[Bioc-devel] [Untrusted Server] Rprintf in a multi-threaded environment

[Shian Su]

Hi Yang,

That was my SO thread you found, and as you can see, the issue was never clearly explained to me besides the warning in the docs. I don’t believe anything’s changed to allow the R API to be called from different threads, so extra effort is still required.

What I ended up doing in my code was the hack shown in the second code-snippet, handling output only in the main thread. For your situation depending on what kind of work you are doing, you may consider a thread safe queue to push your progress messages to and a condition variable to ask the main thread to flush the queue to output. I imagine this would be simpler if your do all your work in spawned threads and leave the main thread free to only print output periodically.

Kind regards,
Shian Su

> On 29 Jan 2019, at 2:24 pm, Yang Liao <liao using wehi.edu.au> wrote:
>
> Hi,
>
> I'm not sure if some C developers have gone through this problem: it seems that Rprintf cannot work safely in a multi-threaded environment. In particular, if I call Rprintf() from a then-created thread while the stack size checking is enabled (ie the "R_CStackLimit" pointer isn't set to -1), it is very likely to end up with some fatal error messages like:
>
> Error: C stack usage  847645293284 is too close to the limit
>> Error: C stack usage  847336061668 is too close to the limit
>> Error: C stack usage  847666277092 is too close to the limit
>> Error: C stack usage  847346551524 is too close to the limit
>> Error: C stack usage  847367531236 is too close to the limit
>> Error: C stack usage  847357041380 is too close to the limit
>> Error: C stack usage  847378021092 is too close to the limit
>> Error: C stack usage  847655787236 is too close to the limit
>
> , and the R session terminates in a segfault.
> After I used all means to confirm that there was no memory leakage and the real stack use was minimum, I thought it can only be the Rprintf issue. I then disabled all screen outputs from the then-created threads and the error was gone. It was also reported on stackoverflow:
> https://stackoverflow.com/questions/50092949/why-does-rcout-and-rprintf-cause-stack-limit-error-when-multithreading
> I tried using a semaphore to protect all Rprintf calls but it didn't prevent the error.
>
> Since my program needs to report some messages from the worker threads (created by the main thread), I wonder if there is a solution to safely do so, or I have to pipe the messages to the main thread, which in turn calls Rprintf? I hope not to change "R_CStackLimit" to disable the stack size checks because it generates a "NOTE" in R check.
>
> Cheers,
> Yang
>
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