Re: HDF5 error with gmt 4.5.12

Thanks a lot cj for that, I will try it!

Cheers,

Gery

Sent from my iRon

On Aug 16, 2014, at 0:21, "Chenjian Fu" <[email protected]> wrote:

Oops, sorry, re-install your gmt4.

-cj

On Fri, Aug 15, 2014 at 6:19 PM, Chenjian Fu <[email protected]> wrote:
> Hi Gery,
>=20
> Try this: go back to hdf5 1.8.12. Then re-install gmt5.
>=20
> Cheers,
> Chenjian
>=20
> 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 thi=
s
>> message about HDF5:
>>=20
>> -----------------------------------------------------------
>>=20
>> $ pscoast -R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -=
K >
>> ps
>>=20
>> Warning! ***HDF5 library version mismatched error***
>>=20
>> The HDF5 header files used to compile this application do not match
>>=20
>> the version used by the HDF5 library to which this application is linked.=

>>=20
>> Data corruption or segmentation faults may occur if the application
>> continues.
>>=20
>> This can happen when an application was compiled by one version of HDF5 b=
ut
>>=20
>> linked with a different version of static or shared HDF5 library.
>>=20
>> You should recompile the application or check your shared library related=

>>=20
>> settings such as 'LD_LIBRARY_PATH'.
>>=20
>> You can, at your own risk, disable this warning by setting the environmen=
t
>>=20
>> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
>>=20
>> Setting it to 2 or higher will suppress the warning messages totally.
>>=20
>> Headers are 1.8.12, library is 1.8.13
>>=20
>> SUMMARY OF THE HDF5 CONFIGURATION
>>=20
>> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
>>=20
>> General Information:
>>=20
>> -------------------
>>=20
>> HDF5 Version: 1.8.13
>>=20
>> Configured on: Wed Jun 4 15:04:57 CEST 2014
>>=20
>> Configured by: marco@GE-MATZERI-EU
>>=20
>> Configure mode: production
>>=20
>> Host system: i686-pc-cygwin
>>=20
>> Uname information: CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3)
>> 2014-05-23 10:36 i686 Cygwin
>>=20
>> Byte sex: little-endian
>>=20
>> Libraries: shared
>>=20
>> Installation point: /usr
>>=20
>> Compiling Options:
>>=20
>> ------------------
>>=20
>> Compilation Mode: production
>>=20
>> C Compiler: /usr/bin/gcc
>>=20
>> CFLAGS: -ggdb -O2 -pipe -Wimplicit-function-declaration
>> -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/
>> build=3D/usr/src/debug/hdf5-1.8.13-1
>> -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr=
/src/debug/hdf5-1.8.13-1
>>=20
>> H5_CFLAGS: -std=3Dc99 -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=3D2 -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 -W=
st
>> rict-overflow -Wlogical-op -Wlarger-than=3D2048 -Wvla -Wsync-nand
>> -Wframe-larger-than=3D16384 -Wpacked-bitfield-compat -Wstrict-overfl ow=3D=
5
>> -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion
>> -Wsuggest-attribute=3Dconst -Wtrampolines -Wstack-usage=3D8192
>> -Wvector-operation-performance -Wsuggest-attribute=3Dpure
>> -Wsuggest-attribute=3Dnoreturn -Wsuggest-attribute=3Dformat -O3 -fomit-fr=
ame-
>> pointer -finline-functions
>>=20
>> AM_CFLAGS:
>>=20
>> CPPFLAGS:
>>=20
>> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
>>=20
>> AM_CPPFLAGS:
>>=20
>> Shared C Library: yes
>>=20
>> Static C Library: no
>>=20
>> Statically Linked Executables: no
>>=20
>> LDFLAGS:
>>=20
>> H5_LDFLAGS: -no-undefined
>>=20
>> AM_LDFLAGS:
>>=20
>> Extra libraries: -lz -ldl -lm
>>=20
>> Archiver: ar
>>=20
>> Ranlib: ranlib
>>=20
>> Debugged Packages:
>>=20
>> API Tracing: no
>>=20
>> Languages:
>>=20
>> ----------
>>=20
>> Fortran: no
>>=20
>> C++: yes
>>=20
>> C++ Compiler: /usr/bin/g++
>>=20
>> C++ Flags: -ggdb -O2 -pipe
>> -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/build=3D/usr/src/debug=
/hdf5-1.8.13
>> -1
>> -fdebug-prefix-map=3D/pub/devel/hdf5/hdf5-1.8.13-1/src/hdf5-1.8.13=3D/usr=
/src/debug/hdf5-1.8.13-1
>>=20
>> H5 C++ Flags:
>>=20
>> AM C++ Flags:
>>=20
>> Shared C++ Library: yes
>>=20
>> Static C++ Library: no
>>=20
>> Features:
>>=20
>> ---------
>>=20
>> Parallel HDF5: no
>>=20
>> High Level library: yes
>>=20
>> Threadsafety: no
>>=20
>> Default API Mapping: v18
>>=20
>> With Deprecated Public Symbols: yes
>>=20
>> I/O filters (external): deflate(zlib)
>>=20
>> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
>>=20
>> MPE: no
>>=20
>> Direct VFD: yes
>>=20
>> dmalloc: no
>>=20
>> Clear file buffers before write: yes
>>=20
>> Using memory checker: no
>>=20
>> Function Stack Tracing: no
>>=20
>> Strict File Format Checks: no
>>=20
>> Optimization Instrumentation: no
>>=20
>> Large File Support (LFS): yes
>>=20
>> Bye...
>>=20
>> Aborted (core dumped)
>>=20
>> -----------------------------------------------------------
>>=20
>> 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.
>>=20
>> Any ideas?? thank..
>>=20
>> Gery
>>=20
>> Mailing list for GMT discussions of all kinds. If you are not sure you ha=
ve
>> found a bug, discuss it here first. To formally report bugs or request
>> features, please register and add New Issue on gmt.soest.hawaii.edu To
>> unsubscribe, send the message "signoff gmt-help" to
>> [email protected] Note: gmt-help will become obsolete on Sept 1,
>> 2014 - please use forum on gmt.soest.hawaii.edu instead.

Mailing list for GMT discussions of all kinds.  If you are not sure you have=
 found a bug, discuss it here first.
To formally report bugs or request features, please register and add New Iss=
ue on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to [email protected]=
.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gm=
t.soest.hawaii.edu instead.

Mailing list for GMT discussions of all kinds.  If you are not sure you have found a bug, discuss it here first.
To formally report bugs or request features, please register and add New Issue on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to [email protected]
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.