R devel - Jan 2020 - SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()

Henrik,

the example from the post works just fine in CRAN R for me - the post was about
homebrew build so it's conceivably a bug in their libraries. That's
exactly why I was proposing a more general solution where you can simply define
a function in user-space that will issue a warning or stop on fork, it
doesn't have to be part of core R, there are other packages that use fork()
as well, so what I proposed is much safer than hacking the parallel package.

Cheers,
Simon
 

> On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson at
gmail.com> wrote:
> 
> The RStudio GUI was just one example.  AFAIK, and please correct me if
> I'm wrong, another example is where multi-threaded code is used in
> forked processing and that's sometimes unstable.  Yes another, which
> might be multi-thread related or not, is
> https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
> 
> res <- parallel::mclapply(urls, function(url) {
>  download.file(url, basename(url))
> })
> 
> That was reported to fail on macOS with the default
method="libcurl"
> but not for method="curl" or method="wget".
> 
> Further documentation is needed and would help but I don't believe
> it's sufficient to solve everyday problems.  The argument for
> introducing an option/env var to disable forking is to give the end
> user a quick workaround for newly introduced bugs.  Neither the
> develop nor the end user have full control of the R package stack,
> which is always in flux.  For instance, above mclapply() code might
> have been in a package on CRAN and then all of a sudden
> method="libcurl" became the new default in base R.  The above
> mclapply() code is now buggy on macOS, and not necessarily caught by
> CRAN checks.  The package developer might not notice this because they
> are on Linux or Windows.  It can take a very long time before this
> problem is even noticed and even further before it is tracked down and
> fixed.   Similarly, as more and more code turn to native code and it
> becomes easier and easier to implement multi-threading, more and more
> of these bugs across package dependencies risk sneaking in the
> backdoor wherever forked processing is in place.
> 
> For the end user, but also higher-up upstream package developers, the
> quickest workaround would be disable forking.  If you're conservative,
> you could even disable it all of your R processing.  Being able to
> quickly disable forking will also provide a mechanism for quickly
> testing the hypothesis that forking is the underlying problem, i.e.
> "Please retry with options(fork.allowed = FALSE)" will become
handy
> for troubleshooting.
> 
> /Henrik
> 
> On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> If I understand the thread correctly this is an RStudio issue and I
would suggest that the developers consider using pthread_atfork() so RStudio can
handle forking as they deem fit (bail out with an error or make RStudio work). 
Note that in principle the functionality requested here can be easily
implemented in a package so R doesn?t need to be modified.
>> 
>> Cheers,
>> Simon
>> 
>> Sent from my iPhone
>> 
>>>> On Jan 10, 2020, at 04:34, Tomas Kalibera <tomas.kalibera at
gmail.com> wrote:
>>>> 
>>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
>>>> I'd like to pick up this thread started on 2019-04-11
>>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
>>>> Modulo all the other suggestions in this thread, would my
proposal of
>>>> being able to disable forked processing via an option or an
>>>> environment variable make sense?
>>> 
>>> I don't think R should be doing that. There are caveats with
using fork, and they are mentioned in the documentation of the parallel package,
so people can easily avoid functions that use it, and this all has been
discussed here recently.
>>> 
>>> If it is the case, we can expand the documentation in parallel
package, add a warning against the use of forking with RStudio, but for that I
it would be good to know at least why it is not working. From the github issue I
have the impression that it is not really known why, whether it could be fixed,
and if so, where. The same github issue reflects also that some people want to
use forking for performance reasons, and even with RStudio, at least on Linux.
Perhaps it could be fixed? Perhaps it is just some race condition somewhere?
>>> 
>>> Tomas
>>> 
>>>> I've prototyped a working patch that
>>>> works like:
>>>>> options(fork.allowed = FALSE)
>>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
>>>> [1] 14058 14058
>>>>> parallel::mcmapply(1:2, FUN = function(x) Sys.getpid())
>>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
>>>> +++ src/library/parallel/R/unix/forkCluster.R (working copy)
>>>> @@ -30,6 +30,7 @@
>>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
>>>> {
>>>> +    allowFork(assert = TRUE)
>>>>    options <- addClusterOptions(options, list(...))
>>>>    outfile <- getClusterOption("outfile", options)
>>>>    port <- getClusterOption("port", options)
>>>> Index: src/library/parallel/R/unix/mclapply.R
>>>>
==================================================================>>>>
--- src/library/parallel/R/unix/mclapply.R (revision 77648)
>>>> +++ src/library/parallel/R/unix/mclapply.R (working copy)
>>>> @@ -28,7 +28,7 @@
>>>>        stop("'mc.cores' must be >= 1")
>>>>    .check_ncores(cores)
>>>> -    if (isChild() && !isTRUE(mc.allow.recursive))
>>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
>>>>        return(lapply(X = X, FUN = FUN, ...))
>>>>    ## Follow lapply
>>>> Index: src/library/parallel/R/unix/mcparallel.R
>>>>
==================================================================>>>>
--- src/library/parallel/R/unix/mcparallel.R (revision 77648)
>>>> +++ src/library/parallel/R/unix/mcparallel.R (working copy)
>>>> @@ -20,6 +20,7 @@
>>>> mcparallel <- function(expr, name, mc.set.seed = TRUE,
silent >>>> FALSE, mc.affinity = NULL, mc.interactive = FALSE,
detached = FALSE)
>>>> {
>>>> +    allowFork(assert = TRUE)
>>>>    f <- mcfork(detached)
>>>>    env <- parent.frame()
>>>>    if (isTRUE(mc.set.seed)) mc.advance.stream()
>>>> Index: src/library/parallel/R/unix/pvec.R
>>>>
==================================================================>>>>
--- src/library/parallel/R/unix/pvec.R (revision 77648)
>>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
>>>> @@ -25,7 +25,7 @@
>>>>    cores <- as.integer(mc.cores)
>>>>    if(cores < 1L) stop("'mc.cores' must be
>= 1")
>>>> -    if(cores == 1L) return(FUN(v, ...))
>>>> +    if(cores == 1L || !allowFork()) return(FUN(v, ...))
>>>>    .check_ncores(cores)
>>>>    if(mc.set.seed) mc.reset.stream()
>>>> with a new file src/library/parallel/R/unix/allowFork.R:
>>>> allowFork <- function(assert = FALSE) {
>>>>   value <- Sys.getenv("R_FORK_ALLOWED")
>>>>   if (nzchar(value)) {
>>>>       value <- switch(value,
>>>>          "1"=, "TRUE"=, "true"=,
"True"=, "yes"=, "Yes"= TRUE,
>>>>          "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
>>>>           stop(gettextf("invalid environment variable
value: %s==%s",
>>>>          "R_FORK_ALLOWED", value)))
>>>> value <- as.logical(value)
>>>>   } else {
>>>>       value <- TRUE
>>>>   }
>>>>   value <- getOption("fork.allowed", value)
>>>>   if (is.na(value)) {
>>>>       stop(gettextf("invalid option value: %s==%s",
"fork.allowed", value))
>>>>   }
>>>>   if (assert && !value) {
>>>>     stop(gettextf("Forked processing is not allowed per
option %s or
>>>> environment variable %s",
sQuote("fork.allowed"),
>>>> sQuote("R_FORK_ALLOWED")))
>>>>   }
>>>>   value
>>>> }
>>>> /Henrik
>>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
>>>>>> 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
>>>>>>>> overcommitment, and that this means that it may
work nicely or fail
>>>>>>>> spectacularly depending on whether, e.g., you
operate on a long
>>>>>>>> vector.
>>>>>>> R cannot possibly replicate documentation of the
underlying operating
>>>>>>> systems. It clearly says that fork() is used and
readers who may not
>>>>>>> know what fork() is need to learn it from external
sources.
>>>>>>> Copy-on-write is an elementary property of fork().
>>>>>> Just to be precise, copy-on-write is an optimization
widely deployed
>>>>>> in most modern *nixes, particularly for the
architectures in which R
>>>>>> usually runs. But it is not an elementary property; it
is not even
>>>>>> possible without an MMU.
>>>>> Yes, old Unix systems without virtual memory had fork
eagerly copying.
>>>>> Not relevant today, and certainly not for systems that run
R, but indeed
>>>>> people interested in OS internals can look elsewhere for
more precise
>>>>> information.
>>>>> Tomas
>>> 
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> Henrik,
>
> the example from the post works just fine in CRAN R for me - the post was
about homebrew build so it's conceivably a bug in their libraries.
I think it works now, because Apple switched to a different SSL
library for libcurl. It usually crashes or fails on older macOS
versions, with the CRAN build of R as well.

