bugy 1.1.0

[Wei-keng Liao]

Hi, Lie-Quan,

Thanks for reporting this bug. Here is a quick fix.
Please replace the following in file parallel-netcdf-1.1.0/src/lib/nc.c

old nc.c:
line 916          alignment = 1;
new nc.c:
line 916          alignment = NC_ALIGN_CHUNK;

Please let us know if that solves your problem.

Wei-keng

On Dec 5, 2009, at 2:14 AM, Lie-Quan Lee wrote:

> Oops, I guess that I may not understand how to run test_double.
>
> Anyhow, the redef problem is true. Attached is the testing program  
> to show the probelm. Please help. Thanks.
>
> Best regards,
> Lie-Quan
>
>
> On Fri, Dec 4, 2009 at 10:30 PM, Lie-Quan Lee <liequan at gmail.com>  
> wrote:
> Dear Parallel-netcdf Developers,
>
> I really would like to use version 1.1.0 for its CDF-5 format in our  
> simulation. However, there are some issues (unrelated to CDF-5) in  
> the release 1.1.0. For example, the test_write program under test/ 
> test_double failed to generated the right data file (as in test/data/ 
> test_double.nc). Here is the ncdump of the resuting data file:
>
> netcdf t {
> dimensions:
>     x = 100 ;
>     y = 100 ;
>     z = 100 ;
>     time = UNLIMITED ; // (100 currently)
> variables:
>     double square(x, y) ;
>         square:description = "2-D integer array" ;
>     double cube(x, y, z) ;
>     double time(time) ;
>     double xytime(time, x, y) ;
>
> // global attributes:
>         :title = "example netCDF dataset" ;
> data:
>
>  square =
>   0, nan, 2, nan, 4, nan, 6, nan, 8, nan, 10, nan, 12, nan, 14, nan,  
> 16, nan,
>     18, nan, 20, nan, 22, nan, 24, nan, 26, nan, 28, nan, 30, nan,  
> 32, nan,
>     34, nan, 36, nan, 38, nan, 40, nan, 42, nan, 44, nan, 46, nan,  
> 48, nan,
>     50, nan, 52, nan, 54, nan, 56, nan, 58, nan, 60, nan, 62, nan,  
> 64, nan,
>     66, nan, 68, nan, 70, nan, 72, nan, 74, nan, 76, nan, 78, nan,  
> 80, nan,
>     82, nan, 84, nan, 86, nan, 88, nan, 90, nan, 92, nan, 94, nan,  
> 96, nan,
>     98, nan,
>   nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan, nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan,
>     nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,  
> nan, nan,
>   200, nan, 202, nan, 204, nan, 206, nan, 208, nan, 210, nan, 212,  
> nan, 214,
>
> ,,,
>
> The testing environment is:
> OS: Linux x64 (RHEL4)
> Compiler: gcc 4.2.2
> MPI: mpich2 1.0.7
>
> Also, in my application, open an existing netcdf and add a new  
> variable (2-d) messed up the existing data somehow.  The same code  
> works when parallel-netcdf release 1.0.3 or early is used.
>
> --
> Best regards,
>
> Lie-Quan Lee
> SLAC National Accelerator Laboratory
>
> <test.cpp>