[FLASH-USERS] Question re Parallel-NetCDF PM / UG

[Klaus Weide]

On Tue, 28 Feb 2017, Schmid  Pirmin wrote:

> Dear Flash users,
> 
> I am a fresh user of FLASH 4.4, which works great so far. I would like 
> to use it with parallel NetCDF, too. Despite having compiled and 
> installed all dependencies, the modules PM and UG seem to be missing 
> that are mentioned in the manual. See example there:
> 
> 
> ./setup Sod -2d -auto -unit=IO/IOMain/pnetcdf/PM
> ./setup Sod -2d -auto -unit=Grid/GridMain/UG -unit=IO/IOMain/pnetcdf/UG

The directories 

 source/IO/IOMain/pnetcdf/PM
 source/IO/IOMain/pnetcdf/UG

have been removed from the FLASH source between FLASH 4 and FLASH 4.2. 
But this was just in the course of a reorganization and cleanup of the 
code; the corresponding features have not been removed but are just 
organized differently now.

You should just use either +pnetcdf or +pnetTypeIO in the setup command, 
possibly in connection with other flags or shortcuts to select a Grid 
implementation, and all the necessary code should get included.

I realize that the IO section in the User's Guide has not been properly 
updated, and still refers to the old directory names. Most other 
information there, including the shortcuts, should still be applicable.
Please let me know if you find outdated information in other parts of the 
Users Guide.

> 
> Compilation of other examples without pnetcdf or compilation of the example with +pnettypeio works. And the generated output file has a CDF in the magic number part.
> However, ncdump cannot read the files, which is suspicious. VisIt can read the files but I am not so sure whether the data are really OK.

I don't know whether ncdump is SUPPOSED to be able to read those files.
We don't use PnectCDF checkpoint or plot files at the FLASH Center, even 
though we regularly runs test (so we know in particular that restarting 
from PnetCDF checkpoint files works).

I was assuming that VisIt is not able to read PnetCDF files from FLASH 
properly, but I may be wrong. All use of VisIt for visualization of
FLASH-generated data that I am aware of is employing HDF5.

Klaus