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Tasklist

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
Task Type Bug Report
Category Packages
Status Closed
Assigned To Ronald van Haren (pressh)
Bruno Pagani (ArchangeGabriel)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

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
Comment by Bruno Pagani (ArchangeGabriel) - Saturday, 02 June 2018, 08:22 GMT
Rebuild on the way…
Comment by Bruno Pagani (ArchangeGabriel) - Sunday, 03 June 2018, 18:05 GMT
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.

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