Re: [netcdfgroup] apparent bug in the latest beta snapshot of nccopy

• To: ed zaron <zaron@xxxxxxxxxxxx>
• Subject: Re: [netcdfgroup] apparent bug in the latest beta snapshot of nccopy
• From: Dennis Heimbigner <dmh@xxxxxxxxxxxxxxxx>
• Date: Fri, 14 Jan 2011 11:21:57 -0700

I will investigate.

=Dennis Heimbigner
 Unidata

ed zaron wrote:

Hi James and Dennis,

I discovered an apparent bug in the latest beta snapshot concerning nccopy.

I have two builds of netcdf, and I executed the following commands and obtained 
different results:

USING LATEST BUILD (latest beta referenced in previous email)
ezaron$ ~/opt/bin/nccopy 
http://omglnx1.meas.ncsu.edu:8080/thredds/dodsC/gomexppp/2010_June/avg/N N.nc

USING AN OLDER BUILD:
ezaron$ /opt/local/bin/nccopy 
http://omglnx1.meas.ncsu.edu:8080/thredds/dodsC/gomexppp/2010_June/avg/N N.nc


The latest build fails to copy all the variables correctly. For some reason the 
file it creates discards all the time variability of the 3-dimensional fields 
(u,v, temp, and salt). I have attached the output of ncdump -h for the files. I 
can post the entire files if needed, they are about 1GB.

Please see below the nc-config information for both netcdf builds.



Here's the config info on the LATEST BUILD:
ezaron$ ~/opt/bin/nc-config --all

This netCDF 4.1.2-beta2-snapshot2011011022 has been built with the following features:

  --cc        -> cc
  --cflags    ->  -I/Users/ezaron/opt/include  -I/opt/local/include 
-I/opt/local/include -I/opt/local/include
  --libs      -> -L/Users/ezaron/opt/lib -lnetcdf  -L/opt/local/lib -lhdf5_hl 
-lhdf5 -L/opt/local/lib -lz -L/opt/local/lib -lcurl -L/opt/local/lib 
-L/opt/local/lib -L/opt/local/lib -lidn -lssl -lcrypto -lssl -lcrypto -lz -lz -lz

  --cxx       -> g++
  --has-c++   -> yes

  --fc        -> g95
  --fflags    -> -g -O2 /Users/ezaron/opt/include
  --flibs     -> -L/Users/ezaron/opt/lib -lnetcdff -lnetcdf
  --has-f77   -> no
  --has-f90   -> no

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no
  --has-szlib -> no

  --prefix    -> /Users/ezaron/opt
  --includedir-> /Users/ezaron/opt/include
  --version   -> netCDF 4.1.2-beta2-snapshot2011011022


Here's the config info on the working OLDER BUILD:
ezaron$ /opt/local/bin/nc-config --all

This netCDF 4.1.1 has been built with the following features:

  --cc        -> /opt/local/bin/gcc-mp-4.3
  --cflags    ->  -I/opt/local/include
  --libs      -> -L/opt/local/lib -lnetcdf

  --cxx       -> /opt/local/bin/g++-mp-4.3
  --has-c++   -> yes

  --fc        -> /opt/local/bin/gfortran-mp-4.3
  --fflags    -> -O2 -m64 -I/opt/local/include
  --flibs     -> -L/opt/local/lib -lnetcdff -lnetcdf
  --has-f77   -> yes
  --has-f90   -> yes

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-szlib -> yes

  --prefix    -> /opt/local
  --includedir-> /opt/local/include
  --version   -> netCDF 4.1.1


Please forgive me if this is not the right place to post a bug report.

All the best,

-Ed



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On Jan 10, 2011, at 4:21 PM, Dennis Heimbigner wrote:

The netcdf snapshot
(ftp://ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-4-daily.tar.gz)
available TOMORROW (Tuesday)
now supports the ability to access opendap data stored in files.

If you have a file called, say, dataset.dods, it is expected that
it contains the on-the-wire data for a request to an opendap server.
Such a file can be created using, for example, wget or a web browser.
Similarly, one can save .das and .dds data in files.

Suppose you have such a file at absolute path /home/abc/dapdata.dods.
You should now be able to access it using, for example the command:
   ncdump file:///home/abs/dapdata
You could also use nccopy instead of ncdump.
NOTE: the final .dods is left off.

There are some things to note:
1. You must have at least a .dods file (e.g. dataset.dods).

2. If there is also a /home/abs/dapdata.das,
  it will be used to obtain attributes.

3. If there is a /home/abs/dapdata.dds
  it will be used.  If this does not exist,
  then the dds part of the .dods file will be used.

If you are in a position to try this out, please do so
and let me know if there are any problems.

=Dennis Heimbigner (dmh@xxxxxxxx)
Unidata

• References:
  • [netcdfgroup] Using file:// protocol to retrieve opendap data...
    • From: Dennis Heimbigner
  • [netcdfgroup] apparent bug in the latest beta snapshot of nccopy
    • From: ed zaron