Re: HDF5 error with gmt 4.5.12

Hi Gery,

Try this: go back to hdf5 1.8.12. Then re-install gmt5.

Cheers,
Chenjian

On Fri, Aug 15, 2014 at 12:57 PM, Gery . <[email protected]> wrote:
> Sorry for the last noisy message, but things were smooth finally, the
> solution was to install without gdal. Now things work, but I received this
> message about HDF5:
>
> -----------------------------------------------------------
>
> $ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -K >
> ps
>
> 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 1.8.12, library is 1.8.13
>
> SUMMARY OF THE HDF5 CONFIGURATION
>
> =================================
>
> General Information:
>
> -------------------
>
> HDF5 Version: 1.8.13
>
> Configured on: Wed Jun 4 15:04:57 CEST 2014
>
> Configured by: marco@GE-MATZERI-EU
>
> Configure mode: production
>
> Host system: i686-pc-cygwin
>
> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3)
> 2014-05-23 10:36 i686 Cygwin
>
> Byte sex: little-endian
>
> Libraries: shared
>
> Installation point: /usr
>
> Compiling Options:
>
> ------------------
>
> Compilation Mode: production
>
> C Compiler: /usr/bin/gcc
>
> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-declaration
> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/
> build=/usr/src/debug/hdf5-1.8.13-1
> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=/usr/src/debug/hdf5-1.8.13-1
>
> H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith
> -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion
> -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes
> -Wmissing-declarations -Wre dundant-decls -Wnested-externs -Winline
> -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked
> -Wdisabled-optimizati on -Wformat=2 -Wunreachable-code -Wendif-labels
> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch
> -Wvariadic-macr os -Winit-self -Wmissing-include-dirs -Wswitch-default
> -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wst
> rict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand
> -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overfl ow=5
> -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion
> -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192
> -Wvector-operation-performance -Wsuggest-attribute=pure
> -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame-
> pointer -finline-functions
>
> AM_CFLAGS:
>
> CPPFLAGS:
>
> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
>
> AM_CPPFLAGS:
>
> Shared C Library: yes
>
> Static C Library: no
>
> Statically Linked Executables: no
>
> LDFLAGS:
>
> H5_LDFLAGS: -no-undefined
>
> AM_LDFLAGS:
>
> Extra libraries: -lz -ldl -lm
>
> Archiver: ar
>
> Ranlib: ranlib
>
> Debugged Packages:
>
> API Tracing: no
>
> Languages:
>
> ----------
>
> Fortran: no
>
> C++: yes
>
> C++ Compiler: /usr/bin/g++
>
> C++ Flags: -ggdb -O2 -pipe
> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/build=/usr/src/debug/hdf5-1.8.13
> -1
> -fdebug-prefix-map=/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=/usr/src/debug/hdf5-1.8.13-1
>
> H5 C++ Flags:
>
> AM C++ Flags:
>
> Shared C++ Library: yes
>
> Static C++ Library: no
>
> Features:
>
> ---------
>
> Parallel HDF5: no
>
> High Level library: yes
>
> Threadsafety: no
>
> Default API Mapping: v18
>
> With Deprecated Public Symbols: yes
>
> I/O filters (external): deflate(zlib)
>
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
>
> MPE: no
>
> Direct VFD: yes
>
> dmalloc: no
>
> Clear file buffers before write: yes
>
> Using memory checker: no
>
> Function Stack Tracing: no
>
> Strict File Format Checks: no
>
> Optimization Instrumentation: no
>
> Large File Support (LFS): yes
>
> Bye...
>
> Aborted (core dumped)
>
> -----------------------------------------------------------
>
> I have the latest Cygwin 32-bit version. Which HDF5 version should I use?
> this Cygwin comes with hdf5 1.8.13-1, netcdf 4.3.2-1 and zlib 1.2.8-1.
>
> Any ideas?? thank..
>
> Gery
>
> Mailing list for GMT discussions of all kinds. If you are not sure you have
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> [email protected] Note: gmt-help will become obsolete on Sept 1,
> 2014 - please use forum on gmt.soest.hawaii.edu instead.

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