building version 5.7.0 on cluster (2)

Rigel · February 3, 2020, 12:44pm

Hi,

I am having problems to build version 5.7.0 of ParaView on my home directory in the Dresden University’s cluster, Taurus. taurus.sh (1.7 KB) is the script I am using. The building process gets pretty close to its end, but then fails:

[  0%] Built target ParaViewData
[  0%] Built target loguru
[  0%] Built target vtksys
[  1%] Built target CommonCore
[  1%] Built target ClientServer
[  1%] Built target WrappingTools
[  1%] Built target WrapHierarchy
[  1%] Built target CommonCore-hierarchy
[  1%] Built target WrapClientServer
[  5%] Built target vtkCommonCoreCS
[  5%] Built target CommonMath
[  5%] Built target CommonTransforms
[  5%] Built target CommonMath-hierarchy
[  5%] Built target CommonTransforms-hierarchy
[  5%] Built target vtkCommonTransformsCS
[  5%] Built target CommonSystem
[  6%] Built target CommonSystem-hierarchy
[  7%] Built target vtkCommonSystemCS
[  7%] Built target CommonMisc
[  9%] Built target CommonDataModel
[  9%] Built target CommonExecutionModel
[  9%] Built target CommonDataModel-hierarchy
[  9%] Built target CommonExecutionModel-hierarchy
[ 10%] Built target vtkCommonExecutionModelCS
[ 10%] Built target CommonMisc-hierarchy
[ 10%] Built target FiltersCore-hierarchy
[ 11%] Built target FiltersCore
[ 13%] Built target vtkFiltersCoreCS
[ 13%] Built target CommonComputationalGeometry-hierarchy
[ 14%] Built target CommonComputationalGeometry
[ 14%] Built target vtkCommonComputationalGeometryCS
[ 14%] Built target ImagingCore-hierarchy
[ 14%] Built target ImagingCore
[ 15%] Built target vtkImagingCoreCS
[ 16%] Built target FiltersGeneral
[ 16%] Built target FiltersGeometry
[ 17%] Built target vtkm_cont
[ 17%] Built target vtkm_worklet
[ 17%] Built target FiltersGeneral-hierarchy
[ 17%] Built target FiltersGeometry-hierarchy
[ 17%] Built target AcceleratorsVTKm-hierarchy
[ 17%] Built target AcceleratorsVTKm
[ 17%] Built target vtkAcceleratorsVTKmCS
[ 17%] Built target CommonColor
[ 17%] Built target CommonColor-hierarchy
[ 17%] Built target vtkCommonColorCS
[ 17%] Built target ImagingSources
[ 17%] Built target ImagingSources-hierarchy
[ 17%] Built target vtkImagingSourcesCS
[ 18%] Built target ImagingFourier
[ 18%] Built target FiltersStatistics
[ 19%] Built target FiltersExtraction
[ 19%] Built target FiltersExtraction-hierarchy
[ 19%] Built target vtkFiltersExtractionCS
[ 21%] Built target vtkFiltersGeneralCS
[ 21%] Built target FiltersSources
[ 21%] Built target FiltersSources-hierarchy
[ 22%] Built target vtkFiltersSourcesCS
[ 23%] Built target RenderingCore
[ 24%] Built target zlib
[ 24%] Built target jpeg
[ 25%] Built target tiff
[ 25%] Built target DICOMParser
[ 25%] Built target metaio
[ 25%] Built target png
[ 25%] Built target IOImage
[ 26%] Built target freetype
[ 26%] Built target RenderingFreeType
[ 26%] Built target InfovisCore
[ 26%] Built target RenderingCore-hierarchy
[ 26%] Built target RenderingFreeType-hierarchy
[ 26%] Built target IOImage-hierarchy
