You may be over-complicating this. Taking mcmc_new in src/lm_lcmc.c
from https://github.com/merliseclyde/BAS, to minimize code changes I
would arrange the memory management along these lines:
SEXP mcmc_new(...)
{
/* ... */
/* create and protect ANS */
SEXP ANS = PROTECT(allocVector(VECSXP, 16));
/* create the work vectors; placing them in ANS protects them */
SEXP modelspace = allocVector(VECSXP, nModels);
SET_VECTOR_ELT(ANS, 1, modelspace);
SEXP logmarg = allocVector(REALSXP, nModels);
SET_VECTOR_ELT(ANS, 2, logmarg);
SEXP modelprobs = allocVector(REALSXP, nModels);
SET_VECTOR_ELT(ANS, 3, modelprobs);
/* etc */
/* do your computations */
if (nUnique < nModels) {
/* new values are protected via ANS;
old ones are immediately available for GC */
SET_VECTOR_ELT(ANS, 1, xlengthgets(modelspace, nUnique));
SET_VECTOR_ELT(ANS, 2, xlengthgets(logmarg, nUnique));
SET_VECTOR_ELT(ANS, 3, xlengthgets(modelprobs, nUnique));
/* etc */
}
/* ... */
UNPROTECT(1); /* ANS */
return ANS;
}
Best,
luke
On Wed, 15 Jan 2025, Merlise Clyde, Ph.D. wrote:
Thanks Luke ! I had seen the usage and discussion of growable vectors, as
well as using SET_TRUELENGTH with SETLENGTH and didn't necessarily want to get
even more out of API compliance :-). but if that looks like it will allowed
(subject to perhaps changes) that seems like the better way forward to handle
the different SEXPs. And switching to smaller vectors and enlarging would be
much more efficient in terms of memory. I'll need to play around with how
much to expand by as the enlargement would need to be in the loop with a final
resizing before returning.
So if I understand the suggestion the use of xlengthgets basically handles the
body of the code in EnlargeVector function for allocation and copying (but now
smaller vectors) with then the extra step to SETLENGTH and SET_TRUELENGTH
If done within a loop over MCMC iterations, then I would need to use
SET_GROWABLE_BIT before the loop or when I encounter the need to enlarge. (so
basically a local implementation of EnlargeVector)
For my non-VECSXP objects (REALSXP, INTSXP) it might be more efficient to use
Realloc on a working array within loops and only allocate and assign after
determining the final length (nUnique), and freeing the memory myself... That
way I avoid SETLENGTH altogether for those types.
best,
Merlise
Merlise Clyde (she/her/hers)
Professor of Statistical Science and Director of Graduate Studies
Duke University
________________________________________
From: luke-tier...@uiowa.edu <luke-tier...@uiowa.edu>
Sent: Wednesday, January 15, 2025 12:34 PM
To: Iris Simmons <ikwsi...@gmail.com>
Cc: Merlise Clyde, Ph.D. <cl...@duke.edu>; List r-package-devel
<r-package-devel@r-project.org>
Subject: Re: [External] Re: [R-pkg-devel] Replacement for SETLENGTH
On Wed, 15 Jan 2025, Iris Simmons wrote:
I don't think memcpy works well for VECSXP. The elements being overwritten
need to have their reference counts decreased and the new elements need to
have theirs increased.
You do not want to use memcpy or inanyother way try to write to the
locations in a VECSXP. It is not jus the reference counts but also the
integrity of the GC write barrier that you would be damaging.
Also, I don't entirely know how accurate everything I'm about to say is,
but I think you need to be using SET_TRUELENGTH and SET_GROWABLE_BIT along
with SETLENGTH. There's an example here:
https://urldefense.com/v3/__https://github.com/wch/r-source/blob/744b5d34e1b8eb839e5d49d91ab21c1fe6800856/src/main/subassign.c*L257__;Iw!!OToaGQ!uACtQIEun1eC8hwn-FzFogXQoPl1wETg9EUSV1NzAif9u15KlRTctzEq1RSA5rcbeVGv0n3geb8UexFngaonYos$
The example uses SET_STDVEC_LENGTH which shouldn't be used, just replace it
with SETLENGTH.
So in your code, I'd replace:
SETLENGTH(modelspace, nUnique);
with
SET_GROWABLE_BIT(modelspace);
SET_TRUELENGTH(modelspace, nModels);
SETLENGTH(modelspace, nUnique);
These are not part of the API.
Support for growable vectors maybe added to the API in the future, but
probably with a more robust interface.
In any case, this mechanism is intended for growing, not shrinking,
vectors.
Initially over-allocating and returning a smaller result is a
reasonable strategy, but the right way to do it is to allocate a new
shorter result. xlengthgets is a convenient way to do this. Tholonger
vector will be subject to garbage collecion once there are no
remaining references to it.
Attempting to keep alive a longer allocation but pretending it is
shorter is mis-guided: it would keep alive a larger object than is
needed and so waste memory.
Best,
luke
On Wed, Jan 15, 2025, 10:30 Merlise Clyde, Ph.D. <cl...@duke.edu> wrote:
Thanks for the added explanation Iris and Tomas!