It is not a bug in any library, it is just that macOS does not support
fork() without an immediate exec().

In general, any code that calls the macOS system libraries might
crash. (Except for CoreFoundation, which seems to be fine, but AFAIR
there is no guarantee for that, either.)

You get crashes in the terminal as well, without multithreading. E.g.
the keyring package links for the Security library on macOS, so you
get:

? R --vanilla -q
> .libPaths("~/R/3.6")
> keyring::key_list()[1:2,]
        service                                                  username
1    CommCenter                             kEntitlementsUniqueIDCacheKey
2           ids                                  
identity-rsa-public-key
> parallel::mclapply(1:10, function(i) keyring::key_list()[1:2,])
 *** caught segfault ***
address 0x110, cause 'memory not mapped'

 *** caught segfault ***
address 0x110, cause 'memory not mapped'

AFAICT only Apple can do anything about this, and they won't.

Gabor
> That's exactly why I was proposing a more general solution where you
can simply define a function in user-space that will issue a warning or stop on
fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
>
> Cheers,
> Simon
>
>
>
> > On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson at
gmail.com> wrote:
> >
> > The RStudio GUI was just one example.  AFAIK, and please correct me if
> > I'm wrong, another example is where multi-threaded code is used in
> > forked processing and that's sometimes unstable.  Yes another,
which
> > might be multi-thread related or not, is
> > https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
> >
> > res <- parallel::mclapply(urls, function(url) {
> >  download.file(url, basename(url))
> > })
> >
> > That was reported to fail on macOS with the default
method="libcurl"
> > but not for method="curl" or method="wget".
> >
> > Further documentation is needed and would help but I don't believe
> > it's sufficient to solve everyday problems.  The argument for
> > introducing an option/env var to disable forking is to give the end
> > user a quick workaround for newly introduced bugs.  Neither the
> > develop nor the end user have full control of the R package stack,
> > which is always in flux.  For instance, above mclapply() code might
> > have been in a package on CRAN and then all of a sudden
> > method="libcurl" became the new default in base R.  The
above
> > mclapply() code is now buggy on macOS, and not necessarily caught by
> > CRAN checks.  The package developer might not notice this because they
> > are on Linux or Windows.  It can take a very long time before this
> > problem is even noticed and even further before it is tracked down and
> > fixed.   Similarly, as more and more code turn to native code and it
> > becomes easier and easier to implement multi-threading, more and more
> > of these bugs across package dependencies risk sneaking in the
> > backdoor wherever forked processing is in place.
> >
> > For the end user, but also higher-up upstream package developers, the
> > quickest workaround would be disable forking.  If you're
conservative,
> > you could even disable it all of your R processing.  Being able to
> > quickly disable forking will also provide a mechanism for quickly
> > testing the hypothesis that forking is the underlying problem, i.e.
> > "Please retry with options(fork.allowed = FALSE)" will
become handy
> > for troubleshooting.
> >
> > /Henrik
> >
> > On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
> > <simon.urbanek at r-project.org> wrote:
> >>
> >> If I understand the thread correctly this is an RStudio issue and
I would suggest that the developers consider using pthread_atfork() so RStudio
can handle forking as they deem fit (bail out with an error or make RStudio
work).  Note that in principle the functionality requested here can be easily
implemented in a package so R doesn?t need to be modified.
> >>
> >> Cheers,
> >> Simon
> >>
> >> Sent from my iPhone
> >>
> >>>> On Jan 10, 2020, at 04:34, Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>>
> >>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
> >>>> I'd like to pick up this thread started on 2019-04-11
> >>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
> >>>> Modulo all the other suggestions in this thread, would my
proposal of
> >>>> being able to disable forked processing via an option or
an
> >>>> environment variable make sense?
> >>>
> >>> I don't think R should be doing that. There are caveats
with using fork, and they are mentioned in the documentation of the parallel
package, so people can easily avoid functions that use it, and this all has been
discussed here recently.
> >>>
> >>> If it is the case, we can expand the documentation in parallel
package, add a warning against the use of forking with RStudio, but for that I
it would be good to know at least why it is not working. From the github issue I
have the impression that it is not really known why, whether it could be fixed,
and if so, where. The same github issue reflects also that some people want to
use forking for performance reasons, and even with RStudio, at least on Linux.
Perhaps it could be fixed? Perhaps it is just some race condition somewhere?
> >>>
> >>> Tomas
> >>>
> >>>> I've prototyped a working patch that
> >>>> works like:
> >>>>> options(fork.allowed = FALSE)
> >>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
> >>>> [1] 14058 14058
> >>>>> parallel::mcmapply(1:2, FUN = function(x)
Sys.getpid())
> >>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/forkCluster.R (working
copy)
> >>>> @@ -30,6 +30,7 @@
> >>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
> >>>> {
> >>>> +    allowFork(assert = TRUE)
> >>>>    options <- addClusterOptions(options, list(...))
> >>>>    outfile <- getClusterOption("outfile",
options)
> >>>>    port <- getClusterOption("port", options)
> >>>> Index: src/library/parallel/R/unix/mclapply.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/mclapply.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/mclapply.R (working copy)
> >>>> @@ -28,7 +28,7 @@
> >>>>        stop("'mc.cores' must be >=
1")
> >>>>    .check_ncores(cores)
> >>>> -    if (isChild() && !isTRUE(mc.allow.recursive))
> >>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
> >>>>        return(lapply(X = X, FUN = FUN, ...))
> >>>>    ## Follow lapply
> >>>> Index: src/library/parallel/R/unix/mcparallel.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/mcparallel.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/mcparallel.R (working
copy)
> >>>> @@ -20,6 +20,7 @@
> >>>> mcparallel <- function(expr, name, mc.set.seed = TRUE,
silent > >>>> FALSE, mc.affinity = NULL, mc.interactive = FALSE,
detached = FALSE)
> >>>> {
> >>>> +    allowFork(assert = TRUE)
> >>>>    f <- mcfork(detached)
> >>>>    env <- parent.frame()
> >>>>    if (isTRUE(mc.set.seed)) mc.advance.stream()
> >>>> Index: src/library/parallel/R/unix/pvec.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/pvec.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
> >>>> @@ -25,7 +25,7 @@
> >>>>    cores <- as.integer(mc.cores)
> >>>>    if(cores < 1L) stop("'mc.cores' must be
>= 1")
> >>>> -    if(cores == 1L) return(FUN(v, ...))
> >>>> +    if(cores == 1L || !allowFork()) return(FUN(v, ...))
> >>>>    .check_ncores(cores)
> >>>>    if(mc.set.seed) mc.reset.stream()
> >>>> with a new file src/library/parallel/R/unix/allowFork.R:
> >>>> allowFork <- function(assert = FALSE) {
> >>>>   value <- Sys.getenv("R_FORK_ALLOWED")
> >>>>   if (nzchar(value)) {
> >>>>       value <- switch(value,
> >>>>          "1"=, "TRUE"=,
"true"=, "True"=, "yes"=, "Yes"= TRUE,
> >>>>          "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
> >>>>           stop(gettextf("invalid environment variable
value: %s==%s",
> >>>>          "R_FORK_ALLOWED", value)))
> >>>> value <- as.logical(value)
> >>>>   } else {
> >>>>       value <- TRUE
> >>>>   }
> >>>>   value <- getOption("fork.allowed", value)
> >>>>   if (is.na(value)) {
> >>>>       stop(gettextf("invalid option value:
%s==%s", "fork.allowed", value))
> >>>>   }
> >>>>   if (assert && !value) {
> >>>>     stop(gettextf("Forked processing is not allowed
per option %s or
> >>>> environment variable %s",
sQuote("fork.allowed"),
> >>>> sQuote("R_FORK_ALLOWED")))
> >>>>   }
> >>>>   value
> >>>> }
> >>>> /Henrik
> >>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
> >>>>>> 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
> >>>>>>>> overcommitment, and that this means that
it may work nicely or fail
> >>>>>>>> spectacularly depending on whether, e.g.,
you operate on a long
> >>>>>>>> vector.
> >>>>>>> R cannot possibly replicate documentation of
the underlying operating
> >>>>>>> systems. It clearly says that fork() is used
and readers who may not
> >>>>>>> know what fork() is need to learn it from
external sources.
> >>>>>>> Copy-on-write is an elementary property of
fork().
> >>>>>> Just to be precise, copy-on-write is an
optimization widely deployed
> >>>>>> in most modern *nixes, particularly for the
architectures in which R
> >>>>>> usually runs. But it is not an elementary
property; it is not even
> >>>>>> possible without an MMU.
> >>>>> Yes, old Unix systems without virtual memory had fork
eagerly copying.
> >>>>> Not relevant today, and certainly not for systems that
run R, but indeed
> >>>>> people interested in OS internals can look elsewhere
for more precise
> >>>>> information.
> >>>>> Tomas
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

