[SAGA-RG] Python bindings: Buffer class issue

[Manuel Franceschini]

On Mon, Nov 9, 2009 at 11:10 PM, Andre Merzky <andre at merzky.net> wrote:
> Quoting [Manuel Franceschini] (Nov 09 2009):
>>
>> Hi all,
>>
>> Quick summary from GFD.90: the SAGA I/O Buffer encapsulates a sequence
>> of bytes to be used for I/O operations, e.g. read()/write() on files
>> and streams, and call() on rpc instances. The recent removal of the
>> buffer class from the Python bindings of the C++ SAGA implementation
>> led us to think again about this issue. The GFD is C/C++ oriented
>
> Well, it should not be C/C++ oriented, but the bias of the authors
> probably shows :-)  The intent was to support binary I/O on any
> language, as that was mentioned in many use cases.
>
>
>> and therefore the Python implementation is all but clear in this regard.
>>
>> Given that that memory management is automatic in Python, the notion
>> of application-managed and implementation-managed Buffer disappears.
>
> From what I learned during the discussion in Banff, this is not
> really true: one *can* allocate an array in user space and pass it
> to an API by-reference, which actually makes it a application
> managed memory segment.  The point in python seems to be that nobody
> is doing that...

Well, in Python there is *only* by-reference parameter passing,
references to objects that is. Version 2.6 introduced an io module
that allows to do what you describe. One problem with this is that our
JySAGA bindings can't support this new feature as Jython just reached
version 2.5.1 and it looks like there is quite a long way to go to
2.6.

I did some memory profiling with large chunks of data copied from one
file to another and the automatic memory management in Python seemed
to be very efficient. In my tests the garbage collection was
instantaneously. In other words, as soon as there was no more
references to a data chunk, memory was deallocated. So when shuffling
1MB chunks 10000 times from one file to another, the memory
consumption of the test program never exceeded 2,5 MB. If somebody can
come up with a test program that shows the advantage of using the new
io module in relevant use cases, we could think about using it in the
C++ bindings. Otherwise, why optimize when there's not real problem?

>> There is no need for a Python SAGA user to tell the bindings who
>> manages the Buffer, since it is managed by the underlying Python VM.
>>
>> Another more critical issue is the data type used to hold binary data
>> in Python. In Python 2.x the immutable 'str' type is used whereas
>> Python 3.x has a newly introduced immutable 'bytes' type. Let's forget
>> about 3.x for a moment, since 2.x will be around for at least a couple
>> of more years. In order to manipulate large binary datasets, the mmap
>> class [0] could be used, which basically transforms a immutable 'str'
>> into a mutable mmap object. In other words it provides the ability to
>> efficiently modify binary data.
>>
>> In the VU Python bindings the buffer class is still present, while, as
>> previously said, in the C++ Python bindings it was removed recently. I
>> do not see any issues with the removal of the Buffer class in the
>> Python bindings. However, I'm not sure whether I am forgetting some
>> corner cases (e.g. async) that would require a dedicated Buffer class.
>> When removing the Buffer class, the user would simply deal with 'str'
>> type data to pass data back and forth to a SAGA file, stream or rpc.
>
> If the bindings decide to go for strings, then that should pose no
> problem for the async calls, as far as I can tell: semantics of sync
> and async calls is identical (apart from synchronization obviously).
>
>
>> Now, I identified the following crucial questions:
>> 1) Can the Buffer class be safely removed from the Python bindings?
>
> According to the original SAGA use cases: no
> According to current SAGA users: yes
>
> So, tough call ;-)

What do other people think?

>> 2) Is handling of large binary datasets a primary concern? If yes, how
>> to handle them?
>
> See above.  How to handle: dunno - that is the question, innit?

The mmap module can be used for modifying binary data in place.

>> 3) Is compliance to Python 3.x a concern right now? In other words, is
>> the eventual migration to 3.x to take into consideration?
>
> If 3.x makes something easier, it might be good to be aware of it at
> least.  I think all agree that 2.x will be around for a long time,
> and that limiting the bindings to 3.x is not an option.  OTOH, it
> should be possible to have slightly differing bindings for 2.x and
> 3.x, depending on the changes in the language itself.

Yeah, I don't think we should think too much about that now. But for
the future it will bring several benefits to the Python bindings.

Cheers,
/Manuel