[ 27%] Built target InfovisCore-hierarchy
[ 28%] Built target vtkInfovisCoreCS
[ 28%] Built target RenderingContext2D
[ 28%] Built target ChartsCore
[ 28%] Built target RenderingContext2D-hierarchy
[ 28%] Built target ChartsCore-hierarchy
[ 29%] Built target vtkChartsCoreCS
[ 30%] Built target lzma
[ 30%] Built target doubleconversion
[ 30%] Built target lz4
[ 30%] Built target IOCore
[ 30%] Built target IOLegacy
[ 30%] Built target IOCore-hierarchy
[ 30%] Built target IOLegacy-hierarchy
[ 31%] Built target vtkIOLegacyCS
[ 31%] Built target glew
[ 32%] Built target RenderingOpenGL2
[ 32%] Built target RenderingOpenGL2-hierarchy
[ 33%] Built target vtkRenderingOpenGL2CS
[ 33%] Built target expat
[ 33%] Built target IOXMLParser
[ 34%] Built target IOXML
[ 34%] Built target IOXMLParser-hierarchy
[ 34%] Built target IOXML-hierarchy
[ 35%] Built target vtkIOXMLCS
[ 35%] Built target FiltersFlowPaths
[ 35%] Built target FiltersFlowPaths-hierarchy
[ 36%] Built target vtkFiltersFlowPathsCS
[ 36%] Built target FiltersHyperTree
[ 36%] Built target FiltersHyperTree-hierarchy
[ 36%] Built target vtkFiltersHyperTreeCS
[ 36%] Built target FiltersStatistics-hierarchy
[ 36%] Built target vtkFiltersStatisticsCS
[ 37%] Built target ParallelCore
[ 37%] Built target FiltersParallelStatistics
[ 37%] Built target FiltersParallelStatistics-hierarchy
[ 38%] Built target vtkFiltersParallelStatisticsCS
[ 38%] Built target DomainsChemistry-hierarchy
[ 38%] Built target DomainsChemistry
[ 38%] Built target vtkDomainsChemistryCS
[ 38%] Built target ImagingMath
[ 38%] Built target ImagingMath-hierarchy
[ 38%] Built target vtkImagingMathCS
[ 38%] Built target ClientServer-hierarchy
[ 38%] Built target Core-hierarchy
[ 38%] Built target Core
[ 38%] Built target vtkPVCoreCS
[ 38%] Built target ParallelCore-hierarchy
[ 38%] Built target VTKExtensionsCore-hierarchy
[ 38%] Built target jsoncpp
[ 38%] Built target VTKExtensionsCore
[ 38%] Built target vtkPVVTKExtensionsCoreCS
[ 42%] Built target vtkCommonDataModelCS
[ 42%] Built target H5make_libsettings
[ 44%] Built target vtkhdf5_src
[ 44%] Built target vtkhdf5_hl_src
[ 44%] Built target IOVeraOut
[ 44%] Built target IOVeraOut-hierarchy
[ 44%] Built target vtkIOVeraOutCS
[ 44%] Built target vtkIOXMLParserCS
[ 44%] Built target VTKExtensionsSIL-hierarchy
[ 44%] Built target FiltersModeling-hierarchy
[ 44%] Built target FiltersParallel-hierarchy
[ 45%] Built target ClientServerCoreCore-hierarchy
[ 46%] Built target FiltersModeling
[ 46%] Built target FiltersParallel
[ 46%] Built target pugixml
[ 46%] Built target VTKExtensionsSIL
[ 46%] Built target ClientServerCoreCore
[ 47%] Built target vtkPVClientServerCoreCoreCS
[ 47%] Built target IOTRUCHAS
[ 47%] Built target IOTRUCHAS-hierarchy
[ 47%] Built target vtkIOTRUCHASCS
[ 47%] Built target InteractionStyle-hierarchy
[ 47%] Built target RenderingAnnotation-hierarchy
[ 47%] Built target InteractionWidgets-hierarchy
[ 47%] Built target RenderingVolume-hierarchy
