Re: HDF5 error with gmt 4.5.12

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Not entirely true: netCDF will likely use HDF, at least if you have =
netCDF4.

But I suggest simply to do what is suggested in the warning message, =
which should be a WARNING not an ERROR:

You can, at your own risk, disable this warning by setting the =
environment

variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.


HDF is way too fussy about this version check. Even for versions that =
SHOULD be compatible it balks on this error.

Remko

On 16 Aug 2014, at 12:18, Joaquim Luis <[email protected]> wrote:

> Well, it wasn't me who said that GMT complained about a HDF version =
mismatch, and GMT doesn't access HDF directly. Only via GDAL.=20
>=20
> Sent from my iDedo
>=20
> No dia 16/08/2014, =C3=A0s 10:51, "Gery ." <[email protected]> =
escreveu:
>=20
>> So, that HDF thing is only to use gdal?? great! because I don't link =
gdal with GMT, so you are wrong Joaquim!! =3D) Cygwin sucks perhaps for =
you, for me it works well. Based on that, why it sucks? why are you guys =
so angry with Cygwin? I think you just need to relief that feeling and =
be free! ;)
>>=20
>> Cheers, and be happy!
>>=20
>> Sent from my iRon
>>=20
>> On Aug 16, 2014, at 1:40, "Joaquim Luis" <[email protected]> wrote:
>>=20
>> Gery,
>>=20
>> That warning from HDF essentially means that you are screwed. The =
computer will blow, or at least you'll get a crash. The HDF version used =
to link GDAL and the one at use must be exactly the same.
>> Still, on the land of opinions, Cygwin sucks compared with with MinGW =
where you can just use the, way faster, GMT5 Win binaries provided by =
us.=20
>>=20
>> Sent from my iPadiola
>>=20
>> On 15/08/2014, at 12:57, "Gery ." <[email protected]> wrote:
>>=20
>>> 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:
>>>=20
>>> -----------------------------------------------------------=E2=80=8B
>>> $ 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 but
>>>=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 =
environment
>>>=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 -Wst rict-overflow -Wlogical-op =
-Wlarger-than=3D2048 -Wvla -Wsync-nand -Wframe-larger-than=3D16384 =
-Wpacked-bitfield-compat -Wstrict-overfl ow=3D5 -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-frame- 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 have found a bug, discuss it here first. To formally report bugs or =
request features, please register and add New Issue =
ongmt.soest.hawaii.edu To unsubscribe, send the message "signoff =
gmt-help" [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 Issue =
ongmt.soest.hawaii.edu To unsubscribe, send the message "signoff =
gmt-help" [email protected] Note: gmt-help will become =
obsolete on Sept 1, 2014 - please use forum ongmt.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 =
ongmt.soest.hawaii.edu To unsubscribe, send the message "signoff =
gmt-help" [email protected] Note: gmt-help will become =
obsolete on Sept 1, 2014 - please use forum ongmt.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 =
ongmt.soest.hawaii.edu To unsubscribe, send the message "signoff =
gmt-help" [email protected] Note: gmt-help will become =
obsolete on Sept 1, 2014 - please use forum ongmt.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.

