Hi All,
I've been looking into speeding up the loading of packages that use a lot
of S4. After profiling I noticed the "exists" function accounts for a
surprising fraction of the time. I have some thoughts about speeding up
exists (below). More to the point of this post, Martin M?chler noted that
'exists' and 'get' are often used in conjunction. Both
functions are
different usages of the do_get C function, so it's a pity to run that twice.
"get" gives an error when a symbol is not found, so you can't just
do a
'get'. With R's C library, one might do
SEXP x = findVarInFrame3(symbol,env);
if (x != R_UnboundValue) {
// do stuff with x
}
It would be very convenient to have something like this at the R level. We
don't want to do any tryCatch stuff or to add args to get (That would kill
any speed advantage. The overhead for handling redundant args accounts for
30% of the time used by "exists"). Michael Lawrence and I worked out
that
we need a function that returns either the desired object, or something
that represents R_UnboundValue. We also need a very cheap way to check if
something equals this new R_UnboundValue. This might look like
if (defined(x <- fetch(symbol, env))) {
do_stuff_with_x(x)
}
A few more thoughts about "exists":
Moving the bit of R in the exists function to C saves 10% of the time.
Dropping the redundant pos and frame args entirely saves 30% of the time
used by this function. I suggest that the arguments of both get and
exists should
be simplified to (x, envir, mode, inherits). The existing C code handles
numeric, character, and environment input for where. The arg frame is
rarely used (0/128 exists calls in the methods package). Users that need to
can call sys.frame themselves. get already lacks a frame argument and the
manpage for exists notes that envir is only there for backwards
compatibility. Let's deprecate the extra args in exists and get and perhaps
move the extra argument handling to C in the interim. Similarly, the
"assign" function does nothing with the "immediate"
argument.
I'd be interested to hear if there is any support for a
"fetch"-like
function (and/or deprecating some unused arguments).
All the best,
Pete
Pete
____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com
[[alternative HTML version deleted]]
I've looked at related speed issues in the past, and have a couple
related points to add. (I've put the info below at
http://rpubs.com/wch/46428.)
There?s a significant amount of overhead just from calling the R
function get(). This is true even when you skip the pos argument and
provide envir. For example, if you call get(), it takes much more time
than .Internal(get()), which is what get() does.
If you already know that the object exists in an environment, it's
faster to use e$x, and slightly faster still to use e[["x"]]:
e <- new.env()
e$a <- 1
# Accessing objects in environments
microbenchmark(
get("a", e, inherits = FALSE),
get("a", envir = e, inherits = FALSE),
.Internal(get("a", e, "any", FALSE)),
e$a,
e[["a"]],
.Primitive("[[")(e, "a"),
unit = "us"
)
#> median name
#> 1 1.0300 get("a", e, inherits = FALSE)
#> 2 0.9425 get("a", envir = e, inherits = FALSE)
#> 3 0.3080 .Internal(get("a", e, "any", FALSE))
#> 4 0.2305 e$a
#> 5 0.1740 e[["a"]]
#> 6 0.2905 .Primitive("[[")(e, "a")
A similar thing happens with exists(): the R function wrapper adds
significant overhead on top of .Internal(exists()). It?s also faster
to use $ and [[, then test for NULL, but of course this won?t
distinguish between objects that don?t exist, and those that do exist
but have a NULL value:
# Test for existence of `a` (which exists), and `c` (which doesn't)
microbenchmark(
exists('a', e, inherits = FALSE),
exists('a', envir = e, inherits = FALSE),
.Internal(exists('a', e, 'any', FALSE)),
'a' %in% ls(e, all.names = TRUE),
is.null(e[['a']]),
is.null(e$a),
exists('c', e, inherits = FALSE),
exists('c', envir = e, inherits = FALSE),
.Internal(exists('c', e, 'any', FALSE)),
'c' %in% ls(e, all.names = TRUE),
is.null(e[['c']]),
is.null(e$c),
unit = "us"
)
#> median name
#> 1 1.2015 exists("a", e, inherits = FALSE)
#> 2 1.0545 exists("a", envir = e, inherits = FALSE)
#> 3 0.3615 .Internal(exists("a", e, "any", FALSE))
#> 4 7.6345 "a" %in% ls(e, all.names = TRUE)
#> 5 0.3055 is.null(e[["a"]])
#> 6 0.3270 is.null(e$a)
#> 7 1.1890 exists("c", e, inherits = FALSE)
#> 8 1.0370 exists("c", envir = e, inherits = FALSE)
#> 9 0.3465 .Internal(exists("c", e, "any", FALSE))
#> 10 7.5475 "c" %in% ls(e, all.names = TRUE)
#> 11 0.2675 is.null(e[["c"]])
#> 12 0.3010 is.null(e$c)
-Winston
On Tue, Dec 2, 2014 at 8:46 PM, Peter Haverty <haverty.peter at gene.com>
wrote:> Hi All,
>
> I've been looking into speeding up the loading of packages that use a
lot
> of S4. After profiling I noticed the "exists" function accounts
for a
> surprising fraction of the time. I have some thoughts about speeding up
> exists (below). More to the point of this post, Martin M?chler noted that
> 'exists' and 'get' are often used in conjunction. Both
functions are
> different usages of the do_get C function, so it's a pity to run that
twice.
