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[netCDF #PVS-842308]: Possible bug in netCDF-4.1?

Hi Sourish,

I verified the problem and see that Jeff Whitaker has reported a simplified 
version of it using the C API.  It appears that the conditions required to 
trigger this are

  - using the netCDF-4 format
  - creating dimensions in one order
  - defining the corresponding coordinate variables in a different order

It's amazing to me that our umpteen thousand tests never tested this
particular case, but a quick workaround would be to define the coordinate 
variables in the same order as the dimensions, until we get this fixed.

Thanks for reporting the bug!

--Russ

> I created the file using python's netCDF4 module, available at
> http://code.google.com/p/netcdf4-python/. The actual code is part of a
> bigger program, so I'm attaching some code that looks similar to the
> relevant part of the program, and reproduces the problem. I'm afraid
> that you might think that this is a python-netcdf4 issue, but I doubt
> that. After all, ncdump and h5dump are giving me different results, and
> neither have anything to do with python.
> 
> To use the code, I did the following from the IPython prompt:
> 
> [1]: %run TestNCDF4
> 
> [2]: x = TesNCDF4()
> 
> [3]: x.WriteFile()
> 
> Then I executed 'ncdump' and 'h5dump' to view the contents. Some more
> information about my libraries you might find useful:
> 
> $ ncdump
> ncdump [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]]
> [-k] [-x] [-s] [-t] [-w] file
> <snip>
> netcdf library version 4.1 of Feb 12 2010 16:32:10 $
> 
> $ ldd `which ncdump`
> linux-vdso.so.1 =>  (0x00007fff18e97000)
> libnetcdf.so.6 => /usr/local/lib/libnetcdf.so.6 (0x00007f093848d000)
> libhdf5_hl.so.6 => /usr/local/lib/libhdf5_hl.so.6
> (0x00007f093825a000)
> libhdf5.so.6 => /usr/local/lib/libhdf5.so.6 (0x00007f0937caa000)
> libsz.so.2 => /usr/local/lib/libsz.so.2 (0x00007f0937a96000)
> libm.so.6 => /lib/libm.so.6 (0x00007f0937812000)
> libz.so.1 => /lib/libz.so.1 (0x00007f09375fb000)
> libc.so.6 => /lib/libc.so.6 (0x00007f093728c000)
> /lib64/ld-linux-x86-64.so.2 (0x00007f09387a0000)
> 
> $ h5dump -V
> h5dump: Version 1.8.4
> 
> $ ldd `which h5dump`
> linux-vdso.so.1 =>  (0x00007fff8ccb5000)
> libhdf5.so.6 => /usr/local/lib/libhdf5.so.6 (0x00007ff87cc9a000)
> libsz.so.2 => /usr/local/lib/libsz.so.2 (0x00007ff87ca86000)
> libz.so.1 => /lib/libz.so.1 (0x00007ff87c86f000)
> libm.so.6 => /lib/libm.so.6 (0x00007ff87c5eb000)
> libc.so.6 => /lib/libc.so.6 (0x00007ff87c27c000)
> /lib64/ld-linux-x86-64.so.2 (0x00007ff87d24a000)
> 
> $ ldd /usr/local/lib/python2.6/dist-packages/netCDF4.so
> linux-vdso.so.1 =>  (0x00007fff4f5ff000)
> libnetcdf.so.6 => /usr/local/lib/libnetcdf.so.6 (0x00007fa860208000)
> libhdf5.so.6 => /usr/local/lib/libhdf5.so.6 (0x00007fa85fc58000)
> libhdf5_hl.so.6 => /usr/local/lib/libhdf5_hl.so.6
> (0x00007fa85fa24000)
> libz.so.1 => /lib/libz.so.1 (0x00007fa85f7e8000)
> libpthread.so.0 => /lib/libpthread.so.0 (0x00007fa85f5cc000)
> libc.so.6 => /lib/libc.so.6 (0x00007fa85f25c000)
> libsz.so.2 => /usr/local/lib/libsz.so.2 (0x00007fa85f048000)
> libm.so.6 => /lib/libm.so.6 (0x00007fa85edc4000)
> /lib64/ld-linux-x86-64.so.2 (0x00007fa8607c5000)
> 
> $ gcc -v
> Using built-in specs.
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> 4.4.1-4ubuntu9' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
> --enable-shared --enable-multiarch --enable-linker-build-id
> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
> --program-suffix=-4.4 --enable-nls --enable-clocale=gnu
> --enable-libstdcxx-debug --enable-objc-gc --disable-werror
> --with-arch-32=i486 --with-tune=generic --enable-checking=release
> --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> Thread model: posix
> gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9)
> 
> $ gfortran -v
> Using built-in specs.
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> 4.4.1-4ubuntu9' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
> --enable-shared --enable-multiarch --enable-linker-build-id
> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
> --program-suffix=-4.4 --enable-nls --enable-clocale=gnu
> --enable-libstdcxx-debug --enable-objc-gc --disable-werror
> --with-arch-32=i486 --with-tune=generic --enable-checking=release
> --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> Thread model: posix
> gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9)
> 
> $ g++ -v
> Using built-in specs.
> Target: x86_64-linux-gnu
> Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> 4.4.1-4ubuntu9' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
> --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
> --enable-shared --enable-multiarch --enable-linker-build-id
> --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
> --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4
> --program-suffix=-4.4 --enable-nls --enable-clocale=gnu
> --enable-libstdcxx-debug --enable-objc-gc --disable-werror
> --with-arch-32=i486 --with-tune=generic --enable-checking=release
> --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
> Thread model: posix
> gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9)
> 
> Thanks,
> 
> -Sourish
> 
> Unidata netCDF Support wrote:
> > Hi Sourish,
> >
> > Can you please make available a copy of the program that created the file?
> > Thanks!
> >
> > --Russ
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: PVS-842308
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> 
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: PVS-842308
Department: Support netCDF
Priority: Normal
Status: Closed