HDF5 error with gmt 4.5.12

Discussion:

Gery .

2014-08-15 16:57:51 UTC

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:

-----------------------------------------------------------â

$ 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: ***@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

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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 ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Gery .

2014-08-15 17:32:12 UTC

Permalink

Even though I use

export HDF5_DISABLE_VERSION_CHECK=1

export HDF5_DISABLE_VERSION_CHECK=2

I am wondering if Cygwin can be eventually unstable? or even my pc explode? 8-)

Thanks for any pointers

Sent from Windows Mail

From: Gery .
Sent: âFridayâ, âAugustâ â15â, â2014 â7â:â05â âPM
To: World-Wide GMT Usage and Help Mailing List

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:

-----------------------------------------------------------â

$ 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: ***@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 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 ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Paul Wessel

2014-08-15 18:25:03 UTC

Permalink

Hi Gery-

While I had to suffer through the indignity of running GMT 5 under Cygwin for a class, I did so without gdal since there was no gdal cygwin package 6 months ago. Are you saying there now is a gdal package via setup.exe? The GMT cygwin install instructions on the GMT wiki are the instructions I wrote after installing it myself so they work as recently as March.

You must have a good reason not to dual-boot your machine into ubuntu since you are willing to put up with cygwin.

-p

Post by Gery .
Even though I use
export HDF5_DISABLE_VERSION_CHECK=1
export HDF5_DISABLE_VERSION_CHECK=2
I am wondering if Cygwin can be eventually unstable? or even my pc explode? 8-)
Thanks for any pointers
Sent from Windows Mail
From: Gery .
Sent: âFridayâ, âAugustâ â15â, â2014 â7â:â05â âPM
To: World-Wide GMT Usage and Help Mailing List
-----------------------------------------------------------â
$ 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
=================================
-------------------
HDF5 Version: 1.8.13
Configured on: Wed Jun 4 15:04:57 CEST 2014
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
------------------
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
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
H5_LDFLAGS: -no-undefined
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
API Tracing: no
----------
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
Shared C++ Library: yes
Static C++ Library: no
---------
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

Gery .

2014-08-15 19:25:33 UTC

Permalink

Hello Paul,

no gdal at all!! in fact I installed gdal myself (latest version). I think now it is possible to use shared libraries in Cygwin, so I will try that again. Well I have, I am tired of booting every single time I need to use gmt/seismic unix/mb/etc, all of them interconnected in shell scripts, so I recently came back to Cygwin again. Actually, I started using Cygwin and I was really happy with it, I just changed to Linux because I needed to use a couple of other seismic processing apps.

indignity haha, I would say âinfinityâ (it takes a lot of time now to install the whole Cygwin, almost 6 GB!!), but Cygwin looks nicer, I like it =)

Cheers,

Gery

Sent from Windows Mail

From: Paul Wessel
Sent: âFridayâ, âAugustâ â15â, â2014 â8â:â25â âPM
To: World-Wide GMT Usage and Help Mailing List

Hi Gery-

While I had to suffer through the indignity of running GMT 5 under Cygwin for a class, I did so without gdal since there was no gdal cygwin package 6 months ago. Are you saying there now is a gdal package via setup.exe? The GMT cygwin install instructions on the GMT wiki are the instructions I wrote after installing it myself so they work as recently as March.

You must have a good reason not to dual-boot your machine into ubuntu since you are willing to put up with cygwin.

-p

On Aug 15, 2014, at 7:32 AM, Gery . <***@HOTMAIL.COM> wrote:

Even though I use

export HDF5_DISABLE_VERSION_CHECK=1

export HDF5_DISABLE_VERSION_CHECK=2

I am wondering if Cygwin can be eventually unstable? or even my pc explode? 8-)

Thanks for any pointers

Sent from Windows Mail

From: Gery .
Sent: âFridayâ, âAugustâ â15â, â2014 â7â:â05â âPM
To: World-Wide GMT Usage and Help Mailing List

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:

-----------------------------------------------------------â

$ 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: ***@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 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 ***@lists.hawaii.edu 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 on gmt.soest.hawaii.edu To unsubscribe, send the message "signoff gmt-help" to ***@lists.hawaii.edu 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 on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Chenjian Fu

2014-08-15 22:19:12 UTC

Permalink

Hi Gery,

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

Cheers,
Chenjian

Post by Gery .
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
-----------------------------------------------------------
$ 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
=================================
-------------------
HDF5 Version: 1.8.13
Configured on: Wed Jun 4 15:04:57 CEST 2014
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
------------------
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
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
H5_LDFLAGS: -no-undefined
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
API Tracing: no
----------
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
Shared C++ Library: yes
Static C++ Library: no
---------
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
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
2014 - please use forum on gmt.soest.hawaii.edu instead.

