Benjamin Caldwell
2013-Mar-05 21:18 UTC
[R] Function completely locks up my computer if the input is too big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a
hard reset every time). I don't know if this is useful description to
anyone - the mouse still responds, but not the keyboard and not windows
explorer.
The script only does this when the input matrix is large, and so my initial
runs didn't catch it as I used a smaller matrix to speed up the test runs.
When I tried an input matrix with a number of dimensions in the same order
of magnitude as the data I want to read in, R and my computer choked. This
was a surprise for me, as I've always been able to break execution in the
past or do other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
loop to do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar <- function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad <- function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg <- function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x & y of equal length
Pol2Car <- function(distance,deg) {
rad <- Deg2Rad(compass2polar(deg))
rad <- rep(rad, length(distance))
x <- ifelse(is.na(distance), NA, distance * cos(rad))
y <- ifelse(is.na(distance), NA, distance * sin(rad))
x<-round(x,2)
y<-round(y,2)
cartes<- list(x,y)
name<-c('x','y')
names(cartes)<-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate <- function(x,y,tilt){ 8
d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)
n <- length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
}
# browser()
tilt.in <- tilt + or.deg
xy<-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) >= 0) {
# shift.frame <- cbind(xy$x, xy$y)
# shift.frame.val <- shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x<- shift.frame.val[1] * -1
# shift.y<- shift.frame.val[2] * -1
# x<-xy$x + shift.x
# y<-xy$y + shift.y
# }
# name <- c('x', 'y')
# xy<-list(x,y)
# names(xy)<-name
xy
}
x <- seq(0,5, .5)
y <- seq(0,5, .5)
z <- seq(0,5, .5)
dquad<-expand.grid(x,y,z)
name<-c("y","x","z")
names(dquad)<-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated<-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof(?myFunction.out?, memory.profiling=T)
y <- myFunction(x)
Rprof(NULL)
summaryRprof(?myFunction.out?, memory=?both?)
#############
x <- seq(0,5, .1)
y <- seq(0,5, .1)
z <- seq(0,5, .1)
dquad<-expand.grid(x,y,z)
name<-c("y","x","z")
names(dquad)<-name
# running the below locks up my machine (commented out to avoid accidental
run)
# rotated<-rotate(dquad$x, dquad$y, 45)
Peter Alspach
2013-Mar-05 21:44 UTC
[R] Function completely locks up my computer if the input is too big
Tena koe Benjamin
I haven't looked at you code in detail, but in general ifelse is slow and
can generally be avoided. For example,
ben <- 1:10^7
system.time(BEN <- ifelse(ben<10, NA, -ben))
user system elapsed
1.31 0.24 1.56
system.time({BEN1 <- -ben; BEN1[BEN1> -10] <- NA})
user system elapsed
0.17 0.03 0.20
all.equal(BEN, BEN1)
[1] TRUE
HTH ...
Peter Alspach
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Benjamin Caldwell
Sent: Wednesday, 6 March 2013 10:18 a.m.
To: r-help
Subject: [R] Function completely locks up my computer if the input is too big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a hard
reset every time). I don't know if this is useful description to anyone -
the mouse still responds, but not the keyboard and not windows explorer.
The script only does this when the input matrix is large, and so my initial runs
didn't catch it as I used a smaller matrix to speed up the test runs.
When I tried an input matrix with a number of dimensions in the same order of
magnitude as the data I want to read in, R and my computer choked. This was a
surprise for me, as I've always been able to break execution in the past or
do other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a loop
to do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar <- function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad <- function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg <- function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x & y of equal length
Pol2Car <- function(distance,deg) {
rad <- Deg2Rad(compass2polar(deg))
rad <- rep(rad, length(distance))
x <- ifelse(is.na(distance), NA, distance * cos(rad))
y <- ifelse(is.na(distance), NA, distance * sin(rad))
x<-round(x,2)
y<-round(y,2)
cartes<- list(x,y)
name<-c('x','y')
names(cartes)<-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate <- function(x,y,tilt){ 8
d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)
n <- length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
}
# browser()
tilt.in <- tilt + or.deg
xy<-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) >= 0) {
# shift.frame <- cbind(xy$x, xy$y)
# shift.frame.val <- shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x<- shift.frame.val[1] * -1
# shift.y<- shift.frame.val[2] * -1
# x<-xy$x + shift.x
# y<-xy$y + shift.y
# }
# name <- c('x', 'y')
# xy<-list(x,y)
# names(xy)<-name
xy
}
x <- seq(0,5, .5)
y <- seq(0,5, .5)
z <- seq(0,5, .5)
dquad<-expand.grid(x,y,z)
name<-c("y","x","z")
names(dquad)<-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated<-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof("myFunction.out", memory.profiling=T)
y <- myFunction(x)
Rprof(NULL)
summaryRprof("myFunction.out", memory="both")
#############
x <- seq(0,5, .1)
y <- seq(0,5, .1)
z <- seq(0,5, .1)
dquad<-expand.grid(x,y,z)
name<-c("y","x","z")
names(dquad)<-name
# running the below locks up my machine (commented out to avoid accidental
run)
# rotated<-rotate(dquad$x, dquad$y, 45)
The contents of this e-mail are confidential and may be ...{{dropped:14}}
William Dunlap
2013-Mar-05 21:50 UTC
[R] Function completely locks up my computer if the input is too big
I see you have profiling calls in there. Have you used them?
