How do I resolve this error?

HDF5 Library
1

Hello, I am running on Ubuntu 18.04.4. I get this error. Could someone please tell me how to resolve this issue. What is causing the problem. Thank you.

HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000: /home/alan/Desktop/hdf5/src/H5Dio.c line 199 in H5Dread(): can’t read data
major: Dataset
minor: Read failed
#001: /home/alan/Desktop/hdf5/src/H5Dio.c line 601 in H5D__read(): can’t read data
major: Dataset
minor: Read failed
#002: /home/alan/Desktop/hdf5/src/H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#003: /home/alan/Desktop/hdf5/src/H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read failed
major: Dataset
minor: Filter operation failed
#004: /home/alan/Desktop/hdf5/src/H5Z.c line 1301 in H5Z_pipeline(): required filter ‘deflate’ is not registered
major: Data filters
minor: Read failed
#005: /home/alan/Desktop/hdf5/src/H5PLint.c line 270 in H5PL_load(): search in path table failed
major: Plugin for dynamically loaded library
minor: Can’t get value
#006: /home/alan/Desktop/hdf5/src/H5PLpath.c line 604 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error
major: Plugin for dynamically loaded library
minor: Can’t get value
#007: /home/alan/Desktop/hdf5/src/H5PLpath.c line 656 in H5PL__find_plugin_in_path(): can’t open directory: /usr/local/hdf5/lib/plugin
major: Plugin for dynamically loaded library
minor: Can’t open directory or file
[TreatmentControlCore.cpp, loadTreatmentFile, 331] ERROR : Failed to load treatment file /home/alan/Desktop/BloodBrainBarrier/FUSArraySystem-issue86_build/TreatmentControl/sampleForRyan.hdf5

2

It’s not finding the shared library for deflate (gzip) compression. How about

sudo apt-get install zlib1g-dev

?

G.

3

Hi gheber,

I already had that package installed, but it still doesn’t work.

4

Which application produces this error stack? What does running ldd your_app show? G.

