parallel-netcdf buffered I/O interface

Sun Aug 19 08:06:03 CDT 2012

Hi Wei-keng,

Here's the problem.   When I updated from subversion and didn't see any
autoconf dependent changes I ran config.status rather than
autoreconf/configure.   The config.status script doesn't have the sed
commands.

On Sat, Aug 18, 2012 at 6:18 PM, Wei-keng Liao
<wkliao at ece.northwestern.edu>wrote:

>
> It is unlikely the autoconf.
>
> In pnetcdf's configure.in, we first generate pnetcdf_inc
> by removing some define macros from pnetcdf_inc.in using
> language C style comment, i.e. /* and */
>
> Then in configure.in line 592, we use command "sed" to
> replace "/*" with F90 style comment "!" and remove "*/".
>
> 592   sed -e "s%/\*%!%g" -e "s%\*/%%g" <src/libf/pnetcdf_inc>pnetcdf_inc
> && mv pnetcdf_inc src/libf/pnetcdf_inc
>
> Could you check if your configure.in file is the same as the SVN's?
>
>
> Wei-keng
>
> On Aug 18, 2012, at 8:37 AM, Jim Edwards wrote:
>
> > They aren't in pnetcdf_inc.in - it seems that configure is generating
> the comments.    I have autoconf 2.67 - could that be the problem?
> >
> > On Fri, Aug 17, 2012 at 8:52 PM, Wei-keng Liao <
> wkliao at ece.northwestern.edu> wrote:
> >
> > Strange. I did not see any c-style comments in the source file
> pnetcdf_inc.in.
> > pnetcdf_inc is generated from pnetcdf_inc.in at the configure time.
> >
> > Could you try a clean build starting from running command "autoreconf"?
> > If the problem persist, please let us know.
> >
> > Wei-keng
> >
> > On Aug 17, 2012, at 12:01 PM, Jim Edwards wrote:
> >
> > > Hi Wei-keng,
> > >
> > > In order to build r1088 using xlf I had to edit the file
> src/libf/pnetcdf_inc and add a ! in front of each of
> > > the c-style comments...
> > >
> > > Jim
> > >
> > > On Thu, Aug 16, 2012 at 5:20 AM, Wei-keng Liao <
> wkliao at ece.northwestern.edu> wrote:
> > > ncmpi_inq_buffer_usage and its fortran API are now added in r1087
> > >
> > > Wei-keng
> > >
> > > On Aug 15, 2012, at 11:27 AM, Rob Latham wrote:
> > >
> > > > On Wed, Aug 15, 2012 at 10:10:02AM -0600, Jim Edwards wrote:
> > > >> Okay, so when do you need to call nfmpi_begin_indep_mode/
> > > >> nfmpi_end_indep_mode?    It doesn't seem to
> > > >> be entirely consistent anymore - is it?
> > > >
> > > > nfmpi_begin_indep_mode and nfmpi_end_indep_mode should continue to
> > > > wrap the blocking and independent nfmpi_put_ and nfmpi_get routines
> > > > (those that do not end in _all).
> > > >
> > > > begin/end should also bracket the independent nfmpi_wait, I think.
> > > >
> > > > If you are interested, I think the reason for all this flipping
> around
> > > > is essentially so we can keep consistent among processors the number
> > > > of records in a record variable.
> > > >
> > > > ==rob
> > > >
> > > >>
> > > >> On Wed, Aug 15, 2012 at 10:01 AM, Rob Latham <robl at mcs.anl.gov>
> wrote:
> > > >>
> > > >>> 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
> > > >>>
> > > >>
> > > >>
> > > >>
> > > >
> > > > --
> > > > Rob Latham
> > > > Mathematics and Computer Science Division
> > > > Argonne National Lab, IL USA
> > >
> > >
> > >
> > >
> > > --
> > > Jim Edwards
> > >
> > >
> > >
> >
> >
> >
> >
> > --
> > Jim Edwards
> >
> >
> >
>
>

-- 

Jim Edwards
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