HDF5 library version mismatched error

mgrddb, anaddb, cut3d, electron-phonon coupling,...

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HDF5 library version mismatched error

Post by polariton » Fri Aug 28, 2020 3:02 am

Dear Developers,

Recently I am trying to run the code for temperature-dependent electronic bandstructures and following the example of tdepes_1.in. I have finished the job for tdepes_1.in, but failed in the postprocessing when using ./temperature_final.py <tdepes_1_temperature.in.

The error message is listed as follows. Could you please tell me how to fix this problem? Thank you!

Best regards,

/THFS/opt/anaconda/2/2019.3/lib/python2.7/site-packages/netCDF4/__init__.py:3: UserWarning:
WARNING: Backwards incompatible files will be created with HDF5 1.10.x
and netCDF < 4.4.1. Upgrading to netCDF4 >= 4.4.1 or downgrading to
to HDF5 version 1.8.x is highly recommended
(see https://github.com/Unidata/netcdf-c/issues/250).
from ._netCDF4 import *
Start on 28/8/2020 at 8h59

____ ____ _ _
| _ \| _ \ | |_ ___ _ __ ___ _ __ ___ _ __ __ _| |_ _ _ _ __ ___
| |_) | |_) |____| __/ _ \ '_ ` _ \| '_ \ / _ \ '__/ _` | __| | | | '__/ _ \
| __/| __/_____| || __/ | | | | | |_) | __/ | | (_| | |_| |_| | | | __/
|_| |_| \__\___|_| |_| |_| .__/ \___|_| \__,_|\__|\__,_|_| \___|
|_| Version 1.3

This script compute the static/dynamic zero-point motion
and the temperature dependence of eigenenergies due to electron-phonon interaction.
The electronic lifetime can also be computed.

WARNING: The first Q-point MUST be the Gamma point.

Enter the number of cpu on which you want to multi-thread
Define the type of calculation you want to perform. Type:
1 if you want to run a non-adiabatic AHC calculation
2 if you want to run a static AHC calculation
3 if you want to run a static AHC calculation without control on active space (not recommended !)
Note that for 1 & 2 you need _EIGR2D.nc and _GKK.nc files obtained through ABINIT option "ieig2rf 5"
Enter name of the output file
Enter value of the smearing parameter for AHC (in eV)
Enter value of the Gaussian broadening for the Eliashberg function and PDOS (in eV)
Enter the energy range for the PDOS and Eliashberg calculations (in eV): [e.g. 0 0.5]
Introduce the min temperature, the max temperature and the temperature steps. e.g. 0 200 50 for (0,50,100,150)
Enter the number of Q-points you have
Enter the name of the 0 DDB file
Enter the name of the 0 eigq file
Enter the name of the 0 EIGR2D file
Enter the name of the 0 GKK file
Enter the name of the unperturbed EIG.nc file at Gamma
Q-point: 0 with wtq = 1.0 and reduced coord. [0. 0. 0.]
Now compute active space ...
Now compute generalized g2F Eliashberg electron-phonon spectral function ...
End on 28/8/2020 at 8 h 59
Runtime: 3 seconds (or 0.05 minutes)
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 1.8.9, library is 1.10.4

General Information:
HDF5 Version: 1.10.4
Configured on: Wed Dec 19 18:26:52 UTC 2018
Configured by: root@3dad7c19-81ba-4672-4f33-547177f88490
Host system: x86_64-conda_cos6-linux-gnu
Uname information: Linux 3dad7c19-81ba-4672-4f33-547177f88490 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /THFS/opt/anaconda/2/2019.3

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,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/THFS/opt/anaconda/2/2019.3/lib -L/THFS/opt/anaconda/2/2019.3/lib
AM_LDFLAGS: -L/THFS/opt/anaconda/2/2019.3/lib
Extra libraries: -lrt -lpthread -lz -ldl -lm
Archiver: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
Ranlib: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib

C: yes
C Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
AM_CPPFLAGS: -I/THFS/opt/anaconda/2/2019.3/include
C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/THFS/opt/anaconda/2/2019.3/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
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: yes

Fortran: yes
Fortran Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
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: yes

C++: yes
C++ Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
C++ Flags: -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/THFS/opt/anaconda/2/2019.3/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
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: yes

Java: no

Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: yes
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: yes
Memory allocation sanity checks: no
Metadata trace file: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Traceback (most recent call last):
File "./temperature_final.py", line 464, in <module>
File "./temperature_final.py", line 282, in main
ncfile = nc.Dataset(str(output)+'_EP.nc','w')
File "netCDF4/_netCDF4.pyx", line 2358, in netCDF4._netCDF4.Dataset.__init__
File "netCDF4/_netCDF4.pyx", line 1926, in netCDF4._netCDF4._ensure_nc_success
IOError: [Errno -101] NetCDF: HDF error: 'temperature_1_EP.nc'

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