From @|mon@urb@nek @end|ng |rom R-project@org  Wed Apr 14 09:35:27 2021
From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek)
Date: Wed, 14 Apr 2021 07:35:27 -0000
Subject: [Rd] custom allocators, Valgrind and uninitialized memory
In-Reply-To: <E1lQyKz-0002vU-AF@rmmprod07.runbox>
References: <E1lQyKz-0002vU-AF@rmmprod07.runbox>
Message-ID: <EE9F6C8C-E540-4310-BD97-B65FE14F58A7@R-project.org>


Andres,

correct me if I'm wrong, but the issue here is not initialisation but rather valgrind flagging. You simply have to call VALGRIND_MAKE_MEM_DEFINED() in your code after allocVector3() to declare that you have initialised the memory - or am I missing something?

Cheers,
Simon



> On 30/03/2021, at 9:18 AM, Andreas Kersting <r-devel at akersting.de> wrote:
> 
> Hi Tomas,
> 
> Thanks for sharing your view on this! I understand your point, but still I think that the current situation is somewhat unfortunate:
> 
> I would argue that mmap() is a natural candidate to be used together with allocVector3(); it is even mentioned explicitly here: https://github.com/wch/r-source/blob/trunk/src/main/memory.c#L2575-L2576
> 
> However, when using a non-anonymous mapping, i.e. we want mmap() to initialize the memory e.g. from a file or a POSIX shared memory object, this means that we need to use MAP_FIXED in case we are obliged to initialize the memory AFTER allocVector3() returned it; at least I cannot think of a different way to achieve this.
> 
> The use of MAP_FIXED
> - is discouraged (e.g. https://developer.apple.com/library/archive/documentation/System/Conceptual/ManPages_iPhoneOS/man2/mmap.2.html)
> - requires two calls to mmap(): (1) to obtain the (anonymous) memory to be handed out by the custom allocater and (2) to actually map the file "over" the just allocated vector (using MAP_FIXED), which will overwrite the vector header; hence, we need to first back it up to later restore it
> 
> I have implemented my function using MAP_FIXED here: https://github.com/gfkse/bettermc/commit/f34c4f4c45c9ab11abe9b9e9b8b48064f128d731#diff-7098a5dde34efab163bbef27fe32f95c29e76236649479985d09c70100e4c737R278-R323
> 
> This solution, to me, is much more complicated and hacky than my previous one, which assumed it is OK to hand out already initialized memory directly from allocVector3().
> 
> Regards,
> Andreas
> 
> 
> 2021-03-29 10:41 GMT+02:00 "Tomas Kalibera" <tomas.kalibera at gmail.com>:
>> Hi Andreas,
>> On 3/26/21 8:48 PM, Andreas Kersting wrote:
>>> Hi Dirk,  > > Sure, let me try to explain: > > CRAN ran the tests of my package using R which was configured > --with-valgrind-instrumentation > 0. Valgrind reported many errors > related to the use of supposedly uninitialized memory and the CRAN > team asked me to tackle these. > > These errors are false positives, because I pass a custom allocator > to allocVector3() which hands out memory which is already > initialized. However, this memory is explicitly marked for Valgrind > as uninitialized by allocVector3(), and I do not initialize it > subsequently, so Valgrind complains. > > Now I am asking if it is correct that allocVector3() marks memory as > uninitialized/undefined, even if it comes from a custom allocator. > This is because allocVector3() cannot know if the memory might > already by initialized.
>> I think the semantics of allocVector/allocVector3 should be the same regardless of whether custom allocators are used. The semantics of allocVector is to provide uninitialized memory (non-pointer types, Writing R Extensions 5.9.2). Therefore, it is the caller who needs to take care of initialization. This is also the semantics of "malloc" and Rallocators.h says "custom_alloc_t mem_alloc; /* malloc equivalent */".
>> 
>> So I think that your code using your custom allocator needs to initialize allocated memory to be correct. If your allocator initializes the memory, that is fine, but unnecessary.
>> 
>> So technically speaking, the valgrind reports are not false alarms. I think your call sites should initialize.
>> 
>> Best
>> Tomas
>> 
>> 
>> 
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[Rd] custom allocators, Valgrind and uninitialized memory
Simon Urbanek