[ 47%] Built target RenderingVolumeOpenGL2-hierarchy
[ 47%] Built target RenderingVolumeAMR-hierarchy
[ 47%] Built target RenderingParallel-hierarchy
[ 47%] Built target RenderingContextOpenGL2-hierarchy
[ 47%] Built target IOExport-hierarchy
[ 47%] Built target RenderingGL2PSOpenGL2-hierarchy
[ 47%] Built target IOExportGL2PS-hierarchy
[ 47%] Built target FiltersGeneric-hierarchy
[ 47%] Built target VTKExtensionsRendering-hierarchy
[ 47%] Built target ImagingFourier-hierarchy
[ 47%] Built target FiltersAMR-hierarchy
[ 47%] Built target IOParallelXML-hierarchy
[ 47%] Built target IOExodus-hierarchy
[ 47%] Built target IOParallelExodus-hierarchy
[ 47%] Built target IONetCDF-hierarchy
[ 47%] Built target IOGeometry-hierarchy
[ 47%] Built target IOParallel-hierarchy
[ 47%] Built target IOImport-hierarchy
[ 47%] Built target IOEnSight-hierarchy
[ 47%] Built target VTKExtensionsDefault-hierarchy
[ 47%] Built target InteractionStyle
[ 47%] Built target ImagingColor
[ 47%] Built target RenderingAnnotation
[ 48%] Built target RenderingVolume
[ 48%] Built target FiltersHybrid
[ 48%] Built target ImagingGeneral
[ 48%] Built target ImagingHybrid
[ 49%] Built target InteractionWidgets
[ 49%] Built target RenderingVolumeOpenGL2
[ 49%] Built target FiltersAMR
[ 49%] Built target RenderingVolumeAMR
[ 49%] Built target RenderingParallel
[ 49%] Built target RenderingContextOpenGL2
[ 49%] Built target IOParallelXML
[ 50%] Built target netcdf
[ 52%] Built target exodusII
[ 52%] Built target IOExodus
[ 52%] Built target IOParallelExodus
[ 52%] Built target IOGeometry
[ 52%] Built target IONetCDF
[ 52%] Built target IOParallel
[ 52%] Built target IOImport
[ 53%] Built target libharu
[ 54%] Built target IOExport
[ 54%] Built target gl2ps
[ 54%] Built target RenderingGL2PSOpenGL2
[ 54%] Built target IOExportGL2PS
[ 54%] Built target IOEnSight
[ 54%] Built target FiltersGeneric
[ 54%] Built target VTKExtensionsRendering
[ 54%] Built target IOPLY
[ 54%] Built target libxml2
[ 54%] Built target IOInfovis
[ 55%] Built target VTKExtensionsDefault
[ 57%] Built target vtkPVVTKExtensionsDefaultCS
[ 57%] Built target vtkImagingFourierCS
[ 57%] Built target xdmf2
[ 57%] Built target IOXdmf2
[ 57%] Built target IOXdmf2-hierarchy
[ 57%] Built target vtkIOXdmf2CS
[ 57%] Built target vtkIOParallelExodusCS
[ 57%] Built target ImagingGeneral-hierarchy
[ 58%] Built target vtkImagingGeneralCS
[ 58%] Built target vtkPVVTKExtensionsSILCS
[ 58%] Built target VTKExtensionsCGNSReader-hierarchy
[ 58%] Built target cgns
[ 58%] Built target VTKExtensionsCGNSReader
[ 59%] Built target vtkPVVTKExtensionsCGNSReaderCS
[ 59%] Built target FiltersPoints-hierarchy
[ 59%] Built target VTKExtensionsPoints-hierarchy
[ 60%] Built target FiltersPoints
[ 60%] Built target VTKExtensionsPoints
[ 60%] Built target vtkPVVTKExtensionsPointsCS
[ 61%] Built target vtkIOImageCS
[ 61%] Built target IOMovie
[ 61%] Built target IOMovie-hierarchy
[ 61%] Built target vtkIOMovieCS
[ 61%] Built target TestingRendering
[ 61%] Built target TestingRendering-hierarchy
