From @|mon@urb@nek @end|ng |rom R-project@org  Sat Jan 11 05:14:07 2020
From: @|mon@urb@nek @end|ng |rom R-project@org (Simon Urbanek)
Date: Fri, 10 Jan 2020 23:14:07 -0500
Subject: [Rd] SUGGESTION: Settings to disable forked processing in R,
 e.g. parallel::mclapply()
In-Reply-To: <CABtg=Km4GdMC5vGOs0PqvOjqABqcrhOZOqPv=81DuoX75zm8HQ@mail.gmail.com>
References: <84d162f5-dd0d-64e6-e9bf-54b65a10faa6@gmail.com>
 <DCF5422D-5237-48C1-BE51-486CA3C1DD60@r-project.org>
 <CAFDcVCS0RwA0-64FTY6kiOk6=yxy8w4OweVbESa-3G6JHtV6Xg@mail.gmail.com>
 <6D7F010F-60B4-4C51-99B3-D8B51BE7572A@R-project.org>
 <CABtg=Km4GdMC5vGOs0PqvOjqABqcrhOZOqPv=81DuoX75zm8HQ@mail.gmail.com>
Message-ID: <606FA782-721B-443A-9399-9B6CE8AF47DD@R-project.org>



> 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
> 



[Rd] SUGGESTION: Settings to disable forked processing in R, e.g. parallel::mclapply()
Simon Urbanek