On Fri, Jan 10, 2020 at 11:23 AM Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> Henrik,
>
> the example from the post works just fine in CRAN R for me - the post was
about homebrew build so it's conceivably a bug in their libraries.
Thanks for ruling that example out.
> That's exactly why I was proposing a more general solution where you
can simply define a function in user-space that will issue a warning or stop on
fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
I think this is worth pursuing and will help improve and stabilize
things.  But issuing a warning or stop on fork will not allow end
users from running the pipeline, or am I missing something?

I'm trying to argue that this is still a real problem that users and
developers run into on a regular basis.  Since parallel::mclapply() is
such a common and readily available solution it is also a low hanging
fruit to make it possible to have those forking functions fall back to
sequential processing.  The only(*) way to achieve this fall back
right now is to run the same pipeline on MS Windows - I just think it
would be very useful to have the same fallback option available on
Unix and macOS.  Having this in base R could also serve as standard
for other parallel/forking packages/implementations who also wish to
have a fallback to sequential processing.

==> What would the disadvantages be to provide a mechanism/setting for
disabling forking in the parallel::mc*** API? <=
(*) One can also somewhat disable forking in 'parallel' by using
'cgroups' limiting the process to a single core (see also
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17641).  That will
handle code that uses mc.cores = parallel::detectCores(), which there
is a lot of.  I guess it will cause run-time error (on 'mc.cores' must
be >= 1) for code that uses the second most common used mc.cores
parallel::detectCores() - 1, which is unfortunately also very common.
I find the use of hardcoded detectCores() unfortunate but that is a
slightly different topic.  OTH, if there would a standardized option
in R for disabling all types of parallel processing by forcing a
single core, one could imagine other parallel APIs to implement
fallbacks to sequential processing as well. (I'm aware that not all
use cases of async processing is about parallelization, so it might
not apply everywhere).

