UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.12.2, this may cause problems
_warn(("h5py is running against HDF5 {0} when it was built against {1}, "
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'.
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 1.12.2, library is 1.12.1
SUMMARY OF THE HDF5 CONFIGURATION
General Information:
HDF5 Version: 1.12.1
Configured on: Fri Mar 4 16:53:33 UTC 2022
Configured by: runner@Mac-1646412153531.local
Host system: arm64-apple-darwin20.0.0
Uname information: Darwin Mac-1646412153531.local 19.6.0 Darwin Kernel Version 19.6.0: Thu Jan 13 01:26:33 PST 2022; root:xnu-6153.141.51~3/RELEASE_X86_64 x86_64
Byte sex: little-endian
Installation point: /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol
Compiling Options:
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
C: yes
C Compiler: /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_build_env/bin/arm64-apple-darwin20.0.0-clang
CPPFLAGS: -D_FORTIFY_SOURCE=2 -isystem /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -mmacosx-version-min=11.0
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include
C Flags: -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/work=/usr/local/src/conda/hdf5_split-1.12.1 -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix
H5 C Flags: -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-missing-noreturn -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -O3
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_build_env/bin/arm64-apple-darwin20.0.0-gfortran ( GNU Fortran (GCC) 11.0.1 20210403 )
Fortran Flags:
H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange -fdiagnostics-urls=never -fno-diagnostics-color -s -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_build_env/bin/arm64-apple-darwin20.0.0-clang++
C++ Flags: -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/work=/usr/local/src/conda/hdf5_split-1.12.1 -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol=/usr/local/src/conda-prefix
H5 C++ Flags:
AM C++ Flags: -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
Shared C++ Library: yes
Static C++ Library: yes
Java: no
Features:
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Build HDF5 Tests: no
Build HDF5 Tools: yes
Threadsafety: yes (recursive RW locks: no)
Default API mapping: v112
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Map (H5M) API: no
Direct VFD: no
Mirror VFD: no
(Read-Only) S3 VFD: yes
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: yes
Memory allocation sanity checks: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
Bye...
Smiril
commented
1 year ago 
sanamsta
commented
1 year ago
UserWarning: h5py is running against HDF5 1.12.1 when it was built against 1.12.2, this may cause problems _warn(("h5py is running against HDF5 {0} when it was built against {1}, " 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'. 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 1.12.2, library is 1.12.1 SUMMARY OF THE HDF5 CONFIGURATION
General Information:
Compiling Options:
Linking Options:
Statically Linked Executables: LDFLAGS: -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib -L/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib H5_LDFLAGS: -Wl,-commons,use_dylibs AM_LDFLAGS: -L/Users/runner/miniforge3/conda-bld/hdf5_split_1646412372985/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib Extra libraries: -lcrypto -lcurl -lpthread -lz -ldl -lm Archiver: arm64-apple-darwin20.0.0-ar AR_FLAGS: cr Ranlib: arm64-apple-darwin20.0.0-ranlib
Languages:
Features:
Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: no Build HDF5 Tools: yes Threadsafety: yes (recursive RW locks: no) Default API mapping: v112 With deprecated public symbols: yes I/O filters (external): deflate(zlib) MPE: no Map (H5M) API: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: yes (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: yes Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no Bye...