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

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

Paul,

Thanks for the starting points. I have a few more questions, especially
about the parallelization that's necessary for these huge systems. I don't
really care about speed here, I just want to output a 2d slice and I don't
plan on doing it very often.

1.) for z_slice_g(), what is ezi? Say I want to output all the data at z=0
(i.e. the bottom plate). What would I use for ezi? Or do I have to create
some routine to find ezi for this case?

2.) I am a little confused about the parallel version of outfld2d(). It
looks like outfld2d_p gets called by buff_2d_out(). Would you suggest doing
this?

Thanks,

Janet


> 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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-- 
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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