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<html><head><meta http-equiv=3D"Content-Type" content=3D"text/html =
charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space;"><div>Not entirely true: netCDF will likely use HDF, =
at least if you have netCDF4.</div><div><br></div><div>But I suggest =
simply to do what is suggested in the warning message, which should be a =
WARNING not an ERROR:</div><div><br></div><div><p style=3D"font-family: =
Calibri, 'Segoe UI', Meiryo, 'Microsoft YaHei UI', 'Microsoft JhengHei =
UI', 'Malgun Gothic', sans-serif; font-size: 16px;">You can, at your own =
risk, disable this warning by setting the environment</p><p =
style=3D"font-family: Calibri, 'Segoe UI', Meiryo, 'Microsoft YaHei UI', =
'Microsoft JhengHei UI', 'Malgun Gothic', sans-serif; font-size: =
16px;">variable 'HDF5_DISABLE_VERSION_CHECK' to a value of =
'1'.</p><div><br></div></div><div>HDF is way too fussy about this =
version check. Even for versions that SHOULD be compatible it balks on =
this error.</div><div><br></div><div>Remko</div><br><div><div>On 16 Aug =
2014, at 12:18, Joaquim Luis &lt;<a =
href=3D"mailto:[email protected]">[email protected]</a>&gt; =
wrote:</div><br class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite"><div dir=3D"auto" style=3D"font-family: Monaco; font-size: =
12px; font-style: normal; font-variant: normal; font-weight: normal; =
letter-spacing: normal; line-height: normal; orphans: auto; text-align: =
start; text-indent: 0px; text-transform: none; white-space: normal; =
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: =
0px;"><div>Well, it wasn't me who said that GMT complained about a HDF =
version mismatch, and GMT doesn't access HDF directly. Only via =
GDAL.&nbsp;<br><br><div>Sent from my iDedo</div></div><div><br>No dia =
16/08/2014, =C3=A0s 10:51, "Gery ." &lt;<a =
href=3D"mailto:[email protected]">[email protected]</a>&gt; =
escreveu:<br><br></div><blockquote type=3D"cite"><div>So, that HDF thing =
is only to use gdal?? great! because I don't link gdal with GMT, so you =
are wrong Joaquim!! =3D) Cygwin sucks perhaps for you, for me it works =
well. Based on that, why it sucks? why are you guys so angry with =
Cygwin? I think you just need to relief that feeling and be free! =
;)</div><div><br></div><div>Cheers, and be happy!<br><br>Sent from my =
iRon</div><div><br>On Aug 16, 2014, at 1:40, "Joaquim Luis" &lt;<a =
href=3D"mailto:[email protected]">[email protected]</a>&gt; =
wrote:<br><br></div><div><div>Gery,</div><div><br></div><div>That =
warning from HDF essentially means that you are screwed. The computer =
will blow, or at least you'll get a crash. The HDF version used to link =
GDAL and the one at use must be exactly the same.</div><div>Still, on =
the land of opinions, Cygwin sucks compared with with MinGW where you =
can just use the, way faster, GMT5 Win binaries provided by =
us.&nbsp;<br><br>Sent from my iPadiola</div><div><br>On 15/08/2014, at =
12:57, "Gery ." &lt;<a =
href=3D"mailto:[email protected]">[email protected]</a>&gt; =
wrote:<br><br></div><blockquote type=3D"cite"><div =
data-externalstyle=3D"false" dir=3D"ltr" style=3D"font-family: Calibri, =
'Segoe UI', Meiryo, 'Microsoft YaHei UI', 'Microsoft JhengHei UI', =
'Malgun Gothic', sans-serif; font-size: 12pt;"><div>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:</div><div><br></div><div>-------------------------------------------=
----------------=E2=80=8B</div><div><p>$ pscoast =
-R-71.2/-70.9/42.25/42.45 -JM6.0 -Ba0.05f0.01SWen -Ia -Na -W3 -K &gt; =
ps</p><p>Warning! ***HDF5 library version mismatched =
error***</p></div><div><p>The HDF5 header files used to compile this =
application do not match</p><p>the version used by the HDF5 library to =
which this application is linked.</p><p>Data corruption or segmentation =
faults may occur if the application continues.</p><p>This can happen =
when an application was compiled by one version of HDF5 but</p><p>linked =
with a different version of static or shared HDF5 library.</p><p>You =
should recompile the application or check your shared library =