Cheers,

Henrik
>
> Cheers,
> Simon
>
>
>
> > On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson at
gmail.com> wrote:
> >
> > The RStudio GUI was just one example.  AFAIK, and please correct me if
> > I'm wrong, another example is where multi-threaded code is used in
> > forked processing and that's sometimes unstable.  Yes another,
which
> > might be multi-thread related or not, is
> > https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
> >
> > res <- parallel::mclapply(urls, function(url) {
> >  download.file(url, basename(url))
> > })
> >
> > That was reported to fail on macOS with the default
method="libcurl"
> > but not for method="curl" or method="wget".
> >
> > Further documentation is needed and would help but I don't believe
> > it's sufficient to solve everyday problems.  The argument for
> > introducing an option/env var to disable forking is to give the end
> > user a quick workaround for newly introduced bugs.  Neither the
> > develop nor the end user have full control of the R package stack,
> > which is always in flux.  For instance, above mclapply() code might
> > have been in a package on CRAN and then all of a sudden
> > method="libcurl" became the new default in base R.  The
above
> > mclapply() code is now buggy on macOS, and not necessarily caught by
> > CRAN checks.  The package developer might not notice this because they
> > are on Linux or Windows.  It can take a very long time before this
> > problem is even noticed and even further before it is tracked down and
> > fixed.   Similarly, as more and more code turn to native code and it
> > becomes easier and easier to implement multi-threading, more and more
> > of these bugs across package dependencies risk sneaking in the
> > backdoor wherever forked processing is in place.
> >
> > For the end user, but also higher-up upstream package developers, the
> > quickest workaround would be disable forking.  If you're
conservative,
> > you could even disable it all of your R processing.  Being able to
> > quickly disable forking will also provide a mechanism for quickly
> > testing the hypothesis that forking is the underlying problem, i.e.
> > "Please retry with options(fork.allowed = FALSE)" will
become handy
> > for troubleshooting.
> >
> > /Henrik
> >
> > On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
> > <simon.urbanek at r-project.org> wrote:
> >>
> >> If I understand the thread correctly this is an RStudio issue and
I would suggest that the developers consider using pthread_atfork() so RStudio
can handle forking as they deem fit (bail out with an error or make RStudio
work).  Note that in principle the functionality requested here can be easily
implemented in a package so R doesn?t need to be modified.
> >>
> >> Cheers,
> >> Simon
> >>
> >> Sent from my iPhone
> >>
> >>>> On Jan 10, 2020, at 04:34, Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>>
> >>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
> >>>> I'd like to pick up this thread started on 2019-04-11
> >>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
> >>>> Modulo all the other suggestions in this thread, would my
proposal of
> >>>> being able to disable forked processing via an option or
an
> >>>> environment variable make sense?
> >>>
> >>> I don't think R should be doing that. There are caveats
with using fork, and they are mentioned in the documentation of the parallel
package, so people can easily avoid functions that use it, and this all has been
discussed here recently.
> >>>
> >>> If it is the case, we can expand the documentation in parallel
package, add a warning against the use of forking with RStudio, but for that I
it would be good to know at least why it is not working. From the github issue I
have the impression that it is not really known why, whether it could be fixed,
and if so, where. The same github issue reflects also that some people want to
use forking for performance reasons, and even with RStudio, at least on Linux.
Perhaps it could be fixed? Perhaps it is just some race condition somewhere?
> >>>
> >>> Tomas
> >>>
> >>>> I've prototyped a working patch that
> >>>> works like:
> >>>>> options(fork.allowed = FALSE)
> >>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
> >>>> [1] 14058 14058
> >>>>> parallel::mcmapply(1:2, FUN = function(x)
Sys.getpid())
> >>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/forkCluster.R (working
copy)
> >>>> @@ -30,6 +30,7 @@
> >>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
> >>>> {
> >>>> +    allowFork(assert = TRUE)
> >>>>    options <- addClusterOptions(options, list(...))
> >>>>    outfile <- getClusterOption("outfile",
options)
> >>>>    port <- getClusterOption("port", options)
> >>>> Index: src/library/parallel/R/unix/mclapply.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/mclapply.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/mclapply.R (working copy)
> >>>> @@ -28,7 +28,7 @@
> >>>>        stop("'mc.cores' must be >=
1")
> >>>>    .check_ncores(cores)
> >>>> -    if (isChild() && !isTRUE(mc.allow.recursive))
> >>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
> >>>>        return(lapply(X = X, FUN = FUN, ...))
> >>>>    ## Follow lapply
> >>>> Index: src/library/parallel/R/unix/mcparallel.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/mcparallel.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/mcparallel.R (working
copy)
> >>>> @@ -20,6 +20,7 @@
> >>>> mcparallel <- function(expr, name, mc.set.seed = TRUE,
silent > >>>> FALSE, mc.affinity = NULL, mc.interactive = FALSE,
detached = FALSE)
> >>>> {
> >>>> +    allowFork(assert = TRUE)
> >>>>    f <- mcfork(detached)
> >>>>    env <- parent.frame()
> >>>>    if (isTRUE(mc.set.seed)) mc.advance.stream()
> >>>> Index: src/library/parallel/R/unix/pvec.R
> >>>>
==================================================================>
>>>> --- src/library/parallel/R/unix/pvec.R (revision 77648)
> >>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
> >>>> @@ -25,7 +25,7 @@
> >>>>    cores <- as.integer(mc.cores)
> >>>>    if(cores < 1L) stop("'mc.cores' must be
>= 1")
> >>>> -    if(cores == 1L) return(FUN(v, ...))
> >>>> +    if(cores == 1L || !allowFork()) return(FUN(v, ...))
> >>>>    .check_ncores(cores)
> >>>>    if(mc.set.seed) mc.reset.stream()
> >>>> with a new file src/library/parallel/R/unix/allowFork.R:
> >>>> allowFork <- function(assert = FALSE) {
> >>>>   value <- Sys.getenv("R_FORK_ALLOWED")
> >>>>   if (nzchar(value)) {
> >>>>       value <- switch(value,
> >>>>          "1"=, "TRUE"=,
"true"=, "True"=, "yes"=, "Yes"= TRUE,
> >>>>          "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
> >>>>           stop(gettextf("invalid environment variable
value: %s==%s",
> >>>>          "R_FORK_ALLOWED", value)))
> >>>> value <- as.logical(value)
> >>>>   } else {
> >>>>       value <- TRUE
> >>>>   }
> >>>>   value <- getOption("fork.allowed", value)
> >>>>   if (is.na(value)) {
> >>>>       stop(gettextf("invalid option value:
%s==%s", "fork.allowed", value))
> >>>>   }
> >>>>   if (assert && !value) {
> >>>>     stop(gettextf("Forked processing is not allowed
per option %s or
> >>>> environment variable %s",
sQuote("fork.allowed"),
> >>>> sQuote("R_FORK_ALLOWED")))
> >>>>   }
> >>>>   value
> >>>> }
> >>>> /Henrik
> >>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
> >>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
> >>>>>> 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
> >>>>>>>> overcommitment, and that this means that
it may work nicely or fail
> >>>>>>>> spectacularly depending on whether, e.g.,
you operate on a long
> >>>>>>>> vector.
> >>>>>>> R cannot possibly replicate documentation of
the underlying operating
> >>>>>>> systems. It clearly says that fork() is used
and readers who may not
> >>>>>>> know what fork() is need to learn it from
external sources.
> >>>>>>> Copy-on-write is an elementary property of
fork().
> >>>>>> Just to be precise, copy-on-write is an
optimization widely deployed
> >>>>>> in most modern *nixes, particularly for the
architectures in which R
> >>>>>> usually runs. But it is not an elementary
property; it is not even
> >>>>>> possible without an MMU.
> >>>>> Yes, old Unix systems without virtual memory had fork
eagerly copying.
> >>>>> Not relevant today, and certainly not for systems that
run R, but indeed
> >>>>> people interested in OS internals can look elsewhere
for more precise
> >>>>> information.
> >>>>> Tomas
> >>>
> >>> ______________________________________________
> >>> R-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >> ______________________________________________
> >> R-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> Henrik,
>
> the example from the post works just fine in CRAN R for me - the post was
about homebrew build so it's conceivably a bug in their libraries.
That's exactly why I was proposing a more general solution where you can
simply define a function in user-space that will issue a warning or stop on
fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
Btw. what other packages do fork() without an exec() call()?

Gbaor
[...]

Henrik,

the whole point and only purpose of mc* functions is to fork. That's what
the multicore package was about, so if you don't want to fork, don't use
mc* functions - they don't have any other purpose. I really fail to see the
point - if you use mc* functions you're very explicitly asking for forking -
so your argument is like saying that print() should have an option to not print
anything - it just makes no sense. If you have code that is fork-incompatilble,
you clearly cannot use it in mcparallel - that's why there is a very
explicit warning in the documentation. As I said, if you have some software that
embeds R and has issue with forks, then that software should be use
pthread_atfork() to control the behavior.

