parallel-netcdf buffered I/O interface

Rob Latham robl at mcs.anl.gov
Wed Aug 15 11:01:02 CDT 2012 

On Wed, Aug 15, 2012 at 09:32:56AM -0600, Jim Edwards wrote:
> Hi Wei-keng,
> 
> Yes that looks like what I would need.   I have to think about the
> independent aspect - currently i am using collective operations in almost
> all cases.  The performance trade offs of independent vs collective
> operations are not really clear to me.  Why no collective bputs?

Aw, Wei-keng already replied.   Well, here's my answer, which says the
same thing as Wei-keng but emphasises the "put it on a list" and
"execute this list" aspects of these APIs.

The 'buffered put' routines are a variant of the non-blocking
routines.  These routines defer all I/O to the wait or wait_all
routine, where all pending I/O requests for a given process are
stitched together into one bigger request.  

So, issuing an I/O operation under these interfaces is essentially
"put it on a list".  Then, "execute this list" can be done either
independently (ncmpi_wait) or collectively (ncmpi_wait_all).

A very early instance of these routines did the "put it on a list"
collectively.  This approach did not work out so well for applications
(like for example Chombo) where processes make a bunch of small
uncoordinated I/O requests, but still have a clear part of their code
where "collectively wait for everyone to finish" made sense.   

I hope you have enjoyed today's episode of Parallel-NetCDF history
theater.  

