On Unix-like systems profiling uses the profile timer, which works via signals. If a threaded C-level library isn't programmed to be sure to ignore signals it isn't using itself then the signal will go to the wrong thread and the handler and the main R process start messing in the same memory with out synchronization. I believe we should be able to make sure that the handler only does it's work when called from the main R thread (maybe just re-signaling to the main thread if the signal goes to the wrong one). The few other signals we use could probably use this as well. I'll look into this sometime if no one else gets there first; there is a lot of fine print involved in signal/threads interaction so it may take a while.
Of course the current mechanism of profiling on Unix doesn't really make senss for multi-threaded programs as it is based on process user time (I believe); for threaded programs we sould want something based on clock time. Not sure what the options are these days, but worth looking into. Windows uses a different mechnism for profiling so this is not likely to be related to another thread on Windows/Rprof issues. Best, luke On Fri, 14 Dec 2012, Dirk Eddelbuettel wrote:
Paul, On 14 December 2012 at 01:17, Paul Johnson wrote: | Dirk! | | Correct as usual! [...] | Here's the evidence you are right. | | Before starting R, restrict openblas's use of threads in the environment | | $ export GOTO_NUM_THREADS=1 | | After that, HAPPY profiling in R! Right. If one has tried multithreading before as I have with (so-far unsuccessful) endeavours to get OpenMP into one particular package (while maintaining RNG outcomes / reproducibility) then those stack error look eerily familiar. All very frustrating because "it all just works" with one thread. And that is all R can handle, so if you multithread, set proper mutexes. And for profiling that very logic seems to require turning multithreading off. Cheers, Dirk
-- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics and Fax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [email protected] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
