Hi,
When trying to read a NetCDF4 encoded file with the NCL 6.0.0 binary, here
is what I get... a problem of mismatch between HDF5 headers at compile time
and library at link time.
The NCL 6.0.0 binary is the following:
ncl_ncarg-6.0.0.Linux_RedHat_x86_64_gcc412.tar.gz
I verified with ldd that no .so HDF5 library is loaded, it has been linked
statically:
% ldd /usr/local/bin/ncl
libpthread.so.0 => /lib64/libpthread.so.0 (0x00000034f7000000)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000034f8400000)
libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000034f9400000)
libm.so.6 => /lib64/libm.so.6 (0x00000034f6800000)
libdl.so.2 => /lib64/libdl.so.2 (0x00000034f6c00000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003e2fe00000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003e2fa00000)
libc.so.6 => /lib64/libc.so.6 (0x00000034f6400000)
/lib64/ld-linux-x86-64.so.2 (0x00000034f5400000)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000034f8000000)
libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000034f8c00000)
======
Copyright (C) 1995-2011 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.0.0
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 1.8.5, library is 1.8.6
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.6
Configured on: Mon May 23 09:21:22 MDT 2011
Configured by: haley@mirage1
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux mirage1 2.6.18-194.17.4.el5 #1 SMP Wed
Oct 20 13:03:08 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /fs/blizzard/contrib/ncl-6.0.0/external
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
CFLAGS: -fPIC
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 -Wredundant-decls
-Wnested-externs -Winline -Wno-long-long -Wfloat-equal
-Wmissing-format-attribute -Wmissing-noreturn -Wpacked
-Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
-Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch
-Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs
-Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations
-Wc++-compat -Wvolatile-register-var -O3 -fomit-frame-pointer
-finline-functions
AM_CFLAGS:
CPPFLAGS: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-D_LARGEFILE_SOURCE
H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
-I/fs/blizzard/contrib/ncl-6.0.0/external/include
-I/fs/blizzard/contrib/ncl-6.0.0/external/include -D_LARGEFILE_SOURCE
-D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared Libraries: no
Static Libraries: yes
Statically Linked Executables: no
LDFLAGS:
AM_LDFLAGS:
-L/fs/blizzard/contrib/ncl-6.0.0/external/lib
-L/fs/blizzard/contrib/ncl-6.0.0/external/lib
Extra libraries: -lsz -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Languages:
----------
Fortran: no
C++: 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),szip(encoder)
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
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
Christian Pagé
http://meteocentre.com/toulouse/ http://meteoalerte.com/france/
Ingénieur de recherche en climat, CERFACS, Toulouse
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Received on Wed Jul 27 09:46:06 2011
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