parallel-netcdf buffered I/O interface

Sat Aug 18 19:18:34 CDT 2012

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
> 
> 
> 