5 
	linux-vdso.so.1 (0x00007fff1c955000)
libQt5PrintSupport.so.5 => /opt/Qt/5.12.8/gcc_64/lib/libQt5PrintSupport.so.5 (0x00007fe89bcaa000)
libvtkRenderingVolumeOpenGL2-8.2.so.1 => /opt/vtk/lib/libvtkRenderingVolumeOpenGL2-8.2.so.1 (0x00007fe89ba14000)
libvtkInteractionImage-8.2.so.1 => /opt/vtk/lib/libvtkInteractionImage-8.2.so.1 (0x00007fe89b7fd000)
libvtkDICOM-8.2.0.so.0.8 => /opt/vtk/lib/libvtkDICOM-8.2.0.so.0.8 (0x00007fe89b335000)
libhdf5_cpp.so.103 => /opt/hdf5-1_10_5/lib/libhdf5_cpp.so.103 (0x00007fe89b0c4000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe89aea5000)
libcuda.so.1 => /usr/lib/x86_64-linux-gnu/libcuda.so.1 (0x00007fe899c84000)
libfftw3.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007fe899882000)
libfftw3f.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3f.so.3 (0x00007fe899475000)
libhdf5.so.103 => /opt/hdf5-1_10_5/lib/libhdf5.so.103 (0x00007fe898e9e000)
libQt5Sql.so.5 => /opt/Qt/5.12.8/gcc_64/lib/libQt5Sql.so.5 (0x00007fe898c56000)
libvtkRenderingGL2PSOpenGL2-8.2.so.1 => /opt/vtk/lib/libvtkRenderingGL2PSOpenGL2-8.2.so.1 (0x00007fe898a44000)
libvtkIOLegacy-8.2.so.1 => /opt/vtk/lib/libvtkIOLegacy-8.2.so.1 (0x00007fe898794000)
libvtkGUISupportQt-8.2.so.1 => /opt/vtk/lib/libvtkGUISupportQt-8.2.so.1 (0x00007fe898540000)
libvtkRenderingOpenGL2-8.2.so.1 => /opt/vtk/lib/libvtkRenderingOpenGL2-8.2.so.1 (0x00007fe89810e000)
libvtkInteractionWidgets-8.2.so.1 => /opt/vtk/lib/libvtkInteractionWidgets-8.2.so.1 (0x00007fe897c77000)
libvtkInteractionStyle-8.2.so.1 => /opt/vtk/lib/libvtkInteractionStyle-8.2.so.1 (0x00007fe897a26000)
libvtkRenderingAnnotation-8.2.so.1 => /opt/vtk/lib/libvtkRenderingAnnotation-8.2.so.1 (0x00007fe897701000)
libvtkRenderingVolume-8.2.so.1 => /opt/vtk/lib/libvtkRenderingVolume-8.2.so.1 (0x00007fe896fd0000)
libvtkRenderingFreeType-8.2.so.1 => /opt/vtk/lib/libvtkRenderingFreeType-8.2.so.1 (0x00007fe896d25000)
libvtkRenderingCore-8.2.so.1 => /opt/vtk/lib/libvtkRenderingCore-8.2.so.1 (0x00007fe896915000)
libvtkFiltersGeometry-8.2.so.1 => /opt/vtk/lib/libvtkFiltersGeometry-8.2.so.1 (0x00007fe896690000)
libvtkFiltersSources-8.2.so.1 => /opt/vtk/lib/libvtkFiltersSources-8.2.so.1 (0x00007fe8963e7000)
libvtkFiltersGeneral-8.2.so.1 => /opt/vtk/lib/libvtkFiltersGeneral-8.2.so.1 (0x00007fe895eb5000)
libvtkCommonComputationalGeometry-8.2.so.1 => /opt/vtk/lib/libvtkCommonComputationalGeometry-8.2.so.1 (0x00007fe895c80000)
libvtkFiltersCore-8.2.so.1 => /opt/vtk/lib/libvtkFiltersCore-8.2.so.1 (0x00007fe8954f4000)
libvtkImagingCore-8.2.so.1 => /opt/vtk/lib/libvtkImagingCore-8.2.so.1 (0x00007fe895086000)
libvtkCommonExecutionModel-8.2.so.1 => /opt/vtk/lib/libvtkCommonExecutionModel-8.2.so.1 (0x00007fe894dcd000)
libvtkCommonDataModel-8.2.so.1 => /opt/vtk/lib/libvtkCommonDataModel-8.2.so.1 (0x00007fe8947c0000)
libvtkCommonMisc-8.2.so.1 => /opt/vtk/lib/libvtkCommonMisc-8.2.so.1 (0x00007fe8945a3000)
libvtkCommonTransforms-8.2.so.1 => /opt/vtk/lib/libvtkCommonTransforms-8.2.so.1 (0x00007fe894371000)
libvtkCommonMath-8.2.so.1 => /opt/vtk/lib/libvtkCommonMath-8.2.so.1 (0x00007fe894150000)
libvtkCommonCore-8.2.so.1 => /opt/vtk/lib/libvtkCommonCore-8.2.so.1 (0x00007fe893b32000)
libQt5Widgets.so.5 => /opt/Qt/5.12.8/gcc_64/lib/libQt5Widgets.so.5 (0x00007fe8932e3000)
libQt5Gui.so.5 => /opt/Qt/5.12.8/gcc_64/lib/libQt5Gui.so.5 (0x00007fe892a94000)
libQt5Core.so.5 => /opt/Qt/5.12.8/gcc_64/lib/libQt5Core.so.5 (0x00007fe8922f9000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fe891f70000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe891bd2000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe8919ba000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe8915c9000)
libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007fe89133d000)