[ 61%] Built target vtkTestingRenderingCS
[ 63%] Built target vtkRenderingCoreCS
[ 63%] Built target vtkRenderingFreeTypeCS
[ 63%] Built target FiltersProgrammable
[ 63%] Built target FiltersProgrammable-hierarchy
[ 63%] Built target vtkFiltersProgrammableCS
[ 64%] Built target vtkParallelCoreCS
[ 64%] Built target ServerImplementationCore-hierarchy
[ 64%] Built target ViewsCore-hierarchy
[ 64%] Built target ViewsContext2D-hierarchy
[ 64%] Built target RenderingLabel-hierarchy
[ 64%] Built target ClientServerCoreRendering-hierarchy
[ 64%] Built target ServerImplementationRendering-hierarchy
[ 64%] Built target ServerManagerCore-hierarchy
[ 64%] Built target ServerManagerRendering-hierarchy
[ 64%] Built target Animation-hierarchy
[ 65%] Built target ViewsCore
[ 65%] Built target ViewsContext2D
[ 65%] Built target RenderingLabel
[ 65%] Built target ClientServerCoreRendering
[ 66%] Built target protobuf
[ 66%] Built target vtklibprotoc
[ 66%] Built target vtkprotoc
[ 66%] Built target vtkPVMessage_protobuf_compile
[ 66%] Built target ServerImplementationCore
[ 67%] Built target ServerManagerCore
[ 67%] Built target ServerImplementationRendering
[ 67%] Built target ProcessXML
[ 67%] Built target ServerManagerRendering
[ 67%] Built target ClientServerCoreDefault
[ 68%] Built target ServerManagerDefault
[ 68%] Built target Animation
[ 69%] Built target vtkPVAnimationCS
[ 69%] Built target vpic
[ 69%] Built target IOVPIC
[ 69%] Built target IOVPIC-hierarchy
[ 69%] Built target vtkIOVPICCS
[ 69%] Built target vtkCommonMiscCS
[ 69%] Built target vtkIOExportGL2PSCS
[ 70%] Built target vtkIOGeometryCS
[ 70%] Built target vtkCommonMathCS
[ 70%] Built target vtkRenderingVolumeCS
[ 70%] Built target RenderingLICOpenGL2-hierarchy
[ 71%] Built target RenderingLICOpenGL2
[ 71%] Built target vtkRenderingLICOpenGL2CS
[ 71%] Built target vtkPVServerManagerRenderingCS
[ 71%] Built target IOSegY
[ 71%] Built target IOSegY-hierarchy
[ 71%] Built target vtkIOSegYCS
[ 72%] Built target vtkIOEnSightCS
[ 72%] Built target vtkRenderingContext2DCS
[ 72%] Built target vtkRenderingVolumeAMRCS
[ 73%] Built target vtkRenderingParallelCS
[ 73%] Built target FiltersTexture
[ 73%] Built target FiltersTexture-hierarchy
[ 73%] Built target vtkFiltersTextureCS
[ 74%] Built target vtkRenderingVolumeOpenGL2CS
[ 75%] Built target vtkRenderingLabelCS
[ 76%] Built target vtkFiltersModelingCS
[ 76%] Built target ClientServerCoreDefault-hierarchy
[ 76%] Built target vtkPVClientServerCoreDefaultCS
[ 76%] Built target vtkIOExodusCS
[ 76%] Built target vtkIOCoreCS
[ 76%] Built target vtkFiltersParallelCS
[ 77%] Built target vtkRenderingContextOpenGL2CS
[ 77%] Built target IOTecplotTable
[ 77%] Built target IOTecplotTable-hierarchy
[ 77%] Built target vtkIOTecplotTableCS
[ 77%] Built target vtkClientServerCS
[ 77%] Built target vtkPVServerImplementationRenderingCS
[ 78%] Built target vtkIOParallelXMLCS
[ 79%] Built target IOLSDyna
[ 79%] Built target IOLSDyna-hierarchy
[ 79%] Built target vtkIOLSDynaCS