Chenjian Fu

2014-08-15 22:21:01 UTC

Permalink

Oops, sorry, re-install your gmt4.

-cj

Post by Chenjian Fu
Hi Gery,
Try this: go back to hdf5 1.8.12. Then re-install gmt5.
Cheers,
Chenjian

Gery .

2014-08-16 09:52:09 UTC

Permalink

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" <***@KENT.EDU> wrote:

Oops, sorry, re-install your gmt4.

-cj

Post by Chenjian Fu
Hi Gery,
Try this: go back to hdf5 1.8.12. Then re-install gmt5.
Cheers,
Chenjian

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 ***@lists.hawaii.edu
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 on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Joaquim Luis

2014-08-15 23:39:32 UTC

Permalink

Gery,

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.

Sent from my iPadiola

Post by Gery .
-----------------------------------------------------------â
$ 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
=================================
-------------------
HDF5 Version: 1.8.13
Configured on: Wed Jun 4 15:04:57 CEST 2014
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
------------------
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
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
H5_LDFLAGS: -no-undefined
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
API Tracing: no
----------
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
Shared C++ Library: yes
Static C++ Library: no
---------
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

Gery .

2014-08-16 09:51:06 UTC

Permalink

So, that HDF thing is only to use gdal?? great! because I don't link gdal with GMT, so you are wrong Joaquim!! =) 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! ;)

Cheers, and be happy!

Sent from my iRon

On Aug 16, 2014, at 1:40, "Joaquim Luis" <***@GMAIL.COM> wrote:

Gery,

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.

Sent from my iPadiola

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 ***@lists.hawaii.edu 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 on gmt.soest.hawaii.edu
To unsubscribe, send the message "signoff gmt-help" to ***@lists.hawaii.edu
Note: gmt-help will become obsolete on Sept 1, 2014 - please use forum on gmt.soest.hawaii.edu instead.

Joaquim Luis

2014-08-16 11:18:15 UTC

Permalink

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.

Sent from my iDedo

Post by Gery .
So, that HDF thing is only to use gdal?? great! because I don't link gdal with GMT, so you are wrong Joaquim!! =) 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! ;)
Cheers, and be happy!
Sent from my iRon
Gery,
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.
Sent from my iPadiola

Remko Scharroo

2014-08-17 09:19:23 UTC

Permalink

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

Post by Joaquim Luis
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.
Sent from my iDedo

J. Luis

2014-08-17 20:32:39 UTC

Permalink

Ops, off course (vacations-memory-cleaning)
I had once that message that I obviously ignored ... and it crashed on
first access.

Post by Remko Scharroo
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,
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

Post by Joaquim Luis
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.
Sent from my iDedo

Post by Gery .
So, that HDF thing is only to use gdal?? great! because I don't link
gdal with GMT, so you are wrong Joaquim!! =) 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! ;)
Cheers, and be happy!
Sent from my iRon
Gery,
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.
Sent from my iPadiola

Post by Gery .
Sorry for the last noisy message, but things were smooth finally,
the solution was to install without gdal. Now things work, but I
----------------------------------------------------------- â
$ 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
=================================
-------------------
HDF5 Version: 1.8.13
Configured on: Wed Jun 4 15:04:57 CEST 2014
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
------------------
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
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
Shared C Library: yes
Static C Library: no
Statically Linked Executables: no
H5_LDFLAGS: -no-undefined
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
API Tracing: no
----------
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
Shared C++ Library: yes
Static C++ Library: no
---------
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 found a bug, discuss it here first. To formally report
bugs or request features, please register and add New Issue
ongmt.soest.hawaii.edu <http://gmt.soest.hawaii.edu/>To
unsubscribe, send the message "signoff gmt-help"
gmt-help will become obsolete on Sept 1, 2014 - please use forum
ongmt.soest.hawaii.edu <http://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 <http://gmt.soest.hawaii.edu/>To unsubscribe,
obsolete on Sept 1, 2014 - please use forum ongmt.soest.hawaii.edu
<http://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 <http://gmt.soest.hawaii.edu/>To unsubscribe,
obsolete on Sept 1, 2014 - please use forum ongmt.soest.hawaii.edu
<http://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 <http://gmt.soest.hawaii.edu/>To unsubscribe,
on Sept 1, 2014 - please use forum ongmt.soest.hawaii.edu
<http://gmt.soest.hawaii.edu/>instead.