[Rcpp-devel] R Session Sometimes Aborts
Bill Dunlap
williamwdunlap at gmail.com
Mon Dec 13 18:15:46 CET 2021
I ran your example under valgrind on Linux (Ubuntu 20.04) and valgrind
found some memory misuse:
$ R --quiet --no-save --debugger=valgrind
--debugger-args="--track-origins=yes"
==1533== Memcheck, a memory error detector
==1533== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==1533== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==1533== Command: /home/bill/R-devel/R-build/bin/exec/R --quiet --no-save
==1533==
> library(terra)
terra version 1.5.2
> library(raster)
Loading required package: sp
> library(GLCMTextures)
>
> r1a<- raster::raster(volcano)
> r2a<- glcm_textures(r1a, w=c(3,7), n_levels = 16, quantization = "equal
prob", shift=c(0,1))
>
> r1b<- terra::rast(volcano)
> r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = "equal
prob", shift=c(0,1)) #Often leads to Rsession Aborted
==1533== Invalid read of size 4
==1533== at 0x1C1ADA01: C_make_glcm(Rcpp::Matrix<13,
Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>,
Rcpp::String) (glcm_cpp_functions.cpp:73)
==1533== by 0x1C1B2237: C_glcm_textures_helper2(Rcpp::Vector<13,
Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int,
Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long,
unsigned long) (glcm_cpp_functions.cpp:218)
==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2
(RcppExports.cpp:94)
==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622)
==1533== by 0x2637C9: bcEval (eval.c:7695)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x240E06: Rf_eval (eval.c:871)
==1533== by 0x246CD6: do_set (eval.c:2990)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x2457DA: do_begin (eval.c:2538)
==1533== Address 0xa59c0c4 is 28 bytes before a block of size 64 in arena
"client"
==1533==
==1533== Invalid write of size 4
==1533== at 0x1C1ADA44: C_make_glcm(Rcpp::Matrix<13,
Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>,
Rcpp::String) (glcm_cpp_functions.cpp:73)
==1533== by 0x1C1B2237: C_glcm_textures_helper2(Rcpp::Vector<13,
Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int,
Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long,
unsigned long) (glcm_cpp_functions.cpp:218)
==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2
(RcppExports.cpp:94)
==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622)
==1533== by 0x2637C9: bcEval (eval.c:7695)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x240E06: Rf_eval (eval.c:871)
==1533== by 0x246CD6: do_set (eval.c:2990)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x2457DA: do_begin (eval.c:2538)
==1533== Address 0xa59c0c4 is 28 bytes before a block of size 64 in arena
"client"
==1533==
--1533-- VALGRIND INTERNAL ERROR: Valgrind received a signal 11 (SIGSEGV) -
exiting
--1533-- si_code=1; Faulting address: 0x10A59C138; sp: 0x10090e2e20
valgrind: the 'impossible' happened:
Killed by fatal signal
host stacktrace:
==1533== at 0x580505C4: ??? (in
/usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux)
==1533== by 0x58004EBB: ??? (in
/usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux)
==1533== by 0x58005DA7: ??? (in
/usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux)
==1533== by 0x580A7204: ??? (in
/usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux)
==1533== by 0x580F5FD4: ??? (in
/usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux)
sched status:
running_tid=1
Thread 1: status = VgTs_Runnable (lwpid 1533)
==1533== at 0x483BE63: operator new(unsigned long) (in
/usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==1533== by 0x6E92D3C: void std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >::_M_construct<char
const*>(char const*, char const*, std::forward_iterator_tag) (in
/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28)
==1533== by 0x1C1B2377: C_glcm_textures_helper2(Rcpp::Vector<13,
Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int,
Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long,
unsigned long) (glcm_cpp_functions.cpp:221)
==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2
(RcppExports.cpp:94)
==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622)
==1533== by 0x2637C9: bcEval (eval.c:7695)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x240E06: Rf_eval (eval.c:871)
