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cdo merge leading to "Aborted (core dumped)"- How to fix it?

Added by Behzad Navidi over 4 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 4 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

    (1-1/1)