[MacPorts] #47797: ncarg ncl fails on hdf5 mismatch
MacPorts
noreply at macports.org
Thu May 21 08:42:13 PDT 2015
#47797: ncarg ncl fails on hdf5 mismatch
--------------------------------+-----------------------
Reporter: barry.j.mcinnes@… | Owner: takeshi@…
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.3.3
Resolution: | Keywords:
Port: ncarg |
--------------------------------+-----------------------
Description changed by mf2k@…:
Old description:
> The update of ncarg to ncarg @6.3.0_1 (science), refers to libraries
> libhdf5.9.dylib and libhdf5_hl.9.dylib, which I do not have currently in
> macports install.
> I copied them from an old macports install and then ncl runs, but with
> the following warnings, which can be turned off, but user has to force
> quit.
> Also tried linking the libs to version 10, with the same result.
> With HDF5_DISABLE_VERSION_CHECK set to 1 or 2, ncl runs ok.
>
> ncl stationTS_compare.ncl
>
> Copyright (C) 1995-2015 - All Rights Reserved
>
> University Corporation for Atmospheric Research
>
> NCAR Command Language Version 6.3.0
>
> The use of this software is governed by a License Agreement.
>
> See http://www.ncl.ucar.edu/ for more details.
>
> 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 1.8.15, library is 1.8.14
>
> SUMMARY OF THE HDF5 CONFIGURATION
>
> =================================
>
> General Information:
>
> -------------------
>
> HDF5 Version: 1.8.14
>
> Configured on: Mon Jan 5 09:39:26 PST 2015
>
> Configured by: macports at tenten-slave.macports.org
>
> Configure mode: production
>
> Host system: i386-apple-darwin14.0.0
>
> Uname information: Darwin tenten-slave.macports.org 14.0.0 Darwin
> Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014;
> root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
>
> Byte sex: little-endian
>
> Libraries: static, shared
>
> Installation point: /opt/local
>
> Compiling Options:
>
> ------------------
>
> Compilation Mode: production
>
> C Compiler: /usr/bin/clang
>
> CFLAGS: -pipe -Os
>
> H5_CFLAGS:
>
> AM_CFLAGS:
>
> CPPFLAGS: -I/opt/local/include
>
> H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
>
> AM_CPPFLAGS:
>
> Shared C Library: yes
>
> Static C Library: yes
>
> Statically Linked Executables: no
>
> LDFLAGS: -L/opt/local/lib
> -Wl,-headerpad_max_install_names
>
> H5_LDFLAGS:
>
> AM_LDFLAGS: -L/opt/local/lib
>
> Extra libraries: -lz -ldl -lm
>
> Archiver: ar
>
> Ranlib: ranlib
>
> Debugged Packages:
>
> API Tracing: no
>
> Languages:
>
> ----------
>
> Fortran: no
>
> C++: yes
>
> C++ Compiler: /usr/bin/clang++
>
> C++ Flags: -pipe -Os -stdlib=libc++
>
> H5 C++ Flags:
>
> AM C++ Flags:
>
> Shared C++ Library: yes
>
> Static C++ Library: yes
>
> 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: no
>
> 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...
>
> Abort
New description:
The update of ncarg to ncarg @6.3.0_1 (science), refers to libraries
libhdf5.9.dylib and libhdf5_hl.9.dylib, which I do not have currently in
macports install.
I copied them from an old macports install and then ncl runs, but with the
following warnings, which can be turned off, but user has to force quit.
Also tried linking the libs to version 10, with the same result.
With HDF5_DISABLE_VERSION_CHECK set to 1 or 2, ncl runs ok.
{{{
ncl stationTS_compare.ncl
Copyright (C) 1995-2015 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.3.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
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 1.8.15, library is 1.8.14
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.14
Configured on: Mon Jan 5 09:39:26 PST 2015
Configured by: macports at tenten-slave.macports.org
Configure mode: production
Host system: i386-apple-darwin14.0.0
Uname information: Darwin tenten-slave.macports.org 14.0.0 Darwin
Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014;
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
Byte sex: little-endian
Libraries: static, shared
Installation point: /opt/local
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/clang
CFLAGS: -pipe -Os
H5_CFLAGS:
AM_CFLAGS:
CPPFLAGS: -I/opt/local/include
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS: -L/opt/local/lib
-Wl,-headerpad_max_install_names
H5_LDFLAGS:
AM_LDFLAGS: -L/opt/local/lib
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: yes
C++ Compiler: /usr/bin/clang++
C++ Flags: -pipe -Os -stdlib=libc++
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
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: no
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...
Abort
}}}
--
--
Ticket URL: <https://trac.macports.org/ticket/47797#comment:2>
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