search for: makeforkclust

Dear all, I?m working as an administrator of a High-Performance Computing (HPC) Cluster which runs on Linux. A lot of people are using R on this Linux cluster and, of course, the *parallel* package to speed up their computations. It has been our collective experience, that using |makeForkCluster| yields an overall better experience /on Linux/ than the |makePSOCKcluster|, for whatever definition of better. Let me just summarize that it works smoother. I believe, other people working with *parallel* on Linux can share this experience Also, we did really welcome the environment variable |M...

...ing users will increasingly start to run into forking related problems in RKWard and other environments. Therefore, I wish: - The warning from ?mcfork about potential complications should also be visible on the documentation pages for the higher level functions mcparallel(), mclapply(), but also makeForkCluster(). - It would be nice to have a way to tell library(parallel) that forking is a bad idea in the current session, so that - mcfork() could stop with an informative error message, or at least produce a warning; mclapply() could fall back to mc.cores=1 with a warning. - third party packages wh...

...14058 > parallel::pvec(1:2, FUN = function(x) Sys.getpid() + x/10) [1] 14058.1 14058.2 > f <- parallel::mcparallel(Sys.getpid()) Error in allowFork(assert = TRUE) : Forked processing is not allowed per option ?fork.allowed? or environment variable ?R_FORK_ALLOWED? > cl <- parallel::makeForkCluster(1L) Error in allowFork(assert = TRUE) : Forked processing is not allowed per option ?fork.allowed? or environment variable ?R_FORK_ALLOWED? > The patch is: Index: src/library/parallel/R/unix/forkCluster.R =================================================================== --- src/library/...

...s.getpid() + x/10) >> [1] 14058.1 14058.2 >>> f <- parallel::mcparallel(Sys.getpid()) >> Error in allowFork(assert = TRUE) : >> Forked processing is not allowed per option ?fork.allowed? or >> environment variable ?R_FORK_ALLOWED? >>> cl <- parallel::makeForkCluster(1L) >> Error in allowFork(assert = TRUE) : >> Forked processing is not allowed per option ?fork.allowed? or >> environment variable ?R_FORK_ALLOWED? >> The patch is: >> Index: src/library/parallel/R/unix/forkCluster.R >> =======================================...

..., FUN = function(x) Sys.getpid() + x/10) > [1] 14058.1 14058.2 >> f <- parallel::mcparallel(Sys.getpid()) > Error in allowFork(assert = TRUE) : > Forked processing is not allowed per option ?fork.allowed? or > environment variable ?R_FORK_ALLOWED? >> cl <- parallel::makeForkCluster(1L) > Error in allowFork(assert = TRUE) : > Forked processing is not allowed per option ?fork.allowed? or > environment variable ?R_FORK_ALLOWED? > > The patch is: > > Index: src/library/parallel/R/unix/forkCluster.R > ===================================================...

...14058.2 >>>>> f <- parallel::mcparallel(Sys.getpid()) >>>> Error in allowFork(assert = TRUE) : >>>> Forked processing is not allowed per option ?fork.allowed? or >>>> environment variable ?R_FORK_ALLOWED? >>>>> cl <- parallel::makeForkCluster(1L) >>>> Error in allowFork(assert = TRUE) : >>>> Forked processing is not allowed per option ?fork.allowed? or >>>> environment variable ?R_FORK_ALLOWED? >>>> The patch is: >>>> Index: src/library/parallel/R/unix/forkCluster.R >>&...

On Mon, 15 Apr 2019 at 08:44, Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > > On 4/13/19 12:05 PM, I?aki Ucar wrote: > > On Sat, 13 Apr 2019 at 03:51, Kevin Ushey <kevinushey at gmail.com> wrote: > >> I think it's worth saying that mclapply() works as documented > > Mostly, yes. But it says nothing about fork's copy-on-write and memory >

...<- parallel::mcparallel(Sys.getpid()) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>>> cl <- parallel::makeForkCluster(1L) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>> The patch is: >>>>>> Index: src/library...

...t; [1] 14058.1 14058.2 > >>> f <- parallel::mcparallel(Sys.getpid()) > >> Error in allowFork(assert = TRUE) : > >> Forked processing is not allowed per option ?fork.allowed? or > >> environment variable ?R_FORK_ALLOWED? > >>> cl <- parallel::makeForkCluster(1L) > >> Error in allowFork(assert = TRUE) : > >> Forked processing is not allowed per option ?fork.allowed? or > >> environment variable ?R_FORK_ALLOWED? > >> The patch is: > >> Index: src/library/parallel/R/unix/forkCluster.R > >> =========...

...;>> f <- parallel::mcparallel(Sys.getpid()) > >>>> Error in allowFork(assert = TRUE) : > >>>> Forked processing is not allowed per option ?fork.allowed? or > >>>> environment variable ?R_FORK_ALLOWED? > >>>>> cl <- parallel::makeForkCluster(1L) > >>>> Error in allowFork(assert = TRUE) : > >>>> Forked processing is not allowed per option ?fork.allowed? or > >>>> environment variable ?R_FORK_ALLOWED? > >>>> The patch is: > >>>> Index: src/library/parallel/R/uni...

...<- parallel::mcparallel(Sys.getpid()) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>>> cl <- parallel::makeForkCluster(1L) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>> The patch is: >>>>>> Index: src/library...

...;>> f <- parallel::mcparallel(Sys.getpid()) > >>>> Error in allowFork(assert = TRUE) : > >>>> Forked processing is not allowed per option ?fork.allowed? or > >>>> environment variable ?R_FORK_ALLOWED? > >>>>> cl <- parallel::makeForkCluster(1L) > >>>> Error in allowFork(assert = TRUE) : > >>>> Forked processing is not allowed per option ?fork.allowed? or > >>>> environment variable ?R_FORK_ALLOWED? > >>>> The patch is: > >>>> Index: src/library/parallel/R/uni...

...values are supported as well; see ?options.) o The NA warning messages from e.g. pchisq() now report the call to the closure and not that of the .Internal. o Added Polish translations by <c5><81>ukasz Daniel. PERFORMANCE IMPROVEMENTS: o In package parallel, makeForkCluster() and the multicore-based functions use native byte-order for serialization (deferred from 2.15.0). o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of objects, mainly by using .Call() rather than .Fortran(). o .C() and .Fortran() do less copying: arguments...

...values are supported as well; see ?options.) o The NA warning messages from e.g. pchisq() now report the call to the closure and not that of the .Internal. o Added Polish translations by <c5><81>ukasz Daniel. PERFORMANCE IMPROVEMENTS: o In package parallel, makeForkCluster() and the multicore-based functions use native byte-order for serialization (deferred from 2.15.0). o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of objects, mainly by using .Call() rather than .Fortran(). o .C() and .Fortran() do less copying: arguments...

...<- parallel::mcparallel(Sys.getpid()) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>>> cl <- parallel::makeForkCluster(1L) >>>>>> Error in allowFork(assert = TRUE) : >>>>>> Forked processing is not allowed per option ?fork.allowed? or >>>>>> environment variable ?R_FORK_ALLOWED? >>>>>> The patch is: >>>>>> Index: src/library...

...rallel(Sys.getpid()) > >>>>>> Error in allowFork(assert = TRUE) : > >>>>>> Forked processing is not allowed per option ?fork.allowed? or > >>>>>> environment variable ?R_FORK_ALLOWED? > >>>>>>> cl <- parallel::makeForkCluster(1L) > >>>>>> Error in allowFork(assert = TRUE) : > >>>>>> Forked processing is not allowed per option ?fork.allowed? or > >>>>>> environment variable ?R_FORK_ALLOWED? > >>>>>> The patch is: > >>>>&g...