On Fri, 2013-12-27 at 16:47 -0600, Hadley Wickham wrote:
> For your original case, you may find it more useful to do memory +
> line profiling (e.g. as visualised by
> https://github.com/hadley/lineprof) to figure out what's going on.
>
> Hadley
I've been trying memory and line profiling, but memory="stats" or
"tseries" doesn't seem to work in summaryRProf. I'm not sure if I've
misunderstood something or there are bugs:
> Rprof(memory.profiling=TRUE, gc.profiling=TRUE,
line.profiling=TRUE)
> system.time(r <- Reduce(addResults,
bigr[1:10]))
user system elapsed
3.408 0.000 3.415
> Rprof(NULL)
> summaryRprof(memory="both")
$by.self
self.time self.pct total.time total.pct mem.total
"<GC>" 4.06 100 4.06 100 3.2
$by.total
total.time total.pct mem.total self.time self.pct
"<GC>" 4.06 100.00 3.2 4.06 100
"gc" 4.06 100.00 3.2 0.00 0
"system.time" 4.06 100.00 3.2 0.00 0
"f" 3.42 84.24 3.2 0.00 0
"Reduce" 3.42 84.24 3.2 0.00 0
$sample.interval
[1] 0.02
$sampling.time
[1] 4.06
> summaryRprof(memory="tseries")
Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] :
non-numeric argument to binary operator
In addition: Warning message:
In data.frame(..., check.names = FALSE) :
row names were found from a short variable and have been discarded
> summaryRprof(memory="tseries", index=2)
Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] :
non-numeric argument to binary operator
In addition: Warning message:
In data.frame(..., check.names = FALSE) :
row names were found from a short variable and have been discarded
> summaryRprof(memory="both", diff=TRUE) # diff=TRUE doesn't seem to
matter
$by.self
self.time self.pct total.time total.pct mem.total
"<GC>" 4.06 100 4.06 100 3.2
$by.total
total.time total.pct mem.total self.time self.pct
"<GC>" 4.06 100.00 3.2 4.06 100
"gc" 4.06 100.00 3.2 0.00 0
"system.time" 4.06 100.00 3.2 0.00 0
"f" 3.42 84.24 3.2 0.00 0
"Reduce" 3.42 84.24 3.2 0.00 0
$sample.interval
[1] 0.02
$sampling.time
[1] 4.06
> summaryRprof(memory="stats", diff=TRUE)
Error in tapply(seq_len(1L), list(index = c("\"system.time\":\"gc
\"", :
arguments must have same length
> summaryRprof(memory="stats")
Error in tapply(seq_len(1L), list(index = c("\"system.time\":\"gc
\"", :
! arguments must have same length
Even the memory="both", which at least runs, is not illuminating to me.
I guess it's saying that all the time is going to garbage collection. I
may try your tool to see if that helps.
Thanks.
Ross
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