[ 79%] Built target IOPLY-hierarchy
[ 79%] Built target vtkIOPLYCS
[ 79%] Built target vtkFiltersGeometryCS
[ 80%] Built target vtkPVServerImplementationCoreCS
[ 80%] Built target ServerManagerDefault-hierarchy
[ 81%] Built target vtkPVServerManagerDefaultCS
[ 81%] Built target vtkIOParallelCS
[ 81%] Built target vtkIOImportCS
[ 81%] Built target FiltersHybrid-hierarchy
[ 82%] Built target vtkFiltersHybridCS
[ 82%] Built target ImagingColor-hierarchy
[ 82%] Built target vtkImagingColorCS
[ 84%] Built target vtkPVServerManagerCoreCS
[ 84%] Built target IOInfovis-hierarchy
[ 84%] Built target vtkIOInfovisCS
[ 84%] Built target vtkViewsContext2DCS
[ 84%] Built target vtkFiltersPointsCS
[ 84%] Built target h5part
[ 84%] Built target IOH5part
[ 84%] Built target IOH5part-hierarchy
[ 84%] Built target vtkIOH5partCS
[ 84%] Built target vtkRenderingGL2PSOpenGL2CS
[ 84%] Built target vtkFiltersGenericCS
[ 84%] Built target vtkIONetCDFCS
[ 84%] Built target vtkIOExportCS
[ 85%] Built target vtkPVVTKExtensionsRenderingCS
[ 88%] Built target vtkInteractionWidgetsCS
[ 88%] Built target IOAMR
[ 88%] Built target IOAMR-hierarchy
[ 88%] Built target vtkIOAMRCS
[ 89%] Built target vtkViewsCoreCS
[ 89%] Built target IOParallelLSDyna
[ 89%] Built target IOParallelLSDyna-hierarchy
[ 89%] Built target vtkIOParallelLSDynaCS
[ 89%] Built target ImagingHybrid-hierarchy
[ 89%] Built target vtkImagingHybridCS
[ 89%] Built target vtkFiltersAMRCS
[ 90%] Built target vtkPVClientServerCoreRenderingCS
[ 90%] Built target IOAsynchronous
[ 90%] Built target IOAsynchronous-hierarchy
[ 90%] Built target vtkIOAsynchronousCS
[ 90%] Built target vtkRenderingAnnotationCS
[ 90%] Built target vtkInteractionStyleCS
[ 90%] Built target verdict
[ 90%] Built target FiltersVerdict
[ 90%] Built target FiltersVerdict-hierarchy
[ 91%] Built target vtkFiltersVerdictCS
[ 91%] Built target WrapPythonInit
[ 91%] Built target WrapPython
[ 91%] Built target WrapJava
[ 91%] Built target ParseJava
[ 91%] Built target vtkProbeOpenGLVersion
[ 91%] Built target gen_hdf5
[ 91%] Automatic MOC for target GUISupportQt
[ 91%] Built target GUISupportQt_autogen
[ 92%] Built target GUISupportQt
[ 92%] Built target smTestDriver
[ 92%] Automatic MOC and UIC for target qttesting
[ 92%] Built target qttesting_autogen
[ 92%] Building CXX object ThirdParty/QtTesting/vtkqttesting/CMakeFiles/qttesting.dir/qttesting_autogen/mocs_compilation.cpp.o
In file included from /home/alves/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/mocs_compilation.cpp(2):
/home/alves/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW/moc_pq3DViewEventPlayer.cpp(9): catastrophic error: cannot open source file "../../../../../../../../../h9/alves/paraview/src/ThirdParty/QtTesting/vtkqttesting/pq3DViewEventPlayer.h"
  #include "../../../../../../../../../h9/alves/paraview/src/ThirdParty/QtTesting/vtkqttesting/pq3DViewEventPlayer.h"
                                                                                                                     ^

