Re: [R] parSapply can't find function
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source(funcs.R)')
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--**--**
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.**de lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__**posting-guide.htmlhttp://www.R-project.org/__posting-guide.html
http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parSapply can't find function
On Apr 29, 2013, at 11:16 AM, Kaiyin Zhong (Victor Chung) wrote:
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source(funcs.R)')
Are you sure those outer single quote marks are not the problem?
--
David.
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--**--**
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.**de lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
__**__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/_**_listinfo/r-helphttps://stat.ethz.ch/mailman/__listinfo/r-help
https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__**posting-guide.htmlhttp://www.R-project.org/__posting-guide.html
http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parSapply can't find function
Oh, indeed, that IS the problem. Thank you!!!
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Mon, Apr 29, 2013 at 8:22 PM, David Winsemius dwinsem...@comcast.netwrote:
On Apr 29, 2013, at 11:16 AM, Kaiyin Zhong (Victor Chung) wrote:
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source(funcs.R)')
Are you sure those outer single quote marks are not the problem?
--
David.
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de
wrote:
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--**--**
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.**de lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-**dortmund.de
lig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
__**__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/_**_listinfo/r-help
https://stat.ethz.ch/mailman/__listinfo/r-help
https://stat.ethz.ch/mailman/**listinfo/r-help
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__**posting-guide.html
http://www.R-project.org/__posting-guide.html
http://www.R-project.org/**posting-guide.html
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible
code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
[[alternative HTML
Re: [R] parSapply can't find function
On 29/04/2013 2:16 PM, Kaiyin Zhong (Victor Chung) wrote:
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source(funcs.R)')
The expression being evaluated there is a string,
'source(funcs.R)'
You want an expression, e.g.
clusterEvalQ(cl, source(funcs.R))
Duncan Murdoch
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--**--**
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.**de lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
__**__
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/_**_listinfo/r-helphttps://stat.ethz.ch/mailman/__listinfo/r-help
https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__**posting-guide.htmlhttp://www.R-project.org/__posting-guide.html
http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parSapply can't find function
Sorry, I got some new error:
Error in cut.default(i, breaks) : 'breaks' are not unique
traceback()
20: stop('breaks' are not unique)
19: cut.default(i, breaks)
18: cut(i, breaks)
17: split.default(i, cut(i, breaks))
16: split(i, cut(i, breaks))
15: structure(split(i, cut(i, breaks)), names = NULL)
14: splitIndices(length(x), ncl)
13: lapply(splitIndices(length(x), ncl), function(i) x[i])
12: splitList(x, length(cl))
11: staticClusterApply(cl, fun, length(x), argfun)
10: clusterApply(cl, splitList(x, length(cl)), lapply, fun, ...)
9: lapply(args, enquote)
8: do.call(fun, lapply(args, enquote))
7: docall(c, clusterApply(cl, splitList(x, length(cl)), lapply,
fun, ...))
6: parLapply(cl, as.list(X), FUN, ...)
5: parSapply(cl, eff, pow_error) at testing.R#5
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source(testing.R)
The sequential run was ok.
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Mon, Apr 29, 2013 at 8:26 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote:
On 29/04/2013 2:16 PM, Kaiyin Zhong (Victor Chung) wrote:
Hi, Uwe.
I still don't get how this can be done correctly. Here is what I tried.
In the file funcs.R, define these functions:
library('modeest')
x = vector(length=500)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
Then do the following:
library('snow')
cl = makeCluster(rep('localhost', 12), 'SOCK')
clusterSetupRNG(cl)
clusterEvalQ(cl, 'source(funcs.R)')
The expression being evaluated there is a string,
'source(funcs.R)'
You want an expression, e.g.
clusterEvalQ(cl, source(funcs.R))
Duncan Murdoch
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
print(r)
}
testK()
stopCluster(cl)
The error still pops up:
Error in checkForRemoteErrors(val) :
12 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 3:44 PM, Uwe Ligges
lig...@statistik.tu-dortmund.**de lig...@statistik.tu-dortmund.de
wrote:
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--**--**
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de lig...@statistik.tu-dortmund.**
de lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-dortmund.de http://dortmund.de
ligges@statistik.**tu-dortmund.de lig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x,
k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have
to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
Re: [R] parSapply can't find function
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parSapply can't find function
Thanks for the reply.
How can i make the functions known to all nodes?
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges lig...@statistik.tu-dortmund.de
wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find function predR
predR is not yet known on all nodes, just on the master. You have to tell
the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
[[alternative HTML version deleted]]
__**
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] parSapply can't find function
On 23.04.2013 15:00, Kaiyin Zhong (Victor Chung) wrote:
Thanks for the reply.
How can i make the functions known to all nodes?
See ?clusterEvalQ
you may also want to try the parallel packages.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
On Tue, Apr 23, 2013 at 2:43 PM, Uwe Ligges
lig...@statistik.tu-dortmund.de
mailto:lig...@statistik.tu-dortmund.de wrote:
On 18.04.2013 11:11, Kaiyin Zhong (Victor Chung) wrote:
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na
http://is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find
function predR
predR is not yet known on all nodes, just on the master. You have to
tell the nodes about the definition first.
Best,
Uwe Ligges
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl mailto:k.zh...@erasmusmc.nl
kindlych...@gmail.com mailto:kindlych...@gmail.com
[[alternative HTML version deleted]]
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/__listinfo/r-help
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__posting-guide.html
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] parSapply can't find function
Here is the code, assuming 8 cores in the cpu.
library('modeest')
library('snow')
cl = makeCluster(rep('localhost', 8), 'SOCK')
x = vector(length=50)
x = sapply(x, function(i) i=sample(c(1,0), 1))
pastK = function(n, x, k) {
if (nk) { return(x[(n-k):(n-1)]) }
else {return(NA)}
}
predR = function(x, k) {
pastList = lapply(1:length(x), function(n) pastK(n, x, k))
pred = sapply(pastList, function(v) mfv(v)[1])
ratio = sum(pred==x, na.rm=T)/(length(pred) - sum(is.na(pred)))
}
testK = function() {
k = seq(3, 25, 2)
r = parSapply(cl, k, function(i) predR(x, i))
#r = sapply(k, function(i) predR(x, i))
}
r = testK()
stopCluster(cl)
Here is the error:
Error in checkForRemoteErrors(val) :
8 nodes produced errors; first error: could not find function predR
Best regards,
Kaiyin ZHONG
--
FMB, Erasmus MC
k.zh...@erasmusmc.nl
kindlych...@gmail.com
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
