R devel - May 2017 - R 3.4 and mclapply assertion failure - is this a bug?

Dear all,?
I am not sure if this is a bug, so I prefer to post it here before filing.
After upgrading to 3.4 I encounter the following message with mclapply:
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.OMP:
Error #13: Assertion failure at kmp_runtime.cpp(6480).OMP: Hint: Please submit a
bug report with this message, compile and run commands used, and machine
configuration info including native compiler and operating system versions.
Faster response will be obtained by including all program sources. For
information on submitting this issue, please
see?http://www.intel.com/software/products/support/.
The complete pdf of what console produces is
here:https://www.dropbox.com/s/navugg28gqne14p/R%20Console.pdf?dl=0
The batch with commands to (hopefully) reproduce it is
here:https://www.dropbox.com/s/8pd0ij3kowigdlc/20170430%20-%20R%20mclapply%20bug%20report.r?dl=0
The data for the reproducible example is here:
https://www.dropbox.com/s/2enoeapu7jgcxwd/z.Rdata?dl=0
Note that this behavior was not present in R 3.3.3 on the same machine and all
the batch was working without any errors.
The sessionInfo():
R version 3.4.0 (2017-04-21)Platform: x86_64-apple-darwin15.6.0 (64-bit)Running
under: macOS Sierra 10.12.4
Matrix products: defaultBLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylibLAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:[1] parallel ?compiler ?stats ? ? graphics ?grDevices
utils ? ? datasets ?methods ? base ? ??
other attached packages:?[1] data.table_1.10.4 ? ? ?numbers_0.6-6 ? ? ? ?
?microbenchmark_1.4-2.1 zoo_1.8-0 ? ? ? ? ? ? ?doParallel_1.0.10 ? ?
?iterators_1.0.8 ? ? ???[7] foreach_1.4.3 ? ? ? ? ?RSclient_0.7-3 ? ? ? ?
stringi_1.1.5 ? ? ? ? ?stringr_1.2.0 ? ? ? ? ?lubridate_1.6.0 ? ? ? ?plyr_1.8.4
? ? ? ? ? ?
loaded via a namespace (and not attached):?[1] Rcpp_0.12.10 ? ? lattice_0.20-35
?codetools_0.2-15 grid_3.4.0 ? ? ? gtable_0.2.0 ? ? magrittr_1.5 ? ?
scales_0.4.1 ? ? ggplot2_2.2.1 ???[9] lazyeval_0.2.0 ? tools_3.4.0 ? ?
?munsell_0.4.3 ? ?colorspace_1.3-2 tibble_1.3.0 ? ?

Thank you in advance for help/hints,?Yan
	[[alternative HTML version deleted]]

Yan,

this looks like an interaction of OpenMP in data.table and forking - you may
want to report that to Matt as he can shed more light on that. He has been
complaining that we didn't enable OpenMP before 3.4 so he probably knows
about the issue and how to fix it.

Cheers,
Simon

> On May 2, 2017, at 7:12 AM, Yan Alperovych via R-devel <r-devel at
r-project.org> wrote:
> 
> Dear all, 
> I am not sure if this is a bug, so I prefer to post it here before filing.
> After upgrading to 3.4 I encounter the following message with mclapply:
> Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool ==
__null.OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).OMP: Hint:
Please submit a bug report with this message, compile and run commands used, and
machine configuration info including native compiler and operating system
versions. Faster response will be obtained by including all program sources. For
information on submitting this issue, please see
http://www.intel.com/software/products/support/.
> The complete pdf of what console produces is
here:https://www.dropbox.com/s/navugg28gqne14p/R%20Console.pdf?dl=0
> The batch with commands to (hopefully) reproduce it is
here:https://www.dropbox.com/s/8pd0ij3kowigdlc/20170430%20-%20R%20mclapply%20bug%20report.r?dl=0
> The data for the reproducible example is here:
> https://www.dropbox.com/s/2enoeapu7jgcxwd/z.Rdata?dl=0
> Note that this behavior was not present in R 3.3.3 on the same machine and
all the batch was working without any errors.
> The sessionInfo():
> R version 3.4.0 (2017-04-21)Platform: x86_64-apple-darwin15.6.0
(64-bit)Running under: macOS Sierra 10.12.4
> Matrix products: defaultBLAS:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylibLAPACK:
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
> locale:[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:[1] parallel  compiler  stats     graphics 
grDevices utils     datasets  methods   base
> other attached packages: [1] data.table_1.10.4      numbers_0.6-6         
microbenchmark_1.4-2.1 zoo_1.8-0              doParallel_1.0.10     
iterators_1.0.8        [7] foreach_1.4.3          RSclient_0.7-3        
stringi_1.1.5          stringr_1.2.0          lubridate_1.6.0        plyr_1.8.4
> loaded via a namespace (and not attached): [1] Rcpp_0.12.10    
lattice_0.20-35  codetools_0.2-15 grid_3.4.0       gtable_0.2.0     magrittr_1.5
scales_0.4.1     ggplot2_2.2.1    [9] lazyeval_0.2.0   tools_3.4.0     
munsell_0.4.3    colorspace_1.3-2 tibble_1.3.0
> 
> Thank you in advance for help/hints, Yan
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel