[Nek5000-users] Writing 2d output files for 3d data

[nek5000-users at lists.mcs.anl.gov]

Hi Janet,

I added z_slice_g, a generalized z_slice() extraction routine
to the repo in navier5.f.

I've not tested it.

Please let me know if this works for you.   Note that all it
does is to extract a scalar.  You would call this once for each
variable of interest and then dump them as a field using some
type of output routine --- outfld2d() and outfld2d_p() look
like decent starting points but are not quite what you need.

If I were you, I would start with the binary .fld (not .f0000)
format from a single processor and see how long that takes.

I think the _p() variant does the following ---

For several processors, it holds the data from different output
times (e.g., proc 0 holds time 1, proc 64 holds time 2, etc.).
Then, at an agreed-upon timestep, each of these opens a file,
in parallel, and writes the entire z-slice that it holds as a copy.

Since each processor gets an entire z-slice from the above routine,
this is not a big deal, and you still get parallel I/O --- it's
time parallel instead of space parallel.   Here's a cartoon:


time/space:        p0         p4         p12        p16

step 1000      get slice  get slice  get slice  get slice
step 1000     save slice

step 2000      get slice  get slice  get slice  get slice
step 2000                save slice

step 3000      get slice  get slice  get slice  get slice
step 3000                           save slice

step 4000      get slice  get slice  get slice  get slice
step 4000                                      save slice

step 4000      write f1   write f2   write f3   write f4   <-- Parallel IO

The attraction of this approach is that the write() looks
like serial I/O because the requisite data is fully resident
on the processor that is doing the write, so it is simpler
to code.

Paul

On Tue, 25 Jun 2013, nek5000-users at lists.mcs.anl.gov wrote:

>
> Hi Janet,
>
> I think that z_slice() and outfld2d would be reasonable
> starting points.
>
> As I look at the code, z_slice takes element 1, slice 1
> in the z direction.   You would want to generalize this.
>
> Also, it looks outfld2d() is set up only for ascii output
> at the moment.   I would suggest conversion to binary.
>
> I can take a pass at making these changes but will not have
> time to verify functionality for a few days.  I could however
> work with you on that.
>
> Paul
>
>
> On Tue, 25 Jun 2013, nek5000-users at lists.mcs.anl.gov wrote:
>
>> We are generating huge 3d data files (>8GB with multiple I/O) which are so
>> large, our version of visit does not have enough memory to load them.
>> Oftentimes we only want to visualize a 2d slice anyway. Is there a routine
>> in nek5000 that does this? Or one that can be easily modified? To be more
>> specific, we want to output, for example, the coordinates and the velocity
>> field for some fixed z-value, into a blah.f00001 file that can then be read
>> by visit.
>> 
>> Thanks,
>> 
>> Janet
>> 
>> -- 
>> Janet Scheel
>> Assistant Professor of Physics
>> Occidental College
>> 1600 Campus Road, M21
>> Los Angeles, CA 90041
>> (323) 259-2777
>> jscheel at oxy.edu
>> 
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