So looking at the code for xlengthgets, it does appear that I may take a
memory hit for multiple large objects due to the second allocation before
the old objects are possibly garbage collected. There are about 12 such
instances per function that are returned (I do use a counter for keeping
track of the number of PROTECTED and to UNPROTECT for bookkeeping :-).
For memory limited machines, the alloc/copy was a problem for memory usage
- and if I recall was one of the reasons in 2008 I switched to SETLENGTH,
which doesn't seem to do an allocation ??? If there is going to be an
absolute ban on SETLENGTH in packages I'll probably need to address memory
management differently for those cases.
I did see a note before the function def'n of xlengthgets:
/* (if it is vectorizable). We could probably be fairly */
/* clever with memory here if we wanted to. */
It would seem that memcpy would be more efficient for at least some of the
types (REALSPX, INTSPX) unless I am missing something - but any way to be
more clever with VECSPX ?
best,
Merlise
Merlise Clyde (she/her/hers)
Professor of Statistical Science and Director of Graduate Studies
Duke University
________________________________________
From: Iris Simmons <ikwsi...@gmail.com>
Sent: Wednesday, January 15, 2025 1:00 AM
To: Merlise Clyde, Ph.D. <cl...@duke.edu>
Cc: r-package-devel@r-project.org <r-package-devel@r-project.org>
Subject: Re: [R-pkg-devel] Replacement for SETLENGTH
Hi Merlise!
Referring to here:
https://urldefense.com/v3/__https://github.com/wch/r-source/blob/bb5a829466f77a3e1d03541747d149d65e900f2b/src/main/builtin.c*L834__;Iw!!OToaGQ!uACtQIEun1eC8hwn-FzFogXQoPl1wETg9EUSV1NzAif9u15KlRTctzEq1RSA5rcbeVGv0n3geb8UexFnr_0lCLM$
It seems as though the object is only re-used if the new length is
equal to the old length.
If you use Rf_lengthgets, you will need to protect the return value.
The code you wrote that uses protect indexes looks correct, and the
reprotect is good because you no longer need the old object.
2 is the correct amount to unprotect. PROTECT and PROTECT_WITH_INDEX
(as far as I know) are the only functions that increase the size of
the protect stack, and so the only calls that need to be unprotected.
Typically, people define `int nprotect = 0;` at the start of their
functions, add `nprotect++;` after each PROTECT and PROTECT_WITH_INDEX
call, and add `UNPROTECT(nprotect);` immediately before each return or
function end. That makes it easier to keep track.
I typically use R_PreserveObject and R_ReleaseObject to protect
objects without a need to bind them somewhere in my package's
namespace. This would be that .onLoad() uses R_PreserveObject to
protect some objects, and .onUnload uses R_ReleaseObject to release
the protected objects. I probably would not use that for what you're
describing.
Regards,
Iris
On Tue, Jan 14, 2025 at 11:26 PM Merlise Clyde, Ph.D. <cl...@duke.edu>
wrote:
I am trying to determine the best way to eliminate the use of SETLENGTH
to truncate over allocated vectors in my package BAS to eliminate the NOTES
about non-API calls in anticipation of R 4.5.0.
From WRE: "At times it can be useful to allocate a larger initial
result vector and resize it to a shorter length if that is sufficient. The
functions Rf_lengthgets and Rf_xlengthgets accomplish this; they are
analogous to using length(x) <- n in R. Typically these functions return a
freshly allocated object, but in some cases they may re-use the supplied
object."
it looks like using
x = Rf_lengthgets(x, newsize);
SET_VECTOR_ELT(result, 0, x);
before returning works to resize without a performance hit that incurs
with a copy. (will this always re-use the supplied object if newsize < old
size?)
There is no mention in section 5.9.2 about the need for re-protection of
the object, but it seems to be mentioned in some packages as well as a
really old thread about SET_LENGTH that looks like a non-API MACRO to
lengthgets,
indeed if I call gc() and then rerun my test I have had some
non-reproducible aborts in R Studio on my M3 Mac (caught once in R -d lldb)
Do I need to do something more like
PROTECT_INDEX ipx0;.
PROTECT_WITH_INDEX(x0 = allocVector(REALSXP, old_size), &ipx0);
PROTECT_INDEX ipx1;.
PROTECT_WITH_INDEX(x1 = allocVector(REALSXP, old_size), &ipx1);
# fill in values in x0 and x1up to new_size (random) < old_size
...
REPROTECT(x0 = Rf_lengthgets(x0, new_size), ipx0);
REPROTECT(x1 = Rf_lengthgets(x1, new_size), ipx1);
SET_VECTOR_ELT(result, 0, x0);
SET_VECTOR_ELT(result, 1, x1);
...
UNPROTECT(2); # or is this 4?
return(result);
There is also a mention in WRE of R_PreserveObject and R_ReleaseObject -
looking for advice if this is needed, or which approach is better/more
stable to replace SETLENGTH? (I have many many instances that need to be
updated, so trying to get some clarity here before updating and running
code through valgrind or other sanitizers to catch any memory issues before
submitting an update to CRAN.
best,
Merlise
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Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
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--
Luke Tierney
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-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu/
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