Cheers,
Simon


> On Jan 10, 2020, at 3:34 PM, Henrik Bengtsson <henrik.bengtsson at
gmail.com> wrote:
> 
> On Fri, Jan 10, 2020 at 11:23 AM Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> Henrik,
>> 
>> the example from the post works just fine in CRAN R for me - the post
was about homebrew build so it's conceivably a bug in their libraries.
> 
> Thanks for ruling that example out.
> 
>> That's exactly why I was proposing a more general solution where
you can simply define a function in user-space that will issue a warning or stop
on fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
> 
> I think this is worth pursuing and will help improve and stabilize
> things.  But issuing a warning or stop on fork will not allow end
> users from running the pipeline, or am I missing something?
> 
> I'm trying to argue that this is still a real problem that users and
> developers run into on a regular basis.  Since parallel::mclapply() is
> such a common and readily available solution it is also a low hanging
> fruit to make it possible to have those forking functions fall back to
> sequential processing.  The only(*) way to achieve this fall back
> right now is to run the same pipeline on MS Windows - I just think it
> would be very useful to have the same fallback option available on
> Unix and macOS.  Having this in base R could also serve as standard
> for other parallel/forking packages/implementations who also wish to
> have a fallback to sequential processing.
> 
> ==> What would the disadvantages be to provide a mechanism/setting for
> disabling forking in the parallel::mc*** API? <=> 
> (*) One can also somewhat disable forking in 'parallel' by using
> 'cgroups' limiting the process to a single core (see also
> https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17641).  That will
> handle code that uses mc.cores = parallel::detectCores(), which there
> is a lot of.  I guess it will cause run-time error (on 'mc.cores'
must
> be >= 1) for code that uses the second most common used mc.cores >
parallel::detectCores() - 1, which is unfortunately also very common.
> I find the use of hardcoded detectCores() unfortunate but that is a
> slightly different topic.  OTH, if there would a standardized option
> in R for disabling all types of parallel processing by forcing a
> single core, one could imagine other parallel APIs to implement
> fallbacks to sequential processing as well. (I'm aware that not all
> use cases of async processing is about parallelization, so it might
> not apply everywhere).
> 
> Cheers,
> 
> Henrik
> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson
at gmail.com> wrote:
>>> 
>>> The RStudio GUI was just one example.  AFAIK, and please correct me
if
>>> I'm wrong, another example is where multi-threaded code is used
in
>>> forked processing and that's sometimes unstable.  Yes another,
which
>>> might be multi-thread related or not, is
>>> https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
>>> 
>>> res <- parallel::mclapply(urls, function(url) {
>>> download.file(url, basename(url))
>>> })
>>> 
>>> That was reported to fail on macOS with the default
method="libcurl"
>>> but not for method="curl" or method="wget".
>>> 
>>> Further documentation is needed and would help but I don't
believe
>>> it's sufficient to solve everyday problems.  The argument for
>>> introducing an option/env var to disable forking is to give the end
>>> user a quick workaround for newly introduced bugs.  Neither the
>>> develop nor the end user have full control of the R package stack,
>>> which is always in flux.  For instance, above mclapply() code might
>>> have been in a package on CRAN and then all of a sudden
>>> method="libcurl" became the new default in base R.  The
above
>>> mclapply() code is now buggy on macOS, and not necessarily caught
by
>>> CRAN checks.  The package developer might not notice this because
they
>>> are on Linux or Windows.  It can take a very long time before this
>>> problem is even noticed and even further before it is tracked down
and
>>> fixed.   Similarly, as more and more code turn to native code and
it
>>> becomes easier and easier to implement multi-threading, more and
more
>>> of these bugs across package dependencies risk sneaking in the
>>> backdoor wherever forked processing is in place.
>>> 
>>> For the end user, but also higher-up upstream package developers,
the
>>> quickest workaround would be disable forking.  If you're
conservative,
>>> you could even disable it all of your R processing.  Being able to
>>> quickly disable forking will also provide a mechanism for quickly
>>> testing the hypothesis that forking is the underlying problem, i.e.
>>> "Please retry with options(fork.allowed = FALSE)" will
become handy
>>> for troubleshooting.
>>> 
>>> /Henrik
>>> 
>>> On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
>>> <simon.urbanek at r-project.org> wrote:
>>>> 
>>>> If I understand the thread correctly this is an RStudio issue
and I would suggest that the developers consider using pthread_atfork() so
RStudio can handle forking as they deem fit (bail out with an error or make
RStudio work).  Note that in principle the functionality requested here can be
easily implemented in a package so R doesn?t need to be modified.
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>>>> On Jan 10, 2020, at 04:34, Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>> 
>>>>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
>>>>>> I'd like to pick up this thread started on
2019-04-11
>>>>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
>>>>>> Modulo all the other suggestions in this thread, would
my proposal of
>>>>>> being able to disable forked processing via an option
or an
>>>>>> environment variable make sense?
>>>>> 
>>>>> I don't think R should be doing that. There are caveats
with using fork, and they are mentioned in the documentation of the parallel
package, so people can easily avoid functions that use it, and this all has been
discussed here recently.
>>>>> 
>>>>> If it is the case, we can expand the documentation in
parallel package, add a warning against the use of forking with RStudio, but for
that I it would be good to know at least why it is not working. From the github
issue I have the impression that it is not really known why, whether it could be
fixed, and if so, where. The same github issue reflects also that some people
want to use forking for performance reasons, and even with RStudio, at least on
Linux. Perhaps it could be fixed? Perhaps it is just some race condition
somewhere?
>>>>> 
>>>>> Tomas
>>>>> 
>>>>>> I've prototyped a working patch that
>>>>>> works like:
>>>>>>> options(fork.allowed = FALSE)
>>>>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
>>>>>> [1] 14058 14058
>>>>>>> parallel::mcmapply(1:2, FUN = function(x)
Sys.getpid())
>>>>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/forkCluster.R (working
copy)
>>>>>> @@ -30,6 +30,7 @@
>>>>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   options <- addClusterOptions(options, list(...))
>>>>>>   outfile <- getClusterOption("outfile",
options)
>>>>>>   port <- getClusterOption("port",
options)
>>>>>> Index: src/library/parallel/R/unix/mclapply.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mclapply.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mclapply.R (working
copy)
>>>>>> @@ -28,7 +28,7 @@
>>>>>>       stop("'mc.cores' must be >=
1")
>>>>>>   .check_ncores(cores)
>>>>>> -    if (isChild() &&
!isTRUE(mc.allow.recursive))
>>>>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
>>>>>>       return(lapply(X = X, FUN = FUN, ...))
>>>>>>   ## Follow lapply
>>>>>> Index: src/library/parallel/R/unix/mcparallel.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mcparallel.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mcparallel.R (working
copy)
>>>>>> @@ -20,6 +20,7 @@
>>>>>> mcparallel <- function(expr, name, mc.set.seed =
TRUE, silent >>>>>> FALSE, mc.affinity = NULL, mc.interactive
= FALSE, detached = FALSE)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   f <- mcfork(detached)
>>>>>>   env <- parent.frame()
>>>>>>   if (isTRUE(mc.set.seed)) mc.advance.stream()
>>>>>> Index: src/library/parallel/R/unix/pvec.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/pvec.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
>>>>>> @@ -25,7 +25,7 @@
>>>>>>   cores <- as.integer(mc.cores)
>>>>>>   if(cores < 1L) stop("'mc.cores' must
be >= 1")
>>>>>> -    if(cores == 1L) return(FUN(v, ...))
>>>>>> +    if(cores == 1L || !allowFork()) return(FUN(v,
...))
>>>>>>   .check_ncores(cores)
>>>>>>   if(mc.set.seed) mc.reset.stream()
>>>>>> with a new file
src/library/parallel/R/unix/allowFork.R:
>>>>>> allowFork <- function(assert = FALSE) {
>>>>>>  value <- Sys.getenv("R_FORK_ALLOWED")
>>>>>>  if (nzchar(value)) {
>>>>>>      value <- switch(value,
>>>>>>         "1"=, "TRUE"=,
"true"=, "True"=, "yes"=, "Yes"= TRUE,
>>>>>>         "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
>>>>>>          stop(gettextf("invalid environment
variable value: %s==%s",
>>>>>>         "R_FORK_ALLOWED", value)))
>>>>>> value <- as.logical(value)
>>>>>>  } else {
>>>>>>      value <- TRUE
>>>>>>  }
>>>>>>  value <- getOption("fork.allowed", value)
>>>>>>  if (is.na(value)) {
>>>>>>      stop(gettextf("invalid option value:
%s==%s", "fork.allowed", value))
>>>>>>  }
>>>>>>  if (assert && !value) {
>>>>>>    stop(gettextf("Forked processing is not allowed
per option %s or
>>>>>> environment variable %s",
sQuote("fork.allowed"),
>>>>>> sQuote("R_FORK_ALLOWED")))
>>>>>>  }
>>>>>>  value
>>>>>> }
>>>>>> /Henrik
>>>>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
>>>>>>>> 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
>>>>>>>>>> overcommitment, and that this means
that it may work nicely or fail
>>>>>>>>>> spectacularly depending on whether,
e.g., you operate on a long
>>>>>>>>>> vector.
>>>>>>>>> R cannot possibly replicate documentation
of the underlying operating
>>>>>>>>> systems. It clearly says that fork() is
used and readers who may not
>>>>>>>>> know what fork() is need to learn it from
external sources.
>>>>>>>>> Copy-on-write is an elementary property of
fork().
>>>>>>>> Just to be precise, copy-on-write is an
optimization widely deployed
>>>>>>>> in most modern *nixes, particularly for the
architectures in which R
>>>>>>>> usually runs. But it is not an elementary
property; it is not even
>>>>>>>> possible without an MMU.
>>>>>>> Yes, old Unix systems without virtual memory had
fork eagerly copying.
>>>>>>> Not relevant today, and certainly not for systems
that run R, but indeed
>>>>>>> people interested in OS internals can look
elsewhere for more precise
>>>>>>> information.
>>>>>>> Tomas
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

