[Bioc-devel] [Untrusted Server] Rprintf in a multi-threaded environment
Thanks, Shian! Yes, I think the only way to make it work is to send the messages to the main thread. Cheers, Yang -----Original Message----- From: Shian Su <su.s at wehi.edu.au> Sent: Tuesday, 29 January 2019 3:22 PM To: Yang Liao <liao at wehi.edu.au> Cc: bioc-devel at r-project.org Subject: Re: [Untrusted Server][Bioc-devel] Rprintf in a multi-threaded environment 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 at 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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