cdo merge leading to "Aborted (core dumped)"- How to fix it?
Added by Behzad Navidi over 5 years ago
hey all
I was trying to merge some netcd4 files but it's leading to this error:
behzad@behzad-x44h:~/Desktop$ cdo -L merge precip.1982.nc precip.1983.nc precip_all.nc
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 1.10.0, library is 1.10.5
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.5
Configured on: Thu Oct 24 21:08:24 +0330 2019
Configured by: behzad@behzad-x44h
Host system: x86_64-unknown-linux-gnu
Uname information: Linux behzad-x44h 5.0.0-32-generic #34~18.04.2-Ubuntu SMP Thu Oct 10 10:36:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /usr/local
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /usr/bin/gcc
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags:
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: no
C++: no
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: no
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: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
Aborted (core dumped)
Thank you
Replies (1)
RE: cdo merge leading to "Aborted (core dumped)"- How to fix it? - Added by Ralf Mueller over 5 years ago
hi!
As suggested in the error message, set the environment variable HDF5_DISABLE_VERSION_CHECK to 1 and rerun the call
- bash-compatible shells (sh/ash/dash/zsh/ksh) :
export HDF5_DISABLE_VERSION_CHECK=1
- csh-compatible shells:
setenv HDF5_DISABLE_VERSION_CHECK 1
hth
ralf