, 4:16pm

Okay, when I run cmake now,

cmake -GNinja -DPARAVIEW_USE_PYTHON=ON -DPARAVIEW_USE_MPI=ON -DVTK_SMP_IMPLEMENTATION_TYPE=TBB -DCMAKE_BUILD_TYPE=Release -DPARAVIEW_USE_VTKM=OFF ../paraview

it completes successfully but when I run:

ninja

It encounters some errors, from which attaching the tail part.

[18127/20145] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/qttesting.dir/pqTreeViewEventPlayer.cxx.o
/home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqTreeViewEventPlayer.cxx: In member function ‘virtual bool pqTreeViewEventPlayer::playEvent(QObject*, const QString&, const QString&, int, bool&)’:
/home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqTreeViewEventPlayer.cxx:79:71: warning: ‘QStringList QString::split(const QString&, QString::SplitBehavior, Qt::CaseSensitivity) const’ is deprecated: Use Qt::SplitBehavior variant instead [-Wdeprecated-declarations]
79 | QStringList indices = str_index.split(“.”, QString::SkipEmptyParts);
| ^
In file included from /usr/include/qt/QtCore/qobject.h:47,
from /usr/include/qt/QtCore/QObject:1,
from /home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqWidgetEventPlayer.h:37,
from /home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqAbstractItemViewEventPlayerBase.h:35,
from /home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqTreeViewEventPlayer.h:35,
from /home/massisenergy/paraview/ThirdParty/QtTesting/vtkqttesting/pqTreeViewEventPlayer.cxx:32:
/usr/include/qt/QtCore/qstring.h:609:17: note: declared here
609 | QStringList split(const QString &sep, SplitBehavior behavior,
| ^~~~~
[19235/20145] Building CXX object Plugins/GMVReader/Reader/CMakeFiles/vtkGMVReader.dir/vtkGMVReader.cxx.o
In file included from /home/massisenergy/paraview/Plugins/GMVReader/Reader/vtkGMVReader.cxx:65:
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c: In function ‘void GMVRead::readunits(FILE*, int)’:
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:3749:17: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
3749 | strncpy(&unitstr[i*MAXCUSTOMNAMELENGTH], unitname, GMV_MIN(strlen(unitname), MAXCUSTOMNAMELENGTH-1));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:3749:75: note: length computed here
45 | #define GMV_MIN(a1,a2) ( ((a1) < (a2)) ? (a1):(a2) )
| ~~~~
…
3749 | strncpy(&unitstr[i*MAXCUSTOMNAMELENGTH], unitname, GMV_MIN(strlen(unitname), MAXCUSTOMNAMELENGTH-1));
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:45:30: note: in definition of macro ‘GMV_MIN’
45 | #define GMV_MIN(a1,a2) ( ((a1) < (a2)) ? (a1):(a2) )
| ^~
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:3694:14: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
3694 | strncpy(gmv_data.chardata2, unitname, GMV_MIN(strlen(unitname), 20-1));
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:3694:59: note: length computed here
45 | #define GMV_MIN(a1,a2) ( ((a1) < (a2)) ? (a1):(a2) )
| ~~~~
…
3694 | strncpy(gmv_data.chardata2, unitname, GMV_MIN(strlen(unitname), 20-1));
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:45:30: note: in definition of macro ‘GMV_MIN’
45 | #define GMV_MIN(a1,a2) ( ((a1) < (a2)) ? (a1):(a2) )
| ^~
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c: In function ‘int GMVRead::checkfromfile.part.0()’:
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:1383:13: warning: ‘char* strcpy(char*, const char*)’ writing one too many bytes into a region of a size that depends on ‘strlen’ [-Wstringop-overflow=]
1383 | strcpy(gmv_data.chardata1,charptr);
| ^~~~~~~~~~~~~~~~~~~~~~
/home/massisenergy/paraview/Plugins/GMVReader/Reader/gmvread.c:1381:42: note: at offset 0 to an object with size at most 299 allocated by ‘void* malloc(size_t)’ here
1381 | gmv_data.chardata1 = (char )malloc(isizeof(char));
| ^~~~~~~~~~
[19871/20145] Building CXX object Qt/Components/CMakeFiles/pqComponents.dir/pqServerLauncher.cxx.o
/home/massisenergy/paraview/Qt/Components/pqServerLauncher.cxx: In member function ‘bool pqServerLauncher::processCommand(QString, double, double, const QProcessEnvironment*)’:
/home/massisenergy/paraview/Qt/Components/pqServerLauncher.cxx:779:25: warning: ‘void QProcess::start(const QString&, QIODevice::OpenMode)’ is deprecated: Use QProcess::start(const QString &program, const QStringList &arguments,OpenMode mode = ReadWrite) instead [-Wdeprecated-declarations]
779 | process->start(command);
| ^
In file included from /usr/include/qt/QtCore/QProcess:1,
from /home/massisenergy/paraview/Qt/Components/pqServerLauncher.h:37,
from /home/massisenergy/paraview/Qt/Components/pqServerLauncher.cxx:32:
/usr/include/qt/QtCore/qprocess.h:168:10: note: declared here
168 | void start(const QString &command, OpenMode mode = ReadWrite);
| ^~~~~
[20145/20145] Linking CXX executable bin/paraview