>
> "get" gives an error when a symbol is not found, so you can't
just do a
> 'get'. With R's C library, one might do
>
> SEXP x = findVarInFrame3(symbol,env);
> if (x != R_UnboundValue) {
> // do stuff with x
> }
>
> It would be very convenient to have something like this at the R level. We
> don't want to do any tryCatch stuff or to add args to get (That would
kill
> any speed advantage. The overhead for handling redundant args accounts for
> 30% of the time used by "exists"). Michael Lawrence and I worked
out that
> we need a function that returns either the desired object, or something
> that represents R_UnboundValue. We also need a very cheap way to check if
> something equals this new R_UnboundValue. This might look like
>
> if (defined(x <- fetch(symbol, env))) {
> do_stuff_with_x(x)
> }
>
> A few more thoughts about "exists":
>
> Moving the bit of R in the exists function to C saves 10% of the time.
> Dropping the redundant pos and frame args entirely saves 30% of the time
> used by this function. I suggest that the arguments of both get and
> exists should
> be simplified to (x, envir, mode, inherits). The existing C code handles
> numeric, character, and environment input for where. The arg frame is
> rarely used (0/128 exists calls in the methods package). Users that need to
> can call sys.frame themselves. get already lacks a frame argument and the
> manpage for exists notes that envir is only there for backwards
> compatibility. Let's deprecate the extra args in exists and get and
perhaps
> move the extra argument handling to C in the interim. Similarly, the
> "assign" function does nothing with the "immediate"
argument.
>
> I'd be interested to hear if there is any support for a
"fetch"-like
> function (and/or deprecating some unused arguments).
>
> All the best,
> Pete
>
>
>
> Pete
>
> ____________________
> Peter M. Haverty, Ph.D.
> Genentech, Inc.
> phaverty at gene.com
>
> [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
Thanks Winston! I'm amazed that "[[" beats calling the .Internal
directly. I guess the difference between .Primitive vs. .Internal is
pretty significant for things on this time scale.
NULL meaning NULL and NULL meaning undefined would lead to the same path
for much of my code. I'll be swapping out many exists and get calls later
today. Thanks!
I do still think it would be very useful to have some way to discriminate
the two NULL cases. I'm reminded of how perl does the same thing. It's
been a while, but it was something like
if (defined(x{'c'})) { print x{'c'}; } # This is still two
lookups, but it
has the "defined" concept.
or maybe even
if (defined( foo = x{'c'} ) ) { print foo; }
Thanks again for the timings!
Pete
____________________
Peter M. Haverty, Ph.D.
Genentech, Inc.
phaverty at gene.com
On Wed, Dec 3, 2014 at 12:48 PM, Winston Chang <winstonchang1 at
gmail.com>
wrote:
> I've looked at related speed issues in the past, and have a couple
> related points to add. (I've put the info below at
> http://rpubs.com/wch/46428.)
>
> There's a significant amount of overhead just from calling the R
> function get(). This is true even when you skip the pos argument and
> provide envir. For example, if you call get(), it takes much more time
> than .Internal(get()), which is what get() does.