> On Jan 10, 2020, at 3:10 PM, G?bor Cs?rdi <csardi.gabor at gmail.com>
wrote:
> 
> On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> Henrik,
>> 
>> the example from the post works just fine in CRAN R for me - the post
was about homebrew build so it's conceivably a bug in their libraries.
> 
> I think it works now, because Apple switched to a different SSL
> library for libcurl. It usually crashes or fails on older macOS
> versions, with the CRAN build of R as well.
> 
That is not true - Apple has not changed the SSL back-end for many years. The
issue in that post is presumably in the homebrew version of SSL.

Cheers,
Simon

> It is not a bug in any library, it is just that macOS does not support
> fork() without an immediate exec().
> 
> In general, any code that calls the macOS system libraries might
> crash. (Except for CoreFoundation, which seems to be fine, but AFAIR
> there is no guarantee for that, either.)
> 
> You get crashes in the terminal as well, without multithreading. E.g.
> the keyring package links for the Security library on macOS, so you
> get:
> 
> ? R --vanilla -q
>> .libPaths("~/R/3.6")
>> keyring::key_list()[1:2,]
>        service                                                  username
> 1    CommCenter                             kEntitlementsUniqueIDCacheKey
> 2           ids                                   identity-rsa-public-key
>> parallel::mclapply(1:10, function(i) keyring::key_list()[1:2,])
> 
> *** caught segfault ***
> address 0x110, cause 'memory not mapped'
> 
> *** caught segfault ***
> address 0x110, cause 'memory not mapped'
> 
> AFAICT only Apple can do anything about this, and they won't.
> 
> Gabor
> 
>> That's exactly why I was proposing a more general solution where
you can simply define a function in user-space that will issue a warning or stop
on fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson
at gmail.com> wrote:
>>> 
>>> The RStudio GUI was just one example.  AFAIK, and please correct me
if
>>> I'm wrong, another example is where multi-threaded code is used
in
>>> forked processing and that's sometimes unstable.  Yes another,
which
>>> might be multi-thread related or not, is
>>> https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
>>> 
>>> res <- parallel::mclapply(urls, function(url) {
>>> download.file(url, basename(url))
>>> })
>>> 
>>> That was reported to fail on macOS with the default
method="libcurl"
>>> but not for method="curl" or method="wget".
>>> 
>>> Further documentation is needed and would help but I don't
believe
>>> it's sufficient to solve everyday problems.  The argument for
>>> introducing an option/env var to disable forking is to give the end
>>> user a quick workaround for newly introduced bugs.  Neither the
>>> develop nor the end user have full control of the R package stack,
>>> which is always in flux.  For instance, above mclapply() code might
>>> have been in a package on CRAN and then all of a sudden
>>> method="libcurl" became the new default in base R.  The
above
>>> mclapply() code is now buggy on macOS, and not necessarily caught
by
>>> CRAN checks.  The package developer might not notice this because
they
>>> are on Linux or Windows.  It can take a very long time before this
>>> problem is even noticed and even further before it is tracked down
and
>>> fixed.   Similarly, as more and more code turn to native code and
it
>>> becomes easier and easier to implement multi-threading, more and
more
>>> of these bugs across package dependencies risk sneaking in the
>>> backdoor wherever forked processing is in place.
>>> 
>>> For the end user, but also higher-up upstream package developers,
the
>>> quickest workaround would be disable forking.  If you're
conservative,
>>> you could even disable it all of your R processing.  Being able to
>>> quickly disable forking will also provide a mechanism for quickly
>>> testing the hypothesis that forking is the underlying problem, i.e.
>>> "Please retry with options(fork.allowed = FALSE)" will
become handy
>>> for troubleshooting.
>>> 
>>> /Henrik
>>> 
>>> On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
>>> <simon.urbanek at r-project.org> wrote:
>>>> 
>>>> If I understand the thread correctly this is an RStudio issue
and I would suggest that the developers consider using pthread_atfork() so
RStudio can handle forking as they deem fit (bail out with an error or make
RStudio work).  Note that in principle the functionality requested here can be
easily implemented in a package so R doesn?t need to be modified.
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>>>> On Jan 10, 2020, at 04:34, Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>> 
>>>>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
>>>>>> I'd like to pick up this thread started on
2019-04-11
>>>>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
>>>>>> Modulo all the other suggestions in this thread, would
my proposal of
>>>>>> being able to disable forked processing via an option
or an
>>>>>> environment variable make sense?
>>>>> 
>>>>> I don't think R should be doing that. There are caveats
with using fork, and they are mentioned in the documentation of the parallel
package, so people can easily avoid functions that use it, and this all has been
discussed here recently.
>>>>> 
>>>>> If it is the case, we can expand the documentation in
parallel package, add a warning against the use of forking with RStudio, but for
that I it would be good to know at least why it is not working. From the github
issue I have the impression that it is not really known why, whether it could be
fixed, and if so, where. The same github issue reflects also that some people
want to use forking for performance reasons, and even with RStudio, at least on
Linux. Perhaps it could be fixed? Perhaps it is just some race condition
somewhere?
>>>>> 
>>>>> Tomas
>>>>> 
>>>>>> I've prototyped a working patch that
>>>>>> works like:
>>>>>>> options(fork.allowed = FALSE)
>>>>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
>>>>>> [1] 14058 14058
>>>>>>> parallel::mcmapply(1:2, FUN = function(x)
Sys.getpid())
>>>>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/forkCluster.R (working
copy)
>>>>>> @@ -30,6 +30,7 @@
>>>>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   options <- addClusterOptions(options, list(...))
>>>>>>   outfile <- getClusterOption("outfile",
options)
>>>>>>   port <- getClusterOption("port",
options)
>>>>>> Index: src/library/parallel/R/unix/mclapply.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mclapply.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mclapply.R (working
copy)
>>>>>> @@ -28,7 +28,7 @@
>>>>>>       stop("'mc.cores' must be >=
1")
>>>>>>   .check_ncores(cores)
>>>>>> -    if (isChild() &&
!isTRUE(mc.allow.recursive))
>>>>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
>>>>>>       return(lapply(X = X, FUN = FUN, ...))
>>>>>>   ## Follow lapply
>>>>>> Index: src/library/parallel/R/unix/mcparallel.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mcparallel.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mcparallel.R (working
copy)
>>>>>> @@ -20,6 +20,7 @@
>>>>>> mcparallel <- function(expr, name, mc.set.seed =
TRUE, silent >>>>>> FALSE, mc.affinity = NULL, mc.interactive
= FALSE, detached = FALSE)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   f <- mcfork(detached)
>>>>>>   env <- parent.frame()
>>>>>>   if (isTRUE(mc.set.seed)) mc.advance.stream()
>>>>>> Index: src/library/parallel/R/unix/pvec.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/pvec.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
>>>>>> @@ -25,7 +25,7 @@
>>>>>>   cores <- as.integer(mc.cores)
>>>>>>   if(cores < 1L) stop("'mc.cores' must
be >= 1")
>>>>>> -    if(cores == 1L) return(FUN(v, ...))
>>>>>> +    if(cores == 1L || !allowFork()) return(FUN(v,
...))
>>>>>>   .check_ncores(cores)
>>>>>>   if(mc.set.seed) mc.reset.stream()
>>>>>> with a new file
src/library/parallel/R/unix/allowFork.R:
>>>>>> allowFork <- function(assert = FALSE) {
>>>>>>  value <- Sys.getenv("R_FORK_ALLOWED")
>>>>>>  if (nzchar(value)) {
>>>>>>      value <- switch(value,
>>>>>>         "1"=, "TRUE"=,
"true"=, "True"=, "yes"=, "Yes"= TRUE,
>>>>>>         "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
>>>>>>          stop(gettextf("invalid environment
variable value: %s==%s",
>>>>>>         "R_FORK_ALLOWED", value)))
>>>>>> value <- as.logical(value)
>>>>>>  } else {
>>>>>>      value <- TRUE
>>>>>>  }
>>>>>>  value <- getOption("fork.allowed", value)
>>>>>>  if (is.na(value)) {
>>>>>>      stop(gettextf("invalid option value:
%s==%s", "fork.allowed", value))
>>>>>>  }
>>>>>>  if (assert && !value) {
>>>>>>    stop(gettextf("Forked processing is not allowed
per option %s or
>>>>>> environment variable %s",
sQuote("fork.allowed"),
>>>>>> sQuote("R_FORK_ALLOWED")))
>>>>>>  }
>>>>>>  value
>>>>>> }
>>>>>> /Henrik
>>>>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
>>>>>>>> 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
>>>>>>>>>> overcommitment, and that this means
that it may work nicely or fail
>>>>>>>>>> spectacularly depending on whether,
e.g., you operate on a long
>>>>>>>>>> vector.
>>>>>>>>> R cannot possibly replicate documentation
of the underlying operating
>>>>>>>>> systems. It clearly says that fork() is
used and readers who may not
>>>>>>>>> know what fork() is need to learn it from
external sources.
>>>>>>>>> Copy-on-write is an elementary property of
fork().
>>>>>>>> Just to be precise, copy-on-write is an
optimization widely deployed
>>>>>>>> in most modern *nixes, particularly for the
architectures in which R
>>>>>>>> usually runs. But it is not an elementary
property; it is not even
>>>>>>>> possible without an MMU.
>>>>>>> Yes, old Unix systems without virtual memory had
fork eagerly copying.
>>>>>>> Not relevant today, and certainly not for systems
that run R, but indeed
>>>>>>> people interested in OS internals can look
elsewhere for more precise
>>>>>>> information.
>>>>>>> Tomas
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>