==rob

> On Wed, Aug 15, 2012 at 9:18 AM, Wei-keng Liao
> <wkliao at ece.northwestern.edu>wrote:
> 
> > > The  NC_EINSUFFBUF error code is returned from the bput call?
> >
> > I found a bug that 1.3.0 fails to return this error code. r1086 fixes this
> > bug.
> >
> >
> > >   If you get that error will you need to make that same bput call again
> > after flushing?  But the other tasks involved in the same bput call who
> > didn't have full buffers would do what?
> >
> > My idea is to skip the bput request when NC_EINSUFFBUF is returned.
> > Flushing at the wait call will only flush those successful bput calls, so
> > yes
> > you need to make the same failed bput call again after flushing.
> >
> > Please note that bput APIs are independent. There is no "other tasks in
> > the same bput call" issue.
> >
> >
> > > I could use a query function and to avoid the independent write calls
> > would do an mpi_allreduce on the max memory used before calling the
> > mpi_waitall.  If the max is approaching the buffer size I would flush all
> > io tasks. This is basically what I have implemented in pio with iput - I
> > have a user determined limit on the size of the buffer and grow the buffer
> > with each iput call, when the buffer meets (or exceeds) the limit on any
> > task I call waitall on all tasks.
> >
> > This is a nice idea.
> >
> >
> > Please let me know if the new query API below will be sufficient for you.
> >
> >   int ncmpi_inq_buffer_usage(int ncid, MPI_Offset *usage);
> >
> >   * "usage" will be returned with the current buffer usage in bytes.
> >   * Error codes may be invalid ncid or no attached buffer found.
> >
> >
> >
> > Wei-keng
> >
> >
> >
> > >
> > >
> > > On Tue, Aug 14, 2012 at 10:07 PM, Wei-keng Liao <
> > wkliao at ece.northwestern.edu> wrote:
> > > Hi, Jim,
> > >
> > > The usage of bput APIs is very similar to iput, except the followings.
> > > 1. users must tell pnetcdf the size of buffer to be used by pnetcdf
> > internally (attach and detach calls).
> > > 2. once a bput API returns, user's buffer can be reused or freed
> > (because the write
> > >   data has been copied to the internal buffer.)
> > >
> > > The internal buffer is per file (as the attach API requires an ncid
> > argument.) It can be used to aggregate
> > > requests to multiple variables defined in the file.
> > >
> > > I did not implement a query API to check the current usage of the
> > buffer. If this query is useful, we
> > > can implement it. Let me know. But please note this query will be an
> > independent call, so you
> > > will have to call independent wait (nfmpi_wait). Independent wait uses
> > MPI independent I/O, causing
> > > poor performance, not recommended. Otherwise, you need an MPI reduce to
> > ensure all processes know
> > > when to call the collective wait_all.
> > >
> > > You are right about flushing. The buffer will not be flushed
> > automatically and all file I/O happens in wait_all.
> > > If the attached buffer ran out of space, NC_EINSUFFBUF error code
> > (non-fatal) will return. It can be
> > > used to determine to call wait API, as described above. However, an
> > automatic flushing would require an MPI
> > > independent I/O, again meaning a poor performance. So, I recommend to
> > make sure the buffer size is
> > > sufficient large. In addition, if you let pnetcdf do type conversion
> > between two types of different size
> > > (e.g. short to int), you must calculate the size of attach buffer using
> > the larger type.
> > >
> > > If automatic flushing is highly desired, we can add it later.
> > >
> > > Once the call to wait/wait_all returns, the internal buffer is marked
> > empty.
> > >
> > > Let me know if the above answers your questions.
> > >
> > > Wei-keng
> > >
> > > On Aug 14, 2012, at 2:04 PM, Jim Edwards wrote:
> > >
> > > > No, the flush must happen in the nfmpi_wait_all.
> > > > But does that call mark the buffer as empty?  I'll wait and bug
> > > > Wei-keng.
> > > >
> > > > On Tue, Aug 14, 2012 at 12:56 PM, Rob Latham <robl at mcs.anl.gov> wrote:
> > > > On Tue, Aug 14, 2012 at 12:52:46PM -0600, Jim Edwards wrote:
> > > >> Hi Rob,
> > > >>
> > > >> I assume that the same buffer can be used for multiple variables (as
> > long
> > > >> as they are associated with the same file).    Is there a query
> > function so
> > > >> that you know when you've used the entire buffer and it's time to
> > flush?
> > > >
> > > > It does not appear to be so.  The only non-data-movement routines in
> > > > the API are these:
> > > >
> > > > int ncmpi_buffer_attach(int ncid, MPI_Offset bufsize);
> > > > int ncmpi_buffer_detach(int ncid);
> > > >
> > > > The end-user doesn't flush, I don't think.  I had the impression that
> > once the
> > > > buffer filled up, the library did the flush, then started filling up
> > the buffer
> > > > again.  This one I'll need Wei-keng to confirm.
> > > >
> > > > ==rob
> > > >
> > > >> Jim
> > > >>
> > > >> On Tue, Aug 14, 2012 at 11:41 AM, Rob Latham <robl at mcs.anl.gov>
> > wrote:
> > > >>
> > > >>> On Tue, Aug 14, 2012 at 10:50:15AM -0600, Jim Edwards wrote:
> > > >>>> No, I'm using iput and blocking get.   I'm doing my own buffereing
> > layer
> > > >>> in
> > > >>>> pio.   I might consider using the bput functions - can you point me
> > to
> > > >>> some
> > > >>>> documentation/examples?
> > > >>>
> > > >>> Sure.  It's too bad Wei-keng is on vacation this month, as he's the
> > > >>> one who designed and implemented this new feature for pnetcdf 1.3.0.
> > > >>> Wei-keng: i'm not expecting you to reply while on vacation.  I'm just
> > > >>> CCing you so you know I'm talking about your work :>
> > > >>>
> > > >>> I think this might be the entire contents of our documentation:
> > > >>>
> > > >>> "A new set of buffered put APIs (eg. ncmpi_bput_vara_float) is added.
> > > >>> They make a copy of the user's buffer internally, so the user's
> > buffer
> > > >>> can be reused when the call returns. Their usage are similar to the
> > > >>> iput APIs. "
> > > >>>
> > > >>> Hey, check that out: Wei-keng wrote up a fortran example:
> > > >>>
> > > >>>
> > > >>>
> > http://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/examples/tutorial/pnetcdf-write-bufferedf.F
> > > >>>
> > > >>> There's also the C version:
> > > >>>
> > > >>>
> > > >>>
> > http://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/examples/tutorial/pnetcdf-write-buffered.c
> > > >>>
> > > >>>
> > > >>> ==rob
> > > >>>
> > > >>>> On Tue, Aug 14, 2012 at 10:16 AM, Rob Latham <robl at mcs.anl.gov>
> > wrote:
> > > >>>>
> > > >>>>> Hi Jim
> > > >>>>>
> > > >>>>> You've been using the new 'bput/bget' routines, right?  Can you
> > tell
> > > >>>>> me a bit about what you are using them for, and what -- if any --
> > > >>>>> benefit they've provided?
> > > >>>>>
> > > >>>>> (Rationale: our program management likes to see papers and
> > > >>>>> presentations, but the most valued contribution is 'science
> > impact').
> > > >>>>>
> > > >>>>> Thanks
> > > >>>>> ==rob
> > > >>>>>
> > > >>>>> --
> > > >>>>> Rob Latham
> > > >>>>> Mathematics and Computer Science Division
> > > >>>>> Argonne National Lab, IL USA
> > > >>>>>
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>
> > > >>> --
> > > >>> Rob Latham
> > > >>> Mathematics and Computer Science Division
> > > >>> Argonne National Lab, IL USA
> > > >>>
> > > >>
> > > >>
> > > >>
> > > >
> > > > --
> > > > Rob Latham
> > > > Mathematics and Computer Science Division
> > > > Argonne National Lab, IL USA
> > > >
> > > >
> > > >
> > > > --
> > > > Jim Edwards
> > > >
> > > > CESM Software Engineering Group
> > > > National Center for Atmospheric Research
> > > > Boulder, CO
> > > > 303-497-1842
> > > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Jim Edwards
> > >
> > >
> > >
> >
> >
> 
> 

-- 
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

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