>
> If you already know that the object exists in an environment, it's
> faster to use e$x, and slightly faster still to use e[["x"]]:
>
> e <- new.env()
> e$a <- 1
>
> # Accessing objects in environments
> microbenchmark(
> get("a", e, inherits = FALSE),
> get("a", envir = e, inherits = FALSE),
> .Internal(get("a", e, "any", FALSE)),
> e$a,
> e[["a"]],
> .Primitive("[[")(e, "a"),
>
> unit = "us"
> )
> #> median name
> #> 1 1.0300 get("a", e, inherits = FALSE)
> #> 2 0.9425 get("a", envir = e, inherits = FALSE)
> #> 3 0.3080 .Internal(get("a", e, "any", FALSE))
> #> 4 0.2305 e$a
> #> 5 0.1740 e[["a"]]
> #> 6 0.2905 .Primitive("[[")(e, "a")
>
>
> A similar thing happens with exists(): the R function wrapper adds
> significant overhead on top of .Internal(exists()). It's also faster
> to use $ and [[, then test for NULL, but of course this won't
> distinguish between objects that don't exist, and those that do exist
> but have a NULL value:
>
> # Test for existence of `a` (which exists), and `c` (which doesn't)
> microbenchmark(
> exists('a', e, inherits = FALSE),
> exists('a', envir = e, inherits = FALSE),
> .Internal(exists('a', e, 'any', FALSE)),
> 'a' %in% ls(e, all.names = TRUE),
> is.null(e[['a']]),
> is.null(e$a),
>
> exists('c', e, inherits = FALSE),
> exists('c', envir = e, inherits = FALSE),
> .Internal(exists('c', e, 'any', FALSE)),
> 'c' %in% ls(e, all.names = TRUE),
> is.null(e[['c']]),
> is.null(e$c),
>
> unit = "us"
> )
> #> median name
> #> 1 1.2015 exists("a", e, inherits = FALSE)
> #> 2 1.0545 exists("a", envir = e, inherits = FALSE)
> #> 3 0.3615 .Internal(exists("a", e, "any",
FALSE))
> #> 4 7.6345 "a" %in% ls(e, all.names = TRUE)
> #> 5 0.3055 is.null(e[["a"]])
> #> 6 0.3270 is.null(e$a)
> #> 7 1.1890 exists("c", e, inherits = FALSE)
> #> 8 1.0370 exists("c", envir = e, inherits = FALSE)
> #> 9 0.3465 .Internal(exists("c", e, "any",
FALSE))
> #> 10 7.5475 "c" %in% ls(e, all.names = TRUE)
> #> 11 0.2675 is.null(e[["c"]])
> #> 12 0.3010 is.null(e$c)
>
>
> -Winston
>
> On Tue, Dec 2, 2014 at 8:46 PM, Peter Haverty <haverty.peter at
gene.com>
> wrote:
> > Hi All,
> >
> > I've been looking into speeding up the loading of packages that
use a lot
> > of S4. After profiling I noticed the "exists" function
accounts for a
> > surprising fraction of the time. I have some thoughts about speeding
up
> > exists (below). More to the point of this post, Martin M?chler noted
that
> > 'exists' and 'get' are often used in conjunction.
Both functions are
> > different usages of the do_get C function, so it's a pity to run
that
> twice.
> >
> > "get" gives an error when a symbol is not found, so you
can't just do a
> > 'get'. With R's C library, one might do
> >
> > SEXP x = findVarInFrame3(symbol,env);
> > if (x != R_UnboundValue) {
> > // do stuff with x
> > }
> >
> > It would be very convenient to have something like this at the R
level.
> We
> > don't want to do any tryCatch stuff or to add args to get (That
would
> kill
> > any speed advantage. The overhead for handling redundant args accounts
> for
> > 30% of the time used by "exists"). Michael Lawrence and I
worked out
> that
> > we need a function that returns either the desired object, or
something
> > that represents R_UnboundValue. We also need a very cheap way to check
if
> > something equals this new R_UnboundValue. This might look like
> >
> > if (defined(x <- fetch(symbol, env))) {
> > do_stuff_with_x(x)
> > }
> >
> > A few more thoughts about "exists":
> >
> > Moving the bit of R in the exists function to C saves 10% of the time.
> > Dropping the redundant pos and frame args entirely saves 30% of the
time
> > used by this function. I suggest that the arguments of both get and
> > exists should
> > be simplified to (x, envir, mode, inherits). The existing C code
handles
> > numeric, character, and environment input for where. The arg frame is
> > rarely used (0/128 exists calls in the methods package). Users that
need
> to
> > can call sys.frame themselves. get already lacks a frame argument and
the
> > manpage for exists notes that envir is only there for backwards
> > compatibility. Let's deprecate the extra args in exists and get
and
> perhaps
> > move the extra argument handling to C in the interim. Similarly, the
> > "assign" function does nothing with the
"immediate" argument.
> >
> > I'd be interested to hear if there is any support for a
"fetch"-like
> > function (and/or deprecating some unused arguments).
> >
> > All the best,
> > Pete
> >
> >
> >
> > Pete
> >
> > ____________________
> > Peter M. Haverty, Ph.D.
> > Genentech, Inc.
> > phaverty at gene.com
> >
> > [[alternative HTML version deleted]]
> >
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
[[alternative HTML version deleted]]