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

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
> _______________________________________________
> ncl-talk mailing list
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Received on Wed Jul 27 10:12:03 2011