Displaying 20 results from an estimated 800 matches similar to: "parLapply - Error in do.call("fun", lapply(args, enquote)) : could not find function "fun""
2010 Apr 09
1
Rsge: recursive parallelization
In principle, I'd like to be able to do something like this:
sge.parLapply(seq(10), function(x) parLapply(seq(x), function(x) x^2))
In practice, however, I have to resort to acrobatics like this:
sge.options(sge.remove.files=FALSE)
sge.options(sge.qsub.options='-cwd -V')
sge.parLapply(seq(10),
function(x) {
sge.options(sge.save.global=TRUE)
2011 Feb 03
1
problem with parLapply from snow
Hi,
The following function use to work, but now it doesn't giving the error
"> CallSnow(, 100)
Using snow package, asking for 2 nodes
2 slaves are spawned successfully. 0 failed.
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: no applicable method for 'lapply' applied to an object of class "list"
".
Where this is the
2005 Nov 11
1
Snow parLapply
Dear R-user,
I am trying to use the function 'parLapply' from the 'snow' package
which is supposed to work the same wys as 'lapply' but for a
parallelized cluster of computers. The function I am trying to call in
parallel is 'dudi.pca' (from the 'ade4' package) which performs
principal component analyses. When I call this function on a list of
2013 Dec 24
2
Parallel computing: how to transmit multiple parameters to a function in parLapply?
Hi R-developers
In the package Parallel, the function parLapply(cl, x, f) seems to allow
transmission of only one parameter (x) to the function f. Hence in order to
compute f(x, y) parallelly, I had to define f(x, y) as f(x) and tried to
access y within the function, whereas y was defined outside of f(x).
Script:
library(parallel)
f <- function(x) {
z <- 2 * x + .GlobalEnv$y # Try to
2007 Mar 27
2
snow parLapply standard output
I am slightly confused by the way the standard output is redirected in a R
snow cluster environment.
I am using parLapply from the snow package to execute a function on my
MPI/LAM cluster. How can I redirect standard output (produced using "cat")
from this function back to the terminal where I invoked it? I intend to
transmit some status information in advance to the final result of the
2012 Aug 21
1
parLapply fails to detect default cluster?
invoking parLapply without a cluster fails to find a previously
registered cluster
> library(parallel)
> setDefaultCluster(makePSOCKcluster(2))
> parLapply(X=1:2, fun=function(...) {})
Error in cut.default(i, breaks) : invalid number of intervals
This is because in parLapply length(cl) is determined before
defaultCluster(cl) is called. By inspection, this appears to be true of
2012 Jan 12
1
parLapply within a function
Dear R users,
I have some problems with the parLapply function from the "parallel"
package:
I use parLapply on a pretty big R object without changing the object
within the called function. If I execute parLapply alone, everything
works fine. It seems that the object resides only once in the memory.
But if I use the same call within another function, the object seems to
be multiplied to
2011 Jun 12
1
snow package
Hi
I try parallelising some code using the snow package and the following lines:
cl <- makeSOCKcluster(8)
pfunc <- function (x) (if(x <= (-th)) 1 else 0) ###correlation coefficient
clusterExport(cl,c("pfunc","th"))
cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc)
The parApply results in the error message:
> cor.c.f <- parApply(cl,tms,c(1,2),FUN=pfunc)
Error
2012 Dec 21
1
Parallel code using parLapply
Dear R-users
I was running into problems with my R code trying to run clh sampling (clhs package) in parallel mode (=on various data sets simultaneously).
Here is the code (which I developed with some help:)):
******************************************
library("clhs")
library("snow")
a <- as.data.frame(replicate(1000, rnorm(20)))
b <- as.data.frame(replicate(1000,
2015 Dec 09
2
Bug: part_set_name does not enquote name
Windows server 2012 sets partition names with spaces.
><fs> part-get-name /dev/sda 3
libguestfs: trace: part_get_name "/dev/sda" 3
guestfsd: main_loop: new request, len 0x38
parted -s -m /dev/null
Error: The device /dev/null is so small that it cannot possibly store a
file system or partition table. Perhaps you selected the wrong device?