libvtkImagingMath-8.2.so.1 => /opt/vtk/lib/libvtkImagingMath-8.2.so.1 (0x00007fe8910f5000)
libvtkglew-8.2.so.1 => /opt/vtk/lib/libvtkglew-8.2.so.1 (0x00007fe890e48000)
libvtkCommonSystem-8.2.so.1 => /opt/vtk/lib/libvtkCommonSystem-8.2.so.1 (0x00007fe890c32000)
libvtkImagingColor-8.2.so.1 => /opt/vtk/lib/libvtkImagingColor-8.2.so.1 (0x00007fe8909db000)
libvtkIOImage-8.2.so.1 => /opt/vtk/lib/libvtkIOImage-8.2.so.1 (0x00007fe89064a000)
libvtkzlib-8.2.so.1 => /opt/vtk/lib/libvtkzlib-8.2.so.1 (0x00007fe89042c000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe89c59f000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe890228000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe890020000)
libvtkgl2ps-8.2.so.1 => /opt/vtk/lib/libvtkgl2ps-8.2.so.1 (0x00007fe88fe07000)
libvtkIOCore-8.2.so.1 => /opt/vtk/lib/libvtkIOCore-8.2.so.1 (0x00007fe88fb97000)
libvtksys-8.2.so.1 => /opt/vtk/lib/libvtksys-8.2.so.1 (0x00007fe88f948000)
libQt5X11Extras.so.5 => /usr/lib/x86_64-linux-gnu/libQt5X11Extras.so.5 (0x00007fe88f744000)
libvtkFiltersExtraction-8.2.so.1 => /opt/vtk/lib/libvtkFiltersExtraction-8.2.so.1 (0x00007fe88f444000)
libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007fe88f10c000)
libXt.so.6 => /usr/lib/x86_64-linux-gnu/libXt.so.6 (0x00007fe88eea3000)
libvtkFiltersHybrid-8.2.so.1 => /opt/vtk/lib/libvtkFiltersHybrid-8.2.so.1 (0x00007fe88ebb7000)
libvtkFiltersModeling-8.2.so.1 => /opt/vtk/lib/libvtkFiltersModeling-8.2.so.1 (0x00007fe88e925000)
libvtkImagingGeneral-8.2.so.1 => /opt/vtk/lib/libvtkImagingGeneral-8.2.so.1 (0x00007fe88e631000)
libvtkfreetype-8.2.so.1 => /opt/vtk/lib/libvtkfreetype-8.2.so.1 (0x00007fe88e39f000)
libvtkCommonColor-8.2.so.1 => /opt/vtk/lib/libvtkCommonColor-8.2.so.1 (0x00007fe88e181000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe88df64000)
libicui18n.so.56 => /opt/Qt/5.12.8/gcc_64/lib/libicui18n.so.56 (0x00007fe88dacb000)
libicuuc.so.56 => /opt/Qt/5.12.8/gcc_64/lib/libicuuc.so.56 (0x00007fe88d713000)
libicudata.so.56 => /opt/Qt/5.12.8/gcc_64/lib/libicudata.so.56 (0x00007fe88bd30000)
libgthread-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgthread-2.0.so.0 (0x00007fe88bb2e000)
libglib-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007fe88b817000)
libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fe88b5e6000)
libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fe88b330000)
libvtkDICOMParser-8.2.so.1 => /opt/vtk/lib/libvtkDICOMParser-8.2.so.1 (0x00007fe88b113000)
libvtkmetaio-8.2.so.1 => /opt/vtk/lib/libvtkmetaio-8.2.so.1 (0x00007fe88ae73000)
libvtkjpeg-8.2.so.1 => /opt/vtk/lib/libvtkjpeg-8.2.so.1 (0x00007fe88ac10000)
libvtkpng-8.2.so.1 => /opt/vtk/lib/libvtkpng-8.2.so.1 (0x00007fe88a9cb000)
libvtktiff-8.2.so.1 => /opt/vtk/lib/libvtktiff-8.2.so.1 (0x00007fe88a74b000)
libvtklz4-8.2.so.1 => /opt/vtk/lib/libvtklz4-8.2.so.1 (0x00007fe88a528000)
libvtklzma-8.2.so.1 => /opt/vtk/lib/libvtklzma-8.2.so.1 (0x00007fe88a2f6000)
libvtkdoubleconversion-8.2.so.1 => /opt/vtk/lib/libvtkdoubleconversion-8.2.so.1 (0x00007fe88a0e6000)
libvtkFiltersStatistics-8.2.so.1 => /opt/vtk/lib/libvtkFiltersStatistics-8.2.so.1 (0x00007fe889e26000)
libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fe889bfe000)
libSM.so.6 => /usr/lib/x86_64-linux-gnu/libSM.so.6 (0x00007fe8899f6000)
libICE.so.6 => /usr/lib/x86_64-linux-gnu/libICE.so.6 (0x00007fe8897db000)
libvtkImagingSources-8.2.so.1 => /opt/vtk/lib/libvtkImagingSources-8.2.so.1 (0x00007fe889589000)
libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007fe889317000)
libvtkImagingFourier-8.2.so.1 => /opt/vtk/lib/libvtkImagingFourier-8.2.so.1 (0x00007fe8890f1000)
libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007fe888eed000)
libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fe888ce7000)
libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007fe888ae0000)
6

