R - cpv (trotter package) and %dopar%
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1
I'd like to know whether the cpv function within the trotter package works with %dopar%? I'm getting the following error:
task 1 failed - "object of type 'S4' is not subsettable"
Here's a small example:
library(doParallel)
library(trotter)
registerDoParallel(cores = 2)
x <- letters
combos <- cpv(2, 1:4)
print(combos)
num_combos <- length(combos)
results_list <- foreach(combo_num=1:num_combos) %dopar% { # many iterations
y <- x[combos[combo_num]]
# time consuming stuff follows that involves using y
}
Replacing %dopar% with %do% (or simply using a for loop) and it works fine.
r foreach doparallel
edited Nov 17 '18 at 6:39
kit
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
add a comment |
1
I'd like to know whether the cpv function within the trotter package works with %dopar%? I'm getting the following error:
task 1 failed - "object of type 'S4' is not subsettable"
Here's a small example:
library(doParallel)
library(trotter)
registerDoParallel(cores = 2)
x <- letters
combos <- cpv(2, 1:4)
print(combos)
num_combos <- length(combos)
results_list <- foreach(combo_num=1:num_combos) %dopar% { # many iterations
y <- x[combos[combo_num]]
# time consuming stuff follows that involves using y
}
Replacing %dopar% with %do% (or simply using a for loop) and it works fine.
r foreach doparallel
edited Nov 17 '18 at 6:39
kit
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04
add a comment |
1
1
1
I'd like to know whether the cpv function within the trotter package works with %dopar%? I'm getting the following error:
task 1 failed - "object of type 'S4' is not subsettable"
Here's a small example:
library(doParallel)
library(trotter)
registerDoParallel(cores = 2)
x <- letters
combos <- cpv(2, 1:4)
print(combos)
num_combos <- length(combos)
results_list <- foreach(combo_num=1:num_combos) %dopar% { # many iterations
y <- x[combos[combo_num]]
# time consuming stuff follows that involves using y
}
Replacing %dopar% with %do% (or simply using a for loop) and it works fine.
r foreach doparallel
edited Nov 17 '18 at 6:39
kit
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
I'd like to know whether the cpv function within the trotter package works with %dopar%? I'm getting the following error:
task 1 failed - "object of type 'S4' is not subsettable"
Here's a small example:
library(doParallel)
library(trotter)
registerDoParallel(cores = 2)
x <- letters
combos <- cpv(2, 1:4)
print(combos)
num_combos <- length(combos)
results_list <- foreach(combo_num=1:num_combos) %dopar% { # many iterations
y <- x[combos[combo_num]]
# time consuming stuff follows that involves using y
}
Replacing %dopar% with %do% (or simply using a for loop) and it works fine.
r foreach doparallel
r foreach doparallel
edited Nov 17 '18 at 6:39
kit
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
edited Nov 17 '18 at 6:39
kit
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
edited Nov 17 '18 at 6:39
kit
1,10431017
edited Nov 17 '18 at 6:39
kit
1,10431017
edited Nov 17 '18 at 6:39
kit
1,10431017
1,10431017
asked Nov 17 '18 at 2:45
user10665650user10665650
82
asked Nov 17 '18 at 2:45
user10665650user10665650
82
asked Nov 17 '18 at 2:45
user10665650user10665650
82
82
Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04
add a comment |
Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04
Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04
add a comment |
1 Answer
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Depending on the cluster type one needs to explicitly specify the used packages via the .packages argument. The following should work:
library(doParallel)
library(trotter)
cl <- makePSOCKcluster(2)
registerDoParallel(cl=cl)
x <- letters
combos <- cpv(2, 1:4)
num_combos <- length(combos)
rl <- foreach(combo_num=1:num_combos, .packages="trotter") %dopar% {
x[combos[combo_num]]
}
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
add a comment |
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1 Answer
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Depending on the cluster type one needs to explicitly specify the used packages via the .packages argument. The following should work:
library(doParallel)
library(trotter)
cl <- makePSOCKcluster(2)
registerDoParallel(cl=cl)
x <- letters
combos <- cpv(2, 1:4)
num_combos <- length(combos)
rl <- foreach(combo_num=1:num_combos, .packages="trotter") %dopar% {
x[combos[combo_num]]
}
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
add a comment |
1
Depending on the cluster type one needs to explicitly specify the used packages via the .packages argument. The following should work:
library(doParallel)
library(trotter)
cl <- makePSOCKcluster(2)
registerDoParallel(cl=cl)
x <- letters
combos <- cpv(2, 1:4)
num_combos <- length(combos)
rl <- foreach(combo_num=1:num_combos, .packages="trotter") %dopar% {
x[combos[combo_num]]
}
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
add a comment |
1
1
1
Depending on the cluster type one needs to explicitly specify the used packages via the .packages argument. The following should work:
library(doParallel)
library(trotter)
cl <- makePSOCKcluster(2)
registerDoParallel(cl=cl)
x <- letters
combos <- cpv(2, 1:4)
num_combos <- length(combos)
rl <- foreach(combo_num=1:num_combos, .packages="trotter") %dopar% {
x[combos[combo_num]]
}
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
Depending on the cluster type one needs to explicitly specify the used packages via the .packages argument. The following should work:
library(doParallel)
library(trotter)
cl <- makePSOCKcluster(2)
registerDoParallel(cl=cl)
x <- letters
combos <- cpv(2, 1:4)
num_combos <- length(combos)
rl <- foreach(combo_num=1:num_combos, .packages="trotter") %dopar% {
x[combos[combo_num]]
}
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
answered Nov 17 '18 at 4:52
FlorianFlorian
1,152818
1,152818
add a comment |
add a comment |
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Hi, from the author of trotter (who has been very lazy in maintaining the R version of this library!). I copied-and-pasted your code and it worked as expected. Might your error come from something else you have done? Try restarting the R session...
– Richard Ambler
Nov 17 '18 at 4:55
I think the difference is that the OP is using windows, and you're not.
– F. Privé
Nov 17 '18 at 7:35
The problem here is that apparently you can't use subsetting on this kind of object without loading the package first. Maybe @RichardAmbler could fixed this, or maybe it's impossible depending on the kind of object system that's used.
– F. Privé
Nov 17 '18 at 7:42
@F.Privé Updating the R package has been added to my list of things to do! :) There shouldn't be an issue with subsetting, though, because the combinations are not actually stored anywhere; rather the cpv instance is just a mapping of integers to combinations that behaves as if it were a list of combinations. As long as the interpreter has a constructed cpv instance it should be able to access any combination "stored" without needing to explicitly partition the combinations for each core.
– Richard Ambler
Nov 17 '18 at 8:04