It is often fruitful to see how the time for a function grows as size of the
input or output grows. Have you tried that?
A concrete suggestion is to change
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
}
to
or.deg[is.na(or.deg)] <- 0
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org] On Behalf
> Of Benjamin Caldwell
> Sent: Tuesday, March 05, 2013 1:18 PM
> To: r-help
> Subject: [R] Function completely locks up my computer if the input is too
big
>
> Dear r-help,
>
>
> Somewhere in my innocuous function to rotate an object in Cartesian space
> I've created a monster that completely locks up my computer (requires a
> hard reset every time). I don't know if this is useful description to
> anyone - the mouse still responds, but not the keyboard and not windows
> explorer.
>
> The script only does this when the input matrix is large, and so my initial
> runs didn't catch it as I used a smaller matrix to speed up the test
runs.
> When I tried an input matrix with a number of dimensions in the same order
> of magnitude as the data I want to read in, R and my computer choked. This
> was a surprise for me, as I've always been able to break execution in
the
> past or do other tasks. So i tried it again, and still no dice.
>
> Now I need the function to work as subsequent functions/functionality are
> dependent, and I can't see anything on the face of it that would likely
> cause the issue.
>
> Any insight on why this happens in general or specifically in my case are
> appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
> windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
> loop to do this function piece-wise for larger data and see if that helps.
>
> Script is attached and appended below.
>
> Thanks
>
> Ben Caldwell
>
>
>
> #compass to polar coordinates
>
> compass2polar <- function(x) {-x+90}
>
>
>
> #degrees (polar) to radians
>
> Deg2Rad <- function(x) {(x*pi)/180}
>
>
>
> # radians to degrees
>
> Rad2Deg <- function (rad) (rad/pi)*180
>
>
>
> # polar to cartesian coordinates - assumes degrees those from a compass.
> output is a list, x & y of equal length
>
> Pol2Car <- function(distance,deg) {
>
>
> rad <- Deg2Rad(compass2polar(deg))
>
> rad <- rep(rad, length(distance))
>
>
> x <- ifelse(is.na(distance), NA, distance * cos(rad))
>
> y <- ifelse(is.na(distance), NA, distance * sin(rad))
>
>
> x<-round(x,2)
>
> y<-round(y,2)
>
>
> cartes<- list(x,y)
>
> name<-c('x','y')
>
> names(cartes)<-name
>
> cartes
>
> }
>
>
>
>
>
> #rotate an object, with assumed origin at 0,0, in any number of degrees
>
> rotate <- function(x,y,tilt){ 8
>
>
> d2 <- x^2+y^2
>
> rotate.dis<-sqrt(d2)
>
> or.rad <- atan(x/y)
>
> or.deg <- Rad2Deg(or.rad)
>
>
> n <- length(or.deg)
>
> for(i in 1:n){
>
> if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
>
> }
>
> # browser()
>
> tilt.in <- tilt + or.deg
>
>
> xy<-Pol2Car (distance=rotate.dis, deg=tilt.in)
>
> # if(abs(tilt) >= 0) {
>
> # shift.frame <- cbind(xy$x, xy$y)
>
> # shift.frame.val <- shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
>
> # shift.x<- shift.frame.val[1] * -1
>
> # shift.y<- shift.frame.val[2] * -1
>
> # x<-xy$x + shift.x
>
> # y<-xy$y + shift.y
>
> # }
>
> # name <- c('x', 'y')
>
> # xy<-list(x,y)
>
> # names(xy)<-name
>
> xy
>
> }
>
>
> x <- seq(0,5, .5)
>
> y <- seq(0,5, .5)
>
> z <- seq(0,5, .5)
>
> dquad<-expand.grid(x,y,z)
>
> name<-c("y","x","z")
>
> names(dquad)<-name
>
>
> plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
>
>
> #this works fine
>
> rotated<-rotate(dquad$x, dquad$y, 45)
>
>
>
> points(rotated$x, rotated$y, col='green')
>
>
> # profiling of both time and memory
>
> Rprof("myFunction.out", memory.profiling=T)
>
> y <- myFunction(x)
>
> Rprof(NULL)
>
> summaryRprof("myFunction.out", memory="both")
>
>
>
> #############
>
> x <- seq(0,5, .1)
>
> y <- seq(0,5, .1)
>
> z <- seq(0,5, .1)
>
> dquad<-expand.grid(x,y,z)
>
> name<-c("y","x","z")
>
> names(dquad)<-name
>
> # running the below locks up my machine (commented out to avoid accidental
> run)
>
> # rotated<-rotate(dquad$x, dquad$y, 45)