FS#58801 - [paraview] HDF5 library version mismatched error
Attached to Project:
Community Packages
Opened by Romain Beucher (oliverjack) - Thursday, 31 May 2018, 06:26 GMT
Last edited by Bruno Pagani (ArchangeGabriel) - Monday, 04 June 2018, 13:56 GMT
Opened by Romain Beucher (oliverjack) - Thursday, 31 May 2018, 06:26 GMT
Last edited by Bruno Pagani (ArchangeGabriel) - Monday, 04 June 2018, 13:56 GMT
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Details
Description:
HDF5 library mismatched error after updating HDF5-openmpi. I believe the solution is to specify the HDF5 library version (=1.10.1) in the pkgconfig. Additional info: * package version(s) Paraview 5.5.0-2 HDF5-openmpi 1.10.2-2 * config and/or log files etc. The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library. You should recompile the application or check your shared library related settings such as 'LD_LIBRARY_PATH'. You can, at your own risk, disable this warning by setting the environment variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. Setting it to 2 or higher will suppress the warning messages totally. Headers are 1.10.1, library is 1.10.2 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.2 Configured on: Wed May 23 16:18:18 CEST 2018 Configured by: builduser@ Host system: x86_64-unknown-linux-gnu Uname information: Linux archange 4.16.10-1-ARCH #1 SMP PREEMPT Mon May 21 07:57:23 UTC 2018 x86_64 GNU/Linux Byte sex: little-endian Installation point: /usr Compiling Options: ------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: high Linking Options: ---------------- Libraries: shared Statically Linked Executables: LDFLAGS: -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now H5_LDFLAGS: AM_LDFLAGS: Extra libraries: -lsz -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib Languages: ---------- C: yes C Compiler: /usr/bin/mpicc ( built with gcc version 8.1.0 (GCC)) CPPFLAGS: -D_FORTIFY_SOURCE=2 H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: C Flags: -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O AM C Flags: Shared C Library: yes Static C Library: no Fortran: yes Fortran Compiler: /usr/bin/mpif90 ( built with gcc version 8.1.0 (GCC)) Fortran Flags: H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 AM Fortran Flags: Shared Fortran Library: yes Static Fortran Library: no C++: yes C++ Compiler: /usr/bin/mpicxx ( built with gcc version 8.1.0 (GCC)) C++ Flags: -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O AM C++ Flags: Shared C++ Library: yes Static C++ Library: no Java: no Features: --------- Parallel HDF5: yes High-level library: yes Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib),szip(encoder) MPE: Direct VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Metadata trace file: no Function stack tracing: no Strict file format checks: no Optimization instrumentation: no Bye... [icarus:23193] *** Process received signal *** [icarus:23193] Signal: Aborted (6) [icarus:23193] Signal code: (-6) [icarus:23193] [ 0] /usr/lib/libc.so.6(+0x368f0)[0x7f9d329968f0] [icarus:23193] [ 1] /usr/lib/libc.so.6(gsignal+0x10b)[0x7f9d3299686b] [icarus:23193] [ 2] /usr/lib/libc.so.6(abort+0x129)[0x7f9d3298140e] [icarus:23193] [ 3] /usr/lib/libhdf5.so.101(H5open+0x0)[0x7f9d10a64b80] [icarus:23193] [ 4] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf27XdmfHDF6DoOpenEPKcS2_+0x47)[0x7f9d0f17fba7] [icarus:23193] [ 5] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf213XdmfValuesHDF4ReadEPNS_9XdmfArrayE+0x270)[0x7f9d0f176370] [icarus:23193] [ 6] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfDataItem6UpdateEv+0xc47)[0x7f9d0f186767] [icarus:23193] [ 7] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfDataItem14UpdateFunctionEv+0x87b)[0x7f9d0f18541b] [icarus:23193] [ 8] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfDataItem6UpdateEv+0x8a1)[0x7f9d0f1863c1] [icarus:23193] [ 9] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfDataItem14UpdateFunctionEv+0x40b)[0x7f9d0f184fab] [icarus:23193] [10] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfDataItem6UpdateEv+0x8a1)[0x7f9d0f1863c1] [icarus:23193] [11] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf212XdmfTopology6UpdateEv+0x14b)[0x7f9d0f19685b] [icarus:23193] [12] /usr/lib/libvtkxdmf2-pv5.5.so.1(_ZN5xdmf28XdmfGrid6UpdateEv+0x65)[0x7f9d0f193fa5] [icarus:23193] [13] /usr/lib/libvtkIOXdmf2-pv5.5.so.1(_ZN16vtkXdmfHeavyData15ReadUniformDataEPN5xdmf28XdmfGridEi+0x61a)[0x7f9d23026a1a] [icarus:23193] [14] /usr/lib/libvtkIOXdmf2-pv5.5.so.1(_ZN16vtkXdmfHeavyData8ReadDataEv+0x319)[0x7f9d23027169] [icarus:23193] [15] /usr/lib/libvtkIOXdmf2-pv5.5.so.1(_ZN13vtkXdmfReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x22e)[0x7f9d2302dcbe] [icarus:23193] [16] /usr/lib/libvtkPVVTKExtensionsCore-pv5.5.so.1(_ZN19vtkFileSeriesReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0xcd)[0x7f9d2cafc14d] [icarus:23193] [17] /usr/lib/libvtkPVVTKExtensionsCore-pv5.5.so.1(_ZN19vtkFileSeriesReader14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x15f)[0x7f9d2cafc3df] [icarus:23193] [18] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x4e)[0x7f9d2c2c385e] [icarus:23193] [19] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x37)[0x7f9d2c2bceb7] [icarus:23193] [20] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN24vtkCompositeDataPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x82)[0x7f9d2c2b9a42] [icarus:23193] [21] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x130)[0x7f9d2c2bfbf0] [icarus:23193] [22] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x21c)[0x7f9d2c2e128c] [icarus:23193] [23] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN24vtkCompositeDataPipeline15ForwardUpstreamEP14vtkInformation+0x182)[0x7f9d2c2b89c2] [icarus:23193] [24] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0xe3)[0x7f9d2c2bfba3] [icarus:23193] [25] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x21c)[0x7f9d2c2e128c] [icarus:23193] [26] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x9c)[0x7f9d2c2be71c] [icarus:23193] [27] /usr/lib/libvtkCommonExecutionModel-pv5.5.so.1(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEiP20vtkInformationVector+0x123)[0x7f9d2c2e2913] [icarus:23193] [28] /usr/lib/libvtkPVServerManagerApplication-pv5.5.so.1(_Z23vtkSISourceProxyCommandP26vtkClientServerInterpreterP13vtkObjectBasePKcRK21vtkClientServerStreamRS5_Pv+0x3a7)[0x7f9d319c1237] [icarus:23193] [29] /usr/lib/libvtkClientServer-pv5.5.so.1(_ZN26vtkClientServerInterpreter19CallCommandFunctionEPKcP13vtkObjectBaseS1_RK21vtkClientServerStreamRS4_+0x1e1)[0x7f9d2adba651] [icarus:23193] *** End of error message *** Aborted (core dumped) |
This task depends upon
Closed by Bruno Pagani (ArchangeGabriel)
Monday, 04 June 2018, 13:56 GMT
Reason for closing: Fixed
Additional comments about closing: paraview-5.5.1-1
Monday, 04 June 2018, 13:56 GMT
Reason for closing: Fixed
Additional comments about closing: paraview-5.5.1-1
Comment by
Bruno Pagani (ArchangeGabriel) -
Saturday, 02 June 2018, 08:22 GMT
Comment by
Bruno Pagani (ArchangeGabriel) -
Sunday, 03 June 2018, 18:05 GMT
Rebuild on the way…
Rebuild failed because of Qt 5.11, even using the newly released
5.5.1 version of Paraview. I’m waiting on upstream answer about
this (https://gitlab.kitware.com/paraview/paraview/issues/18222),
I don’t have the necessary knowledge to fix it myself.