Hi Simon,
I'm having trouble with nested parallel workers, specifically, forking
inside socket connections.
When mclapply is called inside a SOCK, PSOCK or FORK worker I get an
error in unserialize().
cl <- makeCluster(1, "SOCK")
fun = function(i) {
library(parallel)
mclapply(1:2, sqrt)
}
Failure occurs after multiple calls to clusterApply:
> clusterApply(cl, 1, fun)
[[1]]
[[1]][[1]]
[1] 1
[[1]][[2]]
[1] 1.414214
> clusterApply(cl, 1, fun)
[[1]]
[[1]][[1]]
[1] 1
[[1]][[2]]
[1] 1.414214
> clusterApply(cl, 1, fun)
Error in unserialize(node$con) : error reading from connection
This example is from Martin and may be a different problem.
~/tmp >cat test1.R
## like mclapply
## should run 'forever' but terminates semi-randomly
library(parallel)
children <- parallel:::children
while (TRUE) {
n <- 8 ## n == dectectCores()
jobs <- lapply(seq_len(n), function(i) mcparallel(Sys.sleep(20)))
mccollect(children(jobs), FALSE)
parallel:::mckill(children(jobs), tools::SIGTERM)
leni <- length(mccollect(children(jobs)))
message("leni: ", leni)
}
~/tmp >R-dev --vanilla --slave -f test1.R
leni: 6
leni: 7
leni: 7
leni: 7
leni: 7
leni: 7
leni: 7
leni: 7
leni: 8
leni: 7
leni: 7
leni: 7
~/tmp >
Thanks.
Valerie
> sessionInfo()
R Under development (unstable) (2015-03-18 r68009)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Fedora 21 (Twenty One)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] snow_0.3-13
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109
Email: vobencha at fredhutch.org
Phone: (206) 667-3158
On Mar 25, 2015, at 3:46 PM, Valerie Obenchain <vobencha at fredhutch.org> wrote:> Hi Simon, > > I'm having trouble with nested parallel workers, specifically, forking inside socket connections. >You simply can't by definition - when you fork *all* the workers share the same connection inherited from the parent, so you cannot use any I/O operations that you didn't start in the worker since reading in one worker affects all the workers. Cheers, Simon> When mclapply is called inside a SOCK, PSOCK or FORK worker I get an > error in unserialize(). > > cl <- makeCluster(1, "SOCK") > > fun = function(i) { > library(parallel) > mclapply(1:2, sqrt) > } > > Failure occurs after multiple calls to clusterApply: > > > clusterApply(cl, 1, fun) > [[1]] > [[1]][[1]] > [1] 1 > > [[1]][[2]] > [1] 1.414214 > > > clusterApply(cl, 1, fun) > [[1]] > [[1]][[1]] > [1] 1 > > [[1]][[2]] > [1] 1.414214 > > > clusterApply(cl, 1, fun) > Error in unserialize(node$con) : error reading from connection > > > This example is from Martin and may be a different problem. > > ~/tmp >cat test1.R > ## like mclapply > ## should run 'forever' but terminates semi-randomly > library(parallel) > children <- parallel:::children > > while (TRUE) { > n <- 8 ## n == dectectCores() > jobs <- lapply(seq_len(n), function(i) mcparallel(Sys.sleep(20))) > mccollect(children(jobs), FALSE) > parallel:::mckill(children(jobs), tools::SIGTERM) > leni <- length(mccollect(children(jobs))) > message("leni: ", leni) > } > > ~/tmp >R-dev --vanilla --slave -f test1.R > leni: 6 > leni: 7 > leni: 7 > leni: 7 > leni: 7 > leni: 7 > leni: 7 > leni: 7 > leni: 8 > leni: 7 > leni: 7 > leni: 7 > ~/tmp > > > > Thanks. > Valerie > > > > sessionInfo() > R Under development (unstable) (2015-03-18 r68009) > Platform: x86_64-unknown-linux-gnu (64-bit) > Running under: Fedora 21 (Twenty One) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > loaded via a namespace (and not attached): > [1] snow_0.3-13 > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, Seattle, WA 98109 > > Email: vobencha at fredhutch.org > Phone: (206) 667-3158 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
On 03/25/2015 07:48 PM, Simon Urbanek wrote:> On Mar 25, 2015, at 3:46 PM, Valerie Obenchain <vobencha at fredhutch.org> wrote: > >> Hi Simon, >> >> I'm having trouble with nested parallel workers, specifically, forking inside socket connections. >> > > You simply can't by definition - when you fork *all* the workers share the same connection inherited from the parent, so you cannot use any I/O operations that you didn't start in the worker since reading in one worker affects all the workers. >Sorry if I'm missing the obvious here - I thought since the fork workers were shut down by the time the SOCK worker returned to its master conflicting I/O wouldn't be a problem. There are quite a few examples floating around where SOCK workers are spawned on a cluster and multicore workers are called within them. If I understand correctly this should not be done (or at least not encouraged). Instead, nested parallel should only be done with distributed memory workers, SOCK, MPI etc. Thanks. Valerie> Cheers, > Simon > > >> When mclapply is called inside a SOCK, PSOCK or FORK worker I get an >> error in unserialize(). >> >> cl <- makeCluster(1, "SOCK") >> >> fun = function(i) { >> library(parallel) >> mclapply(1:2, sqrt) >> } >> >> Failure occurs after multiple calls to clusterApply: >> >>> clusterApply(cl, 1, fun) >> [[1]] >> [[1]][[1]] >> [1] 1 >> >> [[1]][[2]] >> [1] 1.414214 >> >>> clusterApply(cl, 1, fun) >> [[1]] >> [[1]][[1]] >> [1] 1 >> >> [[1]][[2]] >> [1] 1.414214 >> >>> clusterApply(cl, 1, fun) >> Error in unserialize(node$con) : error reading from connection >> >> >> This example is from Martin and may be a different problem. >> >> ~/tmp >cat test1.R >> ## like mclapply >> ## should run 'forever' but terminates semi-randomly >> library(parallel) >> children <- parallel:::children >> >> while (TRUE) { >> n <- 8 ## n == dectectCores() >> jobs <- lapply(seq_len(n), function(i) mcparallel(Sys.sleep(20))) >> mccollect(children(jobs), FALSE) >> parallel:::mckill(children(jobs), tools::SIGTERM) >> leni <- length(mccollect(children(jobs))) >> message("leni: ", leni) >> } >> >> ~/tmp >R-dev --vanilla --slave -f test1.R >> leni: 6 >> leni: 7 >> leni: 7 >> leni: 7 >> leni: 7 >> leni: 7 >> leni: 7 >> leni: 7 >> leni: 8 >> leni: 7 >> leni: 7 >> leni: 7 >> ~/tmp > >> >> >> Thanks. >> Valerie >> >> >>> sessionInfo() >> R Under development (unstable) (2015-03-18 r68009) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> Running under: Fedora 21 (Twenty One) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> loaded via a namespace (and not attached): >> [1] snow_0.3-13 >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, Seattle, WA 98109 >> >> Email: vobencha at fredhutch.org >> Phone: (206) 667-3158 >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >