From simon.urbanek at r-project.org  Thu Feb 14 21:57:48 2013
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Thu, 14 Feb 2013 15:57:48 -0500
Subject: [Rd] stopping finalizers
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References: <CAJ55+dJogFHu3bXBFSjDGynsH0FKN4A15=5uWg_KS4XTaEOSCA@mail.gmail.com>
	<alpine.DEB.2.02.1302140544570.17940@luke-Latitude>
	<CAJ55+dJVjg9tN9RZB7Fk2twg-vO6zehXKFj2RU+HAhugVm9bsg@mail.gmail.com>
Message-ID: <2F2447A2-CBDB-41E0-8D18-5F90CB61C730@r-project.org>

I would argue that addressing this at a generic R level is the wrong place (almost, see below) -- because this is about *specific* finalizers. You don't mind running other people 's finalizers because they don't mess up your connection. Therefore, I'd argue that primarily the approach should be in your DB driver to synchronize the calls - which is what you did by queueing.

In a sense a more general approach won't be any different - you will need at least a list of *specific* objects that should be deferred - it's either in your driver or in R. I'd argue that the design is much easier in the driver because you know which finalizers to register, whereas R has no concept of finalizer "classes" to group them. You can also do this much more easily in the driver since you know whether they need to be deferred and if they do, you can easily process the deferred once when you get out of your critical section.

Because of this difference between specific finalizers and all GC any R-side solution that doesn't register such finalizers in a special way will be inherently wasteful - as you pointed out in the discussion below - and thus I'd say it's more dangerous than helpful, because R can then lock itself out of memory even if not necessary.

So IMHO the necessary practical way to solve this at R level (if someone wanted to spend the time) would be to create "bags" of finalizers and use those when defining critical regions, something like (pseudocode)

add_fin_bag("myDB", obj1)
// ...
add_fin_bag("myDB", obj2)

critical_fin_section_begin("myDB")
// ... here no finalizers for objects in the bag can be fired
critical_fin_section_end("myDB")

Technically, the simple solution would be to simply preserve the bag in the critical region. However, this would not guarantee that the finalizers get fired at the end of the section even if gc occurred. I suspect it would be harder to guarantee that (other than running gc explicitly or performing explicit de-allocation after the finalizer was detected to be scheduled but not fired).

Cheers,
Simon


On Feb 14, 2013, at 3:12 PM, Thomas Lumley wrote:

> Luke,
> 
> We're actually adopting the first of your generic approaches.
> 
> As a more concrete description:
> 
> There are R objects representing survey data sets, with the data stored in
> a database table.  The subset() method, when applied to these objects,
> creates a new table indicating which rows of the data table are in the
> subset -- we don't modify the original table, because that breaks the
> call-by-value semantics. When the subset object in R goes out of scope, we
> need to delete the extra database table.
> 
> I have been doing this with a finalizer on an environment that's part of
> the subset object in R.   This all worked fine with JDBC, but the native
> database interface requires that all communications with the database come
> in send/receive pairs. Since R is single-threaded, this would normally not
> be any issue. However, since garbage collection can happen at any time, it
> is possible that the send part of the finalizer query "drop table
> _sbs_whatever" comes between the send and receive of some other query, and
> the database connection then falls over.   So, I'm happy for the finalizer
> to run at any time except during a small critical section of R code.
> 
> In this particular case the finalizer only issues "drop table" queries, and
> it doesn't need to know if they succeed, so we can keep a lock in the
> database connection and just store any "drop table" queries that arrive
> during a database operation for later execution.   More generally, though,
> the fact that no R operation is atomic with respect to garbage collection
> seems to make it a bit difficult to use finalizers -- if you need a
> finalizer, it will often be in order to access and free some external
> resource, which is when the race conditions can matter.
> 
> What I was envisaging was something like
> 
> without_gc(expr)
> 
> to evaluate expr with the memory manager set to allocate memory (or attempt
> to do so) without garbage collection.  Even better would be if gc could
> run, but weak references were temporarily treated as strong so that garbage
> without finalizers would be collected but finalizers didn't get triggered.
> Using this facility would be inefficient, because it would allocate more
> memory than necessary and would also mess with the tuning of the garbage
> collector,  but when communicating with other programs it seems it would be
> very useful to have some way of running an R code block and knowing that no
> other R code block would run during it (user interrupts are another issue,
> but they can be caught, and in any case I'm happy to fail when the user
> presses CTRL-C).
> 
>     -thomas
> 
> 
> 
> 
> On Fri, Feb 15, 2013 at 12:53 AM, <luke-tierney at uiowa.edu> wrote:
> 
>> It might help if you could be more specific about what the issue is --
>> if they are out of scope why does it matter whether the finalizers
>> run?
>> 
>> Generically two approaches I can think of:
>> 
>>    you keep track of whenit is safe to fully run your finalizers and have
>>    your finalizers put the objects on a linked list if it isn't safe to
>>    run the finalizer now and clear the list each time you make a new one
>> 
>>    keep track of your objects with a weak list andturn them into strong
>>    references before your calls, then drop the list after.
>> 
>> I'm pretty sure we don't have a mechanism for temporarily suspending
>> running the finalizers but it is probably fairly easy to add if that
>> is the only option.
>> 
>> I might be able to think of other options with more details on the
>> issue.
>> 
>> Best,
>> 
>> luke
>> 
>> 
>> On Tue, 12 Feb 2013, Thomas Lumley wrote:
>> 
>> Is there some way to prevent finalizers running during a section of code?
>>> 
>>> I have a package that includes R objects linked to database tables.  To
>>> maintain the call-by-value semantics, tables are copied rather than
>>> modified, and the extra tables are removed by finalizers during garbage
>>> collection.
>>> 
>>> However, if the garbage collection occurs in the middle of processing
>>> another SQL query (which is relatively likely, since that's where the
>>> memory allocations are) there are problems with the database interface.
>>> 
>>> Since the guarantees for the finalizer are "at most once, not before the
>>> object is out of scope" it seems harmless to be able to prevent finalizers
>>> from running during a particular code block, but I can't see any way to do
>>> it.
>>> 
>>> Suggestions?
>>> 
>>>   -thomas
>>> 
>>> 
>>> 
>>> 
>> --
>> Luke Tierney
>> Chair, Statistics and Actuarial Science
>> Ralph E. Wareham Professor of Mathematical Sciences
>> University of Iowa                  Phone:             319-335-3386
>> Department of Statistics and        Fax:               319-335-3017
>>   Actuarial Science
>> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>> 
> 
> 
> 
> -- 
> Thomas Lumley
> Professor of Biostatistics
> University of Auckland
> 
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[Rd] stopping finalizers
Simon Urbanek