This might be related to #41 but as the error is different, I'm reporting this as a separate issue. In fact, this was the problem I came across first but when trying to boil everything down to a reproducible example, I ran into what is reported in #41. What seems to trigger this more severe issue is simply a larger problem size when compared to what is reported in #41.
set.seed(11)
nrow <- 3000000
ncol <- 1000
mat <- bigmemory::big.matrix(nrow, ncol, type = "double", shared = TRUE)
for (i in seq_len(ncol)) {
mat[, i] <- sample(c(0, 1), nrow, replace = TRUE)
}
res <- biglasso::cv.biglasso(
mat, sample(c(TRUE, FALSE), nrow, replace = TRUE), family = "binomial",
ncores = 8, nlambda = 50, verbose = TRUE
)yielding
Preprocessing start: 2021-09-21 13:23:31.000
Preprocessing end: 2021-09-21 13:23:41.000
-----------------------------------------------
Lambda 1. Now time: 2021-09-21 13:23:42.000
...
Lambda 49. Now time: 2021-09-21 13:51:23.000
Error in structure(new.time - time, class = "proc_time") :
R_Reprotect: only -69 protected items, can't reprotect index -71
Calls: <Anonymous> -> biglasso -> system.time -> structure
Error during wrapup: R_Reprotect: only -53 protected items, can't reprotect index -54
and my sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /cluster/spack/apps/linux-centos7-x86_64/gcc-8.2.0/openblas-0.3.7-aapr6wps44sbmhbedmmigxjk5bhfy5p3/lib/libopenblas_haswell-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] bigmemory.sri_0.1.3 bigmemory_4.5.36 compiler_4.0.2
[4] Matrix_1.2-18 biglasso_1.4.1 parallel_4.0.2
[7] Rcpp_1.0.7 grid_4.0.2 ncvreg_3.13.0
[10] lattice_0.20-41
Happy to share additional info and also to do some further probing of the issue if someone has any pointers.
This might be related to #41 but as the error is different, I'm reporting this as a separate issue. In fact, this was the problem I came across first but when trying to boil everything down to a reproducible example, I ran into what is reported in #41. What seems to trigger this more severe issue is simply a larger problem size when compared to what is reported in #41.
yielding
and my
sessionInfo()Happy to share additional info and also to do some further probing of the issue if someone has any pointers.