problems writing vars with pnetcdf

[Katie Antypas]

Hi All,

I'm not sure if this list gets much traffic but here goes.  I'm having a 
problem writing out data in parallel for a particular case when there are 
zero elements to write on a given processor.

Let me explain a little better.  For a very simple case, a 1 dimensional 
array that we want to write in parallel - we define a dimension say, 
'dim_num_particles' and define a variable, say 'particles' with a unique 
id.

Each processor then writes out its portion of the particles into the 
particles variable with the correct 
starting position and count.  As long as each processor has at least one 
particle to write we have absolutely no problems, but quite often in our 
code there are 
processors that have zero particles for a given checkpoint file and thus 
have nothing to write to 
file.  This is where we hang.


I've tried a couple different hacks to get around this --

* First was to try to write a zero-length array, with the count= zero 
  and the offset or starting point = 'dim_num_particles'  but that 
  returned an error message from the put_vars calls.  
  All other offsets I choose returned errors as well, which is 
  understandable.

* The second thing I tried was to not write the data at all if there 
  were zero particles on a proc.  But that hung.  After talking to some 
  people here they though this also made sense because all procs now would 
  not be doing the same task, a problem we've also seen hang hdf5.

-- I can do a really ugly hack by increasing the dim_num_particles to have 
extra room.  That way if a proc had zero particles it could write out a 
dummy value.  The problem is that messes up our offsets when we need 
to read in the checkpoint file.


Has anyone else seen this problem or know a fix to it?

Thanks,

Katie


____________________________
Katie Antypas
ASC Flash Center
University of Chicago
kantypas at flash.uchicago.edu