Re: Problems with ncl 6.0.0 binary and HDF5: version mismatch

Hi Mary,

This binary does work without the HDF5 error. But it is not opendap enabled?

Christian

On Wed, Jul 27, 2011 at 18:11, Mary Haley <haley@ucar.edu> wrote:

> Hi Christian,
>
> This was reported before, and I suggested the below to the other user. I
> don't remember if it worked, however, so I didn't put this new binary on the
> ESG.
>
> Can you download this new file, and install it the same way you did before,
> and let me know if it works:
>
> ftp ftp.ucar.edu
> <log in as "anonymous">
> <Use email address as password>
> cd /pub/scd/haley
> get ncl_ncarg-6.0.0.Linux_RedHat_x86_64_nodap_gcc412.tar.gz
> quit
>
> The instructions for installing the software are the same as before:
>
> http://www.ncl.ucar.edu/Download/install.shtml
>
> If this works, then let me know and I'll replace the binary on the ESG with
> this one.
>
> Thanks,
>
> --Mary
>
> On Jul 27, 2011, at 9:45 AM, Christian Pagé wrote:
>
> 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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>
>
>

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Received on Wed Jul 27 10:21:10 2011