#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@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@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> MacPorts <https://www.macports.org/> Ports system for OS X

#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 | --------------------------------+----------------------- Comment (by barry.j.mcinnes@…): Currently we have an ncl install in /usr/local. I will try with macports ncl. We do have various versions of libhdf as well as macports [mac27:~/info] bmcinnes% locate libhdf5 /Applications/HDFView.app/Contents/Resources/lib/libhdf5.a /Applications/HDFView.app/Contents/Resources/share/cmake/hdf5/libhdf5.settings /Applications/MATLAB_R2015a.app/bin/maci64/libhdf5.8.dylib /Applications/MATLAB_R2015a.app/bin/maci64/libhdf5.dylib /Applications/MATLAB_R2015a.app/bin/maci64/libhdf5_hl.8.dylib /Applications/MATLAB_R2015a.app/bin/maci64/libhdf5_hl.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.0.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.6.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.0.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.6.dylib /Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.dylib /Volumes/Cluster/opt/local/lib/libhdf5.10.dylib /Volumes/Cluster/opt/local/lib/libhdf5.8.dylib /Volumes/Cluster/opt/local/lib/libhdf5.9.dylib /Volumes/Cluster/opt/local/lib/libhdf5.a /Volumes/Cluster/opt/local/lib/libhdf5.dylib /Volumes/Cluster/opt/local/lib/libhdf5.settings /Volumes/Cluster/opt/local/lib/libhdf5_cpp.10.dylib /Volumes/Cluster/opt/local/lib/libhdf5_cpp.8.dylib /Volumes/Cluster/opt/local/lib/libhdf5_cpp.a /Volumes/Cluster/opt/local/lib/libhdf5_cpp.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl.10.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl.8.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl.9.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl.a /Volumes/Cluster/opt/local/lib/libhdf5_hl.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.10.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.8.dylib /Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.a /Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.dylib /Volumes/Cluster/usr/local/ifort/lib/libhdf5.8.dylib /Volumes/Cluster/usr/local/ifort/lib/libhdf5.a /Volumes/Cluster/usr/local/ifort/lib/libhdf5.dylib /Volumes/Cluster/usr/local/ifort/lib/libhdf5.la /Volumes/Cluster/usr/local/ifort/lib/libhdf5.settings /Volumes/Cluster/usr/local/ifort/lib/libhdf5_fortran.a /Volumes/Cluster/usr/local/ifort/lib/libhdf5_fortran.la /Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.8.dylib /Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.a /Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.dylib /Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.la /Volumes/Cluster/usr/local/ifort/lib/libhdf5hl_fortran.a /Volumes/Cluster/usr/local/ifort/lib/libhdf5hl_fortran.la [mac27:~/info] -- Ticket URL: <https://trac.macports.org/ticket/47797#comment:8> MacPorts <https://www.macports.org/> Ports system for OS X

#47797: ncarg ncl fails on hdf5 mismatch --------------------------------+----------------------- Reporter: barry.j.mcinnes@… | Owner: takeshi@… Type: defect | Status: closed Priority: Normal | Milestone: Component: ports | Version: 2.3.3 Resolution: invalid | Keywords: Port: ncarg | --------------------------------+----------------------- Changes (by takeshi@…): * status: new => closed * resolution: => invalid -- Ticket URL: <https://trac.macports.org/ticket/47797#comment:10> MacPorts <https://www.macports.org/> Ports system for OS X