> On Jan 10, 2020, at 3:10 PM, G?bor Cs?rdi <csardi.gabor at gmail.com>
wrote:
> 
> On Fri, Jan 10, 2020 at 7:23 PM Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> Henrik,
>> 
>> the example from the post works just fine in CRAN R for me - the post
was about homebrew build so it's conceivably a bug in their libraries.
> 
> I think it works now, because Apple switched to a different SSL
> library for libcurl. It usually crashes or fails on older macOS
> versions, with the CRAN build of R as well.
> 
> It is not a bug in any library, it is just that macOS does not support
> fork() without an immediate exec().
> 
> In general, any code that calls the macOS system libraries might
> crash. (Except for CoreFoundation, which seems to be fine, but AFAIR
> there is no guarantee for that, either.)
> 
That is not true, either. macOS itself is fork-safe (it is POSIX-certified after
all), but libraries may or may not. The rules are pretty clear - fork() shares
open descriptors and only inherits the main thread (see the POSIX documentation
for pthread_atfork() - it illustrates the issues nicely). So as a user of APIs
it may be your responsibility to make sure things are handled properly - again,
that's what pthread_atfork() is for. Most libraries don't allow
duplicated fds or have rules about thread safety, so it is your responsibility
in the package to abide by those rules if you want it to function after forking.
Some libraries don't allow forking at all, e.g., JVMs cannot be forked
(because they are too complex to make them fork-safe). In general, you cannot
assume that (non-R) code is fork-safe unless it has been designed to be.
That's why mcparallel() should only be used for pure R code (and even that
is with I/O limitations) and C code that is explicitly fork-safe. As I said,
using mc* functions explicitly says that you are ok with forking, so you if you
run code that is not fork-safe it is clearly a user error.

That's exactly why we have the long "Warning" section in the
documentation. If you have suggestions for its improvements, please feel free to
supply patches.