Then I tired to launch, using:

bin/paraview

Which yields:

bin/paraview: symbol lookup error: /usr/lib64/libvtkIOLegacy-pv5.9.so.1: undefined symbol: _ZN31vtkPartitionedDataSetCollection21GetPartitionedDataSetEj

Still not there yet, but thanks as some improvement towards the goal

mwestphal · April 6, 2021, 8:29am

This is unexpected. in your case I’d:

make sure my repository is clean and there is no changes
update my submodules
build from scratch with the same options as before
build from scratch without any options turned on

massisenergy · April 8, 2021, 4:45pm

I get same result as my last try with those suggestions Makes me think - probably it’s not a vtk-m problem?

I think I need to provide some more information about the dependencies, since all the suggested packages here are not available! When I check the status like this:

❯ pacman -Qi base-devel ninja openmpi tbb qt python python-numpy cmake

error: package ‘base-devel’ was not found
error: package ‘qt’ was not found

I found that base-devel is not a package but a group of packages. Then checked it, and found that all packages are already installed in my system. And I already have qt5-base installed. So, does anything look problematic regarding these?

massisenergy · April 27, 2021, 10:07am

I got it to work finally, with a newer version, through manual building: paraview Build guide ArchLinux and importantly, with VTKM option off.

So, the version that works now:

Client Information:
Version: 5.9.1-RC1-940-g43007029b9
VTK Version: 9.0.0-3883-geb332ee027
Qt Version: 5.15.2
vtkIdType size: 64bits
Embedded Python: On
Python Library Path: /usr/lib/python3.9
Python Library Version: 3.9.4 (default, Apr 20 2021, 15:51:38) [GCC 10.2.0]
Python Numpy Support: On
Python Numpy Path: /usr/lib/python3.9/site-packages/numpy
Python Numpy Version: 1.20.2
Python Matplotlib Support: Off
Python Testing: Off
MPI Enabled: On
Disable Registry: Off
Test Directory:
Data Directory:
OpenGL Vendor: Mesa/X.org
OpenGL Version: 4.5 (Core Profile) Mesa 21.0.3
OpenGL Renderer: llvmpipe (LLVM 11.1.0, 128 bits)

Connection Information:
Remote Connection: No

However, when I install OpenFOAM (any version from AUR or the Arch4Edu repo), it pulls older version of ParaView and this manually installed version stops working. Uninstalling the OpenFOAM and the AUR ParaView brings the manually installed Paraview version to work again. Very cumbersome, looks like I cannot use ParaView & OpenFOAM in a single ArchLinux machine '( . Anyway, that might be a topic of another post. For now, if no OpenFOAM is installed, the manually built ParaView works…

mwestphal · April 27, 2021, 10:11am

This is an issue for the AUR package of OpenFOAM.

massisenergy · April 27, 2021, 10:12am

Okay, then I shall inform the package maintainers over there.

olesenm · April 27, 2021, 11:07am

There is an Arch openfoam package, that is actually from openfoam.org, which very likely tries to provide its own paraview. I have tried to get them to at least rename their package. The Arch openfoam-com package (from openfoam.com) should not be doing anything weird with paraview.

@massisenergy

massisenergy · April 27, 2021, 3:13pm

Great. Now I got the response from the maintainer of aur/openfoam-com package. I uninstalled the ParaView Versions that OpenFOAM installed automatically:

sudo pacman -R --nodeps --nodeps aur/paraview

And then repeated the build & install procedure with ParaView Version: 5.9.1-RC1-942-g7cfe71ad8e. So I can use OpenFoam (any version) along with manually built ParaView

olesenm · April 27, 2021, 3:19pm

Yes, that is exactly what I have been pursuing - eliminating the need for any OpenFOAM-specific build of ParaView. Should make it easier to use the latest ParaView.