R help - May 2023 - mclapply enters into an infinite loop....

Dear Jeff,
                There was a problem in LYGH and lapply threw an error, but
mclapply got stuck in an infinite loop. The doc for mclapply says that mclapply
runs under try() with silent = TRUE. So that means mclapply should run properly,
i.e output a try class object and exit. But it didn't. Can you shed some
light on why this happened?

THanking you,
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: R-help <r-help-bounces at r-project.org> on behalf of Jeff Newmiller
<jdnewmil at dcn.davis.ca.us>
Sent: Wednesday, May 17, 2023 5:24 AM
To: r-help at r-project.org <r-help at r-project.org>
Subject: Re: [R] mclapply enters into an infinite loop....

It does not look to me like you are providing the necessary arguments to arfima.

Try making this work with lapply first... then try mclapply.

On May 16, 2023 3:10:45 PM PDT, akshay kulkarni <akshay_e4 at hotmail.com>
wrote:
>Dear members,
>                         I am using arfima in an mclapply construction (from
the parallel package):
>
>Browse[2]> LYG <- mclapply(LYGH, FUN = arfima, mc.cores =
detectCores())
>^C
>Browse[2]> LYG <- mclapply(LYGH[1:10], FUN = arfima, mc.cores =
detectCores())
>^C
>Browse[2]> LYG <- mclapply(LYGH[1:2], FUN = arfima, mc.cores =
detectCores())
>^C
>
>You can see that I am aborting the execution of mclapply. It doesn't
finish even if I reduce the elements to be iterated over to 2. Why is it
entering an infinite loop?
>
>Please exhort me if this is to be posted in HPC list.
>
>THanking you,
>Yours sincerely,
>ALSHAY M KULKARNI
>
>       [[alternative HTML version deleted]]
>
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>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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--
Sent from my phone. Please excuse my brevity.

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

	[[alternative HTML version deleted]]

On Wed, 17 May 2023 13:55:59 +0000
akshay kulkarni <akshay_e4 at hotmail.com> wrote:
> So that means mclapply should run properly, i.e output a try class
> object and exit. But it didn't. Can you shed some light on why this
> happened?
What's your sessionInfo()? Are you using a GUI frontend?

mclapply() relies on the fork() system call, which is tricky to get
right in a process where other threads may exist at the same time: when
a process calls fork(), the child process ends up with the same
contents of virtual memory but no other threads at all. If a thread was
holding a lock when the process was forked, the lock will never be
released in the child process, leaving it stuck. Depending on how
you're running R, it may be threading issues or something else.

More information may be obtained by looking at traceback() after you
interrupt mclapply() (easy, but low information: did you interrupt
selectChildren() or some other function?) and attaching a C debugger to
the child process when you become sure it's stuck (hard, requires
additional preparation such as installing debugging symbols).

-- 
Best regards,
Ivan