Closed mattdowle closed 5 years ago
awesome of Luke to do all the hard work of identifying the cause! 💯
I'm in process of confirming with Luke that it's fixed before closing ...
Confirmed fixed. Thanks to @ltierney for his help.
For completeness in case we need to refer back... I could not reproduce the problem with R-devel compiled as follows. (I needed to confirm I could reproduce the problem with 1.11.8 before I could confirm 1.11.9 fixes it.)
./configure --without-recommended-packages --disable-byte-compiled-packages --enable-strict-barrier CC="gcc -fsanitize=address -fno-sanitize=float-divide-by-zero -fno-omit-frame-pointer" CFLAGS="-O0 -g -Wall -pedantic"
even with the script that Luke provided :
library(data.table)
library(constellation)
temp <- as.data.table(vitals[VARIABLE == "TEMPERATURE"])
pulse <- as.data.table(vitals[VARIABLE == "PULSE"])
resp <- as.data.table(vitals[VARIABLE == "RESPIRATORY_RATE"])
temp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
pulse[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
resp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
gc()
for (i in 1:10) {
cat("i=",i,"\n")
b1 <- bundle(temp, pulse, resp,
bundle_names = c("PLATELETS", "INR"), window_hours_pre = 24,
window_hours_post = c(6, 6), join_key = "PAT_ID",
time_var = "RECORDED_TIME", event_name = "CREATININE", mult = "all")
}
gc()
As a long shot, I recompiled R-devel more simply as follows, still with --enable-strict-barrier
which is the important thing :
./configure --without-recommended-packages --enable-strict-barrier
reinstalled constellation and all its dependencies and data.table 1.11.8, and this time Luke's script correctly fails :
Fatal error: Wrong thread calling 'RunFinalizers'
Installing data.table-dev (1.11.9) into this R-devel and rerunning, works fine. Reinstalling data.table 1.11.8 again fails. So it's indeed fixed by 1.11.9. In my original R-devel compile, perhaps something there was making 1.11.8 work (disabling byte compiler, -00, ASAN, etc). Anyway, a simpler R-devel compile was needed and was worth trying.
@jangorecki If time allows, it would be great to add --enable-strict-barrier
to the R-devel used in CI pipelines. I don't know if you compile R-devel or not for CI pipelines.
@mattdowle yes I compile R-devel daily, will add this flag there. Added to not forget in #3147
Luke Tierney contacted me about a memory issue in R-devel. Tests are passing both on CRAN and Travis/Appveyor, but memory usage is higher in some cases. As before the garbage collector turns off. Not sure when exactly the R-devel change was made, but some time in the last month or so. It might be that the R-devel change causes the new memory issue, or that the R-devel change reveals the problem that exists already (possibly even with data.table-release on R-release). In any case, it needs to be fixed.
Luke wrote :
Given Luke's detail, it's easy to see the problem in the code without needing to reproduce. All R API usage needs taking outside all parallel regions as Luke requested before. I delayed doing that last time due to time pressure, and now it needs tackling. Last time I just did the first step which was to ensure that DATAPTR inside parallel regions did not receive ALTREP.
This warrants accelerating release of 1.12.0, not least because it impacts Luke.
$ grep "omp.*parallel" *.c
$ grep ALTREP *.c