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

Just a follow-up on this: Christian downloaded the binary again and it worked. I believe the binary was updated after a previous user reported the same problem.

--Mary

On Jul 27, 2011, at 10:20 AM, Christian Pagé wrote:

> 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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Received on Fri Aug 5 07:24:12 2011