related</p><p>settings such as 'LD_LIBRARY_PATH'.</p><p>You can, at your =
own risk, disable this warning by setting the environment</p><p>variable =
'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.</p><p>Setting it to 2 or =
higher will suppress the warning messages totally.</p><p>Headers are =
1.8.12, library is 1.8.13</p><p>SUMMARY OF THE HDF5 =
CONFIGURATION</p><p>=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</p><p>General =
Information:</p><p>-------------------</p><p>HDF5 Version: =
1.8.13</p><p>Configured on: Wed Jun 4 15:04:57 CEST =
2014</p><p>Configured by: marco@GE-MATZERI-EU</p><p>Configure mode: =
production</p><p>Host system: i686-pc-cygwin</p><p>Uname information: =
CYGWIN_NT-6.1-WOW64 GE-MATZERI-EU 1.7.30(0.272/5/3) 2014-05-23 10:36 =
i686 Cygwin</p><p>Byte sex: little-endian</p><p>Libraries: =
shared</p><p>Installation point: /usr</p><p>Compiling =
Options:</p><p>------------------</p><p>Compilation Mode: =
production</p><p>C Compiler: /usr/bin/gcc</p><p>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</p><p>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 =
-Wst rict-overflow -Wlogical-op -Wlarger-than=3D2048 -Wvla -Wsync-nand =
-Wframe-larger-than=3D16384 -Wpacked-bitfield-compat -Wstrict-overfl =
ow=3D5 -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-frame- pointer =
-finline-functions</p><p>AM_CFLAGS:</p><p>CPPFLAGS:</p><p>H5_CPPFLAGS: =
-DNDEBUG -UH5_DEBUG_API</p><p>AM_CPPFLAGS:</p><p>Shared C Library: =
yes</p><p>Static C Library: no</p><p>Statically Linked Executables: =
no</p><p>LDFLAGS:</p><p>H5_LDFLAGS: =
-no-undefined</p><p>AM_LDFLAGS:</p><p>Extra libraries: -lz -ldl =
-lm</p><p>Archiver: ar</p><p>Ranlib: ranlib</p><p>Debugged =
Packages:</p><p>API Tracing: =
no</p><p>Languages:</p><p>----------</p><p>Fortran: no</p><p>C++: =
yes</p><p>C++ Compiler: /usr/bin/g++</p><p>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</p><p>H5 C++ Flags:</p><p>AM C++ =
Flags:</p><p>Shared C++ Library: yes</p><p>Static C++ Library: =
no</p><p>Features:</p><p>---------</p><p>Parallel HDF5: no</p><p>High =
Level library: yes</p><p>Threadsafety: no</p><p>Default API Mapping: =
v18</p><p>With Deprecated Public Symbols: yes</p><p>I/O filters =
(external): deflate(zlib)</p><p>I/O filters (internal): =
shuffle,fletcher32,nbit,scaleoffset</p><p>MPE: no</p><p>Direct VFD: =
yes</p><p>dmalloc: no</p><p>Clear file buffers before write: =
yes</p><p>Using memory checker: no</p><p>Function Stack Tracing: =
no</p><p>Strict File Format Checks: no</p><p>Optimization =
Instrumentation: no</p><p>Large File Support (LFS): =
yes</p><p>Bye...</p><p>Aborted (core =
dumped)</p><p>-----------------------------------------------------------<=
/p></div><div>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&nbsp;zlib 1.2.8-1.</div><div><br></div><div>Any ideas?? =
thank..</div><div><br></div><div>Gery</div><div><br></div></div>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<a =
href=3D"http://gmt.soest.hawaii.edu/">gmt.soest.hawaii.edu</a><span =
class=3D"Apple-converted-space">&nbsp;</span>To unsubscribe, send the =
message "signoff gmt-help" to<a =
href=3D"mailto:[email protected]">[email protected]</a><sp=
an class=3D"Apple-converted-space">&nbsp;</span>Note: gmt-help will =
become obsolete on Sept 1, 2014 - please use forum on<span =
class=3D"Apple-converted-space">&nbsp;</span><a =
href=3D"http://gmt.soest.hawaii.edu/">gmt.soest.hawaii.edu</a><span =
class=3D"Apple-converted-space">&nbsp;</span>instead.</blockquote>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<a =
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href=3D"http://gmt.soest.hawaii.edu/">gmt.soest.hawaii.edu</a><span =
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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<a =
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class=3D"Apple-converted-space">&nbsp;</span>instead.</blockquote>Mailing =
list for GMT discussions of all kinds. If you are not sure you have =
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