Warning: Error fsyncing/closing
2012 Oct 26
0
parallel::pvec FUN types differ when v is a list; code simplifications?
In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas
pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems
consistent with pvec's description.
This came up in a complicated Bioconductor thread about generics and parallel
evaluation
https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html
One relevant point is that a
2017 Dec 11
0
document environment passing in parallel::parLapply
The runtime of parallel::parLapply depends on variables unrelated to
the parLapply call. However, this is not clearly documented. Therefore
I would like to suggest expanding the relevant documentation to
explain this behaviour.
Consider this example:
parallel_demo <- function(random_values_count) {
some_data <- runif(random_values_count)
dummy_function <- function(x) {
x
}
2006 Apr 04
1
Mpirun with R CMD scripts
Hi,
I am working on a 64-bit rocks cluster and am relatively new to the
R package. I am trying to get Snow working with R and Rmpi and have
run into the following issue. R is able to load the Rmpi and snow
libraries and is able to run simple commands both interactively and
batch as follows:
-------------------------------------------------------------------------------------------------------
2006 Mar 14
1
Using up2date to download channels on rhn
Hi all,
i have a problem with centos's up2date tool. I have setup a central
update server with yam (http://dag.wieers.com/home-made/yam/) under
CentOS-4. When yam calls t up2date to download updates, up2date returns
this error:
Traceback (most recent call last):
File "/usr/bin/yam", line 1099, in ?
main()
File "/usr/bin/yam", line 983, in main
2013 Apr 02
1
R doesn't recognize utils functions, such as arrayIndex( )
Hi all,
When I called arrayIndex(20:23, dim=c(4,3,3)), it says "Error: could not
find function "arrayIndex"in R". So I called ls("package:utils") to see the
functions inside:
[1] "?"
[2] "adist"
[3] "alarm"
[4] "apropos"
[5] "aregexec"
[6] "argsAnywhere"
[7] "arrangeWindows"
[8]
2014 Jul 02
1
parLapply on sqlQuery (from package RODBC)
R Version : 2.14.1 x64
Running on Windows 7
Connecting to a database on a remote Microsoft SQL Server 2012
The short form of my problem is the following.
I have an unordered vectors of names, say:
names<-c("A", "B", "A", "C","C")
each of which have an id in a table in my db. I need to convert the names to their corresponding ids.
I
2018 Mar 15
2
clusterApply arguments
Thank you for your answer!
I agree with you except for the 3 (Error) example and
I realize now I should have started with that in the explanation.
>From my point of view
parLapply(cl = clu, X = 1:2, fun = fun, c = 1)
shouldn't give an error.
This could be easily avoided by using all the argument
names in the custerApply call of parLapply which means changing,
parLapply <-
2018 Mar 14
2
clusterApply arguments
Hi!
I recognized that the argument matching of clusterApply (and therefore parLapply) goes wrong when one of the arguments of the function is called "c". In this case, the argument "c" is used as cluster and the functions give the following error message "Error in checkCluster(cl) : not a valid cluster".
Of course, "c" is for many reasons an unfortunate
2006 Oct 13
3
Rmpi performance
Dear R users,
we are trying to do some parallel computing using library(snow).
In particular we have a cluster with 3 nodes
>cl <- makeCluster(3, type = "MPI")
3 slaves are spawned successfully. 0 failed.
and we want to compute the function op_mat (see below) first with the
master and then with the cluster using system.time for checking the
computational performance.
2011 Jun 14
2
Still have problems with tcltk in R 64 bit
Dear R users,
Since a long time now, I have the following error when I want to load
the tcltk library in R 64 bit.
Loading Tcl/Tk interface ...Error : .onLoad failed in loadNamespace()
for 'tcltk', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Program
Files/R/R-2.13.0/library/tcltk/libs/x64/tcltk.dll':
LoadLibrary