Reproducible segfault on setkey() in data.table 1.9.7 development version

[peterlittlejohn]

Dear data.table team,

Here's a reproducible segmentation fault in the current development version (1.9.7):

library(data.table)
test <- data.table(A=rep(letters[1:20],5e07))
setkey(test,A) #  segfault here

## data.table info:
# data.table 1.9.7 IN DEVELOPMENT built 2016-06-22 23:36:56 UTC; travis

## system info:
# R version 3.2.3 (2015-12-10)
# Platform: x86_64-redhat-linux-gnu (64-bit)
# Running under: CentOS Linux 7 (Core)

# 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 

[peterlittlejohn]

Following up on this:
The segfault only occurs with development version, not with CRAN version 1.9.6.

Different machine with 16Gb of RAM; more system info shown below.
library(data.table)
data.table 1.9.6 For help type ?data.table or https://github.com/Rdatatable/data.table/wiki

test <- data.table(A=rep(letters[1:20],5e07))
setkey(test,A)
tables()

NAME NROW NCOL MB COLS KEY
[1,] test 1,000,000,000 1 7,630 A A

Total: 7,630MB

Same commands issued after installing current development version of data.table:
library(data.table)
data.table 1.9.7 IN DEVELOPMENT built 2016-06-24 16:35:29 UTC; travis

test <- data.table(A=rep(letters[1:20],5e07))
setkey(test,A) 

*** caught segfault ***
address 0x7f6ede7e5810, cause 'memory not mapped'

*** caught segfault ***
address 0x7f6ea2e38e10, cause 'memory not mapped'

*** caught segfault ***
address 0x7f6e914eb608, cause 'memory not mapped'

Traceback:
1: setkeyv(x, cols, verbose = verbose, physical = physical)
2: setkey(test, A)

Sysinfo
sysname release
"Linux" "4.5.7-200.fc23.x86_64"
machine login
"x86_64" "ap"

[ChristK]

@arunsrinivasan I can reproduce it on 2 different machines running Scientific Linux release 6.2 (Carbon) x64. One with 256Gb of RAM and one with 2Tb of RAM. However, unlike OP I get segfaults both in CRAN and in latest GitHub data.table version

sessionInfo()
#R version 3.3.0 (2016-05-03)
#Platform: x86_64-pc-linux-gnu (64-bit)
#Running under: Scientific Linux release 6.2 (Carbon)

#locale:
# [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
# [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
# [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
# [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
# [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

#attached base packages:
#[1] stats     graphics  grDevices utils     datasets  methods   base     

#other attached packages:
#[1] data.table_1.9.7

[jangorecki]

reproduced on

R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

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     

other attached packages:
[1] data.table_1.9.7

[mainguyenanhvu]

reproduced on:

R version 4.1.3 (2022-03-10) -- "One Push-Up"
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Platform: x86_64-conda-linux-gnu (64-bit)

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> library(data.table)
data.table 1.14.2 using 128 threads (see ?getDTthreads).  Latest news: r-datatable.com