OK, libz is there:

How about setting the HDF5_PLUGIN_PATH variable, e.g., in Bash

export HDF5_PLUGIN_PATH=/lib/x86_64-linux-gnu:$HDF5_PLUGIN_PATH

Any changes with that?
G.

7

Another possibility would be that your version of the HDF5 library

was built without support for Gzip (deflate) compression. Who built it? Where did you get it? It looks like a custom installation location (for Ubuntu).

G.

8

This is the new error message.

Gtk-Message: 22:44:21.275: GtkDialog mapped without a transient parent. This is discouraged.
[TreatmentControlCore.cpp, loadTreatmentFile, 246] INFO : Reading data for /home/alan/Desktop/BloodBrainBarrier/FUSArraySystem-issue86_build/TreatmentControl/sampleForRyan.hdf5

Memory usage summary: heap total: 0, heap peak: 0, stack peak: 0
total calls total memory failed calls
malloc| 0 0 0
realloc| 0 0 0 (nomove:0, dec:0, free:0)
calloc| 0 0 0
free| 0 0
Histogram for block sizes:
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
#000: /home/alan/Desktop/hdf5/src/H5Dio.c line 199 in H5Dread(): can’t read data
major: Dataset
minor: Read failed
#001: /home/alan/Desktop/hdf5/src/H5Dio.c line 601 in H5D__read(): can’t read data
major: Dataset
minor: Read failed
#002: /home/alan/Desktop/hdf5/src/H5Dchunk.c line 2259 in H5D__chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#003: /home/alan/Desktop/hdf5/src/H5Dchunk.c line 3624 in H5D__chunk_lock(): data pipeline read failed
major: Dataset
minor: Filter operation failed
#004: /home/alan/Desktop/hdf5/src/H5Z.c line 1301 in H5Z_pipeline(): required filter ‘deflate’ is not registered
major: Data filters
minor: Read failed
#005: /home/alan/Desktop/hdf5/src/H5PLint.c line 327 in H5PL__open(): can’t dlopen:/lib/x86_64-linux-gnu/libparted-fs-resize.so.0.0.1: undefined symbol: ped_alignment_any
major: Plugin for dynamically loaded library
minor: Can’t get value
#006: /home/alan/Desktop/hdf5/src/H5PLint.c line 327 in H5PL__open(): can’t dlopen:/lib/x86_64-linux-gnu/libparted-fs-resize.so.0: undefined symbol: ped_alignment_any
major: Plugin for dynamically loaded library
minor: Can’t get value

9

I built HDF5 from source from the link above using CMake and make.

Where do I get the HDF5 library for support with Gzip(deflate) compression?

Thanks.

10

Now there is a separate issue:

It’s not finding libparted-fs-resize.so.

If you followed the CMake instructions, then deflate compression is enabled by default. (Unless it wasn’t found at the time you built HDF5…) Did you run the tests after building HDF5?

G.