compilation aborted for /home/alves/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/mocs_compilation.cpp (code 4)
make[2]: *** [ThirdParty/QtTesting/vtkqttesting/CMakeFiles/qttesting.dir/qttesting_autogen/mocs_compilation.cpp.o] Error 4
make[1]: *** [ThirdParty/QtTesting/vtkqttesting/CMakeFiles/qttesting.dir/all] Error 2
make: *** [all] Error 2

The problem seems to be that the building process is somewhy generating the wrong relative path for the include directive. If I navigate to the folder where moc_pq3DViewEventPlayer.cpp is:

~/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW

I cannot get back to the home directory using the path the build process is attempting to use:

alves@tauruslogin5:~/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW> ll ../../../../../../../../../h9
ls: cannot access ../../../../../../../../../h9: No such file or directory

The following, however, works:

alves@tauruslogin5:~/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW> ll ../../../../../../../../../alves

or

alves@tauruslogin5:~/paraview/5.7.0/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW> ll ../../../../../../../../../../h9/alves

Then I am back in my home directory, and from there I can navigate to the folder where pq3DViewEventPlayer.h is.

This seems to be a bug in the build process; it happens (on the same place) if I attempt to build the master branch. How can we bypass it? By the way, it is worth noticing that, in my system, the directories /home/alves and /home/h9/alves both refer to the same place (the home directory).

Thank you very much,

XavierStuvw · February 13, 2020, 6:50pm

I confirm the issue proceeding from a superbuild.

In the folder [builddir]/superbuild/paraview/build/ThirdParty/QtTesting/vtkqttesting/qttesting_autogen/EWIEGA46WW the file moc_pq3DViewEventPlayer.cpp includes a header file with a lengthy and incorrect path

#include “…/…/…/…/…/…/…/…/…/…/…/…/…/…/…/…/[parent]/[parent]/[parent]/[parent]/[parent]/[builddir]/superbuild/paraview/src/ThirdParty/QtTesting/vtkqttesting/pq3DViewEventPlayer.h”

I can locate that file in [buildir]/superbuild/paraview/src/ThirdParty/QtTesting/vtkqttesting/ instead.

In my case this error occurs while

[ 91%] Performing build step for ‘paraview’
…
[ 6%] Built target CommonCore
…
No such file or directory
…
compilation terminated.
…
CMake Error at [builddir]/superbuild/sb-paraview-build.cmake:47 (message):
Failed with exit code 2

Please advise

ben.boeckel · February 14, 2020, 6:56am

Do you have symlinks somewhere in your build dir path? Do they match the symlinks used in your source dir path?

If not, I suggest doing a cd $(readlink -f $PWD) to go to a path without any symlinks.

If that solves your problem, this is a long standing CMake behavior that is broader than it should be. https://gitlab.kitware.com/cmake/cmake/issues/16228 You can do any of:

not use symlinks
keep all symlinks common between your build and source tree
reference symlink paths by their symlink-free name

to mitigate the issue.

XavierStuvw · February 14, 2020, 10:12am

I do, and indeed this makes the issue common with the original poster. In my situation the home directory is mounted on a data server, like in the issue tracker you mentioned.

I kind of think that the path to the current (build) directory was already in the extended symlink-free form, and for good measure I have applied your command before launching ccmake.

Also, I checked that all paths in the CMakeCache.txt files are in the extended form: only superbuild_download_location:PATH contained a symlink.

In sum, that was the issue. Ben Boeckel’s tips worked for me. Thanks

@Rigel Thanks for sharing your issue. If Ben’s tip works for you, I would recommend to mark that a solution.