Cheers,
Simon

> You get crashes in the terminal as well, without multithreading. E.g.
> the keyring package links for the Security library on macOS, so you
> get:
> 
> ? R --vanilla -q
>> .libPaths("~/R/3.6")
>> keyring::key_list()[1:2,]
>        service                                                  username
> 1    CommCenter                             kEntitlementsUniqueIDCacheKey
> 2           ids                                   identity-rsa-public-key
>> parallel::mclapply(1:10, function(i) keyring::key_list()[1:2,])
> 
> *** caught segfault ***
> address 0x110, cause 'memory not mapped'
> 
> *** caught segfault ***
> address 0x110, cause 'memory not mapped'
> 
> AFAICT only Apple can do anything about this, and they won't.
> 
> Gabor
> 
>> That's exactly why I was proposing a more general solution where
you can simply define a function in user-space that will issue a warning or stop
on fork, it doesn't have to be part of core R, there are other packages that
use fork() as well, so what I proposed is much safer than hacking the parallel
package.
>> 
>> Cheers,
>> Simon
>> 
>> 
>> 
>>> On Jan 10, 2020, at 10:58 AM, Henrik Bengtsson <henrik.bengtsson
at gmail.com> wrote:
>>> 
>>> The RStudio GUI was just one example.  AFAIK, and please correct me
if
>>> I'm wrong, another example is where multi-threaded code is used
in
>>> forked processing and that's sometimes unstable.  Yes another,
which
>>> might be multi-thread related or not, is
>>> https://stat.ethz.ch/pipermail/r-devel/2018-September/076845.html:
>>> 
>>> res <- parallel::mclapply(urls, function(url) {
>>> download.file(url, basename(url))
>>> })
>>> 
>>> That was reported to fail on macOS with the default
method="libcurl"
>>> but not for method="curl" or method="wget".
>>> 
>>> Further documentation is needed and would help but I don't
believe
>>> it's sufficient to solve everyday problems.  The argument for
>>> introducing an option/env var to disable forking is to give the end
>>> user a quick workaround for newly introduced bugs.  Neither the
>>> develop nor the end user have full control of the R package stack,
>>> which is always in flux.  For instance, above mclapply() code might
>>> have been in a package on CRAN and then all of a sudden
>>> method="libcurl" became the new default in base R.  The
above
>>> mclapply() code is now buggy on macOS, and not necessarily caught
by
>>> CRAN checks.  The package developer might not notice this because
they
>>> are on Linux or Windows.  It can take a very long time before this
>>> problem is even noticed and even further before it is tracked down
and
>>> fixed.   Similarly, as more and more code turn to native code and
it
>>> becomes easier and easier to implement multi-threading, more and
more
>>> of these bugs across package dependencies risk sneaking in the
>>> backdoor wherever forked processing is in place.
>>> 
>>> For the end user, but also higher-up upstream package developers,
the
>>> quickest workaround would be disable forking.  If you're
conservative,
>>> you could even disable it all of your R processing.  Being able to
>>> quickly disable forking will also provide a mechanism for quickly
>>> testing the hypothesis that forking is the underlying problem, i.e.
>>> "Please retry with options(fork.allowed = FALSE)" will
become handy
>>> for troubleshooting.
>>> 
>>> /Henrik
>>> 
>>> On Fri, Jan 10, 2020 at 5:31 AM Simon Urbanek
>>> <simon.urbanek at r-project.org> wrote:
>>>> 
>>>> If I understand the thread correctly this is an RStudio issue
and I would suggest that the developers consider using pthread_atfork() so
RStudio can handle forking as they deem fit (bail out with an error or make
RStudio work).  Note that in principle the functionality requested here can be
easily implemented in a package so R doesn?t need to be modified.
>>>> 
>>>> Cheers,
>>>> Simon
>>>> 
>>>> Sent from my iPhone
>>>> 
>>>>>> On Jan 10, 2020, at 04:34, Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>> 
>>>>>> ?On 1/10/20 7:33 AM, Henrik Bengtsson wrote:
>>>>>> I'd like to pick up this thread started on
2019-04-11
>>>>>>
(https://hypatia.math.ethz.ch/pipermail/r-devel/2019-April/077632.html).
>>>>>> Modulo all the other suggestions in this thread, would
my proposal of
>>>>>> being able to disable forked processing via an option
or an
>>>>>> environment variable make sense?
>>>>> 
>>>>> I don't think R should be doing that. There are caveats
with using fork, and they are mentioned in the documentation of the parallel
package, so people can easily avoid functions that use it, and this all has been
discussed here recently.
>>>>> 
>>>>> If it is the case, we can expand the documentation in
parallel package, add a warning against the use of forking with RStudio, but for
that I it would be good to know at least why it is not working. From the github
issue I have the impression that it is not really known why, whether it could be
fixed, and if so, where. The same github issue reflects also that some people
want to use forking for performance reasons, and even with RStudio, at least on
Linux. Perhaps it could be fixed? Perhaps it is just some race condition
somewhere?
>>>>> 
>>>>> Tomas
>>>>> 
>>>>>> I've prototyped a working patch that
>>>>>> works like:
>>>>>>> options(fork.allowed = FALSE)
>>>>>>> unlist(parallel::mclapply(1:2, FUN = function(x)
Sys.getpid()))
>>>>>> [1] 14058 14058
>>>>>>> parallel::mcmapply(1:2, FUN = function(x)
Sys.getpid())
>>>>>> [1] 14058 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/parallel/R/unix/forkCluster.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/forkCluster.R (working
copy)
>>>>>> @@ -30,6 +30,7 @@
>>>>>> newForkNode <- function(..., options =
defaultClusterOptions, rank)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   options <- addClusterOptions(options, list(...))
>>>>>>   outfile <- getClusterOption("outfile",
options)
>>>>>>   port <- getClusterOption("port",
options)
>>>>>> Index: src/library/parallel/R/unix/mclapply.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mclapply.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mclapply.R (working
copy)
>>>>>> @@ -28,7 +28,7 @@
>>>>>>       stop("'mc.cores' must be >=
1")
>>>>>>   .check_ncores(cores)
>>>>>> -    if (isChild() &&
!isTRUE(mc.allow.recursive))
>>>>>> +    if (!allowFork() || (isChild() &&
!isTRUE(mc.allow.recursive)))
>>>>>>       return(lapply(X = X, FUN = FUN, ...))
>>>>>>   ## Follow lapply
>>>>>> Index: src/library/parallel/R/unix/mcparallel.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/mcparallel.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/mcparallel.R (working
copy)
>>>>>> @@ -20,6 +20,7 @@
>>>>>> mcparallel <- function(expr, name, mc.set.seed =
TRUE, silent >>>>>> FALSE, mc.affinity = NULL, mc.interactive
= FALSE, detached = FALSE)
>>>>>> {
>>>>>> +    allowFork(assert = TRUE)
>>>>>>   f <- mcfork(detached)
>>>>>>   env <- parent.frame()
>>>>>>   if (isTRUE(mc.set.seed)) mc.advance.stream()
>>>>>> Index: src/library/parallel/R/unix/pvec.R
>>>>>>
==================================================================>>>>>>
--- src/library/parallel/R/unix/pvec.R (revision 77648)
>>>>>> +++ src/library/parallel/R/unix/pvec.R (working copy)
>>>>>> @@ -25,7 +25,7 @@
>>>>>>   cores <- as.integer(mc.cores)
>>>>>>   if(cores < 1L) stop("'mc.cores' must
be >= 1")
>>>>>> -    if(cores == 1L) return(FUN(v, ...))
>>>>>> +    if(cores == 1L || !allowFork()) return(FUN(v,
...))
>>>>>>   .check_ncores(cores)
>>>>>>   if(mc.set.seed) mc.reset.stream()
>>>>>> with a new file
src/library/parallel/R/unix/allowFork.R:
>>>>>> allowFork <- function(assert = FALSE) {
>>>>>>  value <- Sys.getenv("R_FORK_ALLOWED")
>>>>>>  if (nzchar(value)) {
>>>>>>      value <- switch(value,
>>>>>>         "1"=, "TRUE"=,
"true"=, "True"=, "yes"=, "Yes"= TRUE,
>>>>>>         "0"=,
"FALSE"=,"false"=,"False"=, "no"=,
"No" = FALSE,
>>>>>>          stop(gettextf("invalid environment
variable value: %s==%s",
>>>>>>         "R_FORK_ALLOWED", value)))
>>>>>> value <- as.logical(value)
>>>>>>  } else {
>>>>>>      value <- TRUE
>>>>>>  }
>>>>>>  value <- getOption("fork.allowed", value)
>>>>>>  if (is.na(value)) {
>>>>>>      stop(gettextf("invalid option value:
%s==%s", "fork.allowed", value))
>>>>>>  }
>>>>>>  if (assert && !value) {
>>>>>>    stop(gettextf("Forked processing is not allowed
per option %s or
>>>>>> environment variable %s",
sQuote("fork.allowed"),
>>>>>> sQuote("R_FORK_ALLOWED")))
>>>>>>  }
>>>>>>  value
>>>>>> }
>>>>>> /Henrik
>>>>>>> On Mon, Apr 15, 2019 at 3:12 AM Tomas Kalibera
<tomas.kalibera at gmail.com> wrote:
>>>>>>> On 4/15/19 11:02 AM, I?aki Ucar wrote:
>>>>>>>> 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
>>>>>>>>>> overcommitment, and that this means
that it may work nicely or fail
>>>>>>>>>> spectacularly depending on whether,
e.g., you operate on a long
>>>>>>>>>> vector.
>>>>>>>>> R cannot possibly replicate documentation
of the underlying operating
>>>>>>>>> systems. It clearly says that fork() is
used and readers who may not
>>>>>>>>> know what fork() is need to learn it from
external sources.
>>>>>>>>> Copy-on-write is an elementary property of
fork().
>>>>>>>> Just to be precise, copy-on-write is an
optimization widely deployed
>>>>>>>> in most modern *nixes, particularly for the
architectures in which R
>>>>>>>> usually runs. But it is not an elementary
property; it is not even
>>>>>>>> possible without an MMU.
>>>>>>> Yes, old Unix systems without virtual memory had
fork eagerly copying.
>>>>>>> Not relevant today, and certainly not for systems
that run R, but indeed
>>>>>>> people interested in OS internals can look
elsewhere for more precise
>>>>>>> information.
>>>>>>> Tomas
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> 
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>