h5py - HDF5 library version mismatched error causes crash of QGIS on startup of Box
Issue #747
on hold
A mismatch in HDF library versions might currently cause a crash of QGIS if the EnMAP-Box is started. Usually this happens without any error message (except QGIS is started from the Terminal, see error below).
Observed on Ubuntu 20.04
h5py 3.4.0
root@:/# apt list --installed | grep hdf
hdf5-helpers/focal,now 1.10.4+repack-11ubuntu1 amd64 [installed,automatic]
libhdf4-0-alt/focal,now 4.2.14-1ubuntu1 amd64 [installed,automatic]
libhdf4-alt-dev/focal,now 4.2.14-1ubuntu1 amd64 [installed,automatic]
libhdf5-103/focal,now 1.10.4+repack-11ubuntu1 amd64 [installed,automatic]
libhdf5-cpp-103/focal,now 1.10.4+repack-11ubuntu1 amd64 [installed,automatic]
libhdf5-dev/focal,now 1.10.4+repack-11ubuntu1 amd64 [installed,automatic]
Workaround
Two potential workarounds:
1. Install h5py using your systems package manager (apt on Ubuntu, i.e., apt install python3-h5py). Make sure to uninstall previous pip installation with python3 -m pip uninstall h5py.
OR
2. In QGIS go to Settings --> Options --> System, under Environment add the variable HDF5_DISABLE_VERSION_CHECK with a value of 1. Note that this does not fix potential functionality issues of the h5py library, so be careful when using the PRISMA Import.
Error/crash message
Warning! ***HDF5 library version mismatched error***
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'.
'HDF5_DISABLE_VERSION_CHECK' environment variable is set to 1, application will
continue at your own risk.
Headers are 1.12.1, library is 1.10.4
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.4
Configured on: Mon, 13 Apr 2020 12:15:08 +0000
Configured by: Debian
Host system: x86_64-pc-linux-gnu
Uname information: Debian
Byte sex: little-endian
Installation point: /usr
Flavor name: serial
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
AM_LDFLAGS:
Extra libraries: -lpthread -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: x86_64-linux-gnu-ranlib
Languages:
----------
C: yes
C Compiler: /usr/bin/gcc
CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong -Wfo
rmat -Werror=format-security
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wc
ast-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-prot
otypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-string
s -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-nor
eturn -O
AM C Flags:
Shared C Library: yes
AM C Flags: [0/702]
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /usr/bin/gfortran
Fortran Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong
H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising
-Wno-c-binding-type -s -O2
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /usr/bin/g++
C++ Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong -Wfo
rmat -Werror=format-security
H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcas
t-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: yes
Java: yes
Java Compiler: /usr/bin/java (openjdk 11.0.7-ea 2020-04-14)
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: yes
Default API mapping: v18
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
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
Comments (7)
-
-
-
assigned issue to
Fabian Thiel
-
assigned issue to
-
- changed component to known issue
-
reporter
- changed status to on hold
Current fix/workaround is to set the environment variable or try to (re)install the h5py package
-
reporter
- edited description
-
reporter
- edited description
-
@Fabian Thiel is it possible to reproduce this error in a few lines of bash / python code?
I am asking because this would allow us to open a QGIS issue and might offer a way to sovle it by adding it to the QGIS install dependencies - Log in to comment
- Assignee
- Type
- Priority
- Status
- on hold
- Component
- known issue
- Milestone
- –
- Version
- 3.9
- Votes
- 0
- Watchers
- 1
Fabian, please mention this issue under RTD troubleshooting and put it on hoold afterwards.