==1533== by 0x246CD6: do_set (eval.c:2990)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x2457DA: do_begin (eval.c:2538)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x244FC9: do_for (eval.c:2420)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x2457DA: do_begin (eval.c:2538)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x244FC9: do_for (eval.c:2420)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x2457DA: do_begin (eval.c:2538)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x253F32: bcEval (eval.c:7107)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x243D9C: R_execMethod (eval.c:2094)
==1533== by 0x8800187: R_dispatchGeneric (methods_list_dispatch.c:1145)
==1533== by 0x2B15F4: do_standardGeneric (objects.c:1285)
==1533== by 0x253DB3: bcEval (eval.c:7096)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x253F32: bcEval (eval.c:7107)
==1533== by 0x240653: Rf_eval (eval.c:748)
==1533== by 0x243223: R_execClosure (eval.c:1918)
==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844)
==1533== by 0x240E06: Rf_eval (eval.c:871)
==1533== by 0x246CD6: do_set (eval.c:2990)
==1533== by 0x240A8C: Rf_eval (eval.c:823)
==1533== by 0x28EF5E: Rf_ReplIteration (main.c:264)
==1533== by 0x28F157: R_ReplConsole (main.c:316)
==1533== by 0x290BC0: run_Rmainloop (main.c:1130)
==1533== by 0x290BDA: Rf_mainloop (main.c:1137)
==1533== by 0x16F74B: main (Rmain.c:29)
client stack range: [0x1FFEED3000 0x1FFF000FFF] client SP: 0x1FFEFF35F0
valgrind stack range: [0x1008FE3000 0x10090E2FFF] top usage: 12336 of
1048576
Note: see also the FAQ in the source distribution.
It contains workarounds to several common problems.
In particular, if Valgrind aborted or crashed after
identifying problems in your program, there's a good chance
that fixing those problems will prevent Valgrind aborting or
crashing, especially if it happened in m_mallocfree.c.
If that doesn't help, please report this bug to: www.valgrind.org
In the bug report, send all the above text, the valgrind
version, and what OS and version you are using. Thanks.
On Mon, Dec 13, 2021 at 8:15 AM Alexander Ilich <ailich at mail.usf.edu> wrote:
> Hi, I'm upgrading one of my R packages to rely on the terra package
> instead of the raster package for the handling of spatial raster data.
> Previously when relying on the raster package I had to convert the data to
> a matrix and send it to C++ to loop through the cells manually, but with
> the new features in the terra package I can supply a C++ function that
> returns multiple values directly to terra::focalCpp to perform focal
> operations
> <https://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-focal-statistics-works.htm>.
> I get the same values using both the old and new versions of the functions,
> but the new version often causes the R session to abort, especially at
> larger window sizes. For example, a 3x3 or a 3x5 window seems to always
> run, but a 3x7 window will often cause the R session to abort. However,
> when it doesn't, I get the correct values. Functions followed by 2 are the
> terra versions of the function. By commenting out things and rebuilding I
> was able to determine the line that causes the crash in the terra version
> is "NumericMatrix curr_GLCM = C_make_glcm(curr_window, n_levels, shift,
> na_opt); //Tabulate the GLCM"; however, this line is also included in the
> raster version of the function so I'm not sure why this would happen. Any
> help would be greatly appreciated. Here is the github repository
> <https://github.com/ailich/GLCMTextures/tree/terra>, and I've added some
> sample code below to illustrate the issue.
>
> Thanks,
> Alex
>
> install.packages('raster', repos='https://rspatial.r-universe.dev')
> #install development version of raster
> install.packages('terra', repos='https://rspatial.r-universe.dev')
> #install development version of terra
>
> remotes::install_github("ailich/GLCMTextures", ref = "terra") #Install
> branch of my package testing terra versions of functions
>
> library(terra)
> library(raster)
> library(GLCMTextures)
>
> r1a<- raster::raster(volcano)
> r2a<- glcm_textures(r1a, w=c(3,7), n_levels = 16, quantization = "equal
> prob", shift=c(0,1))
>
> r1b<- terra::rast(volcano)
> r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = "equal
> prob", shift=c(0,1)) #Often leads to Rsession Aborted
>
> all.equal(values(r2a),values(r2b)) #TRUE
>
>
>
> #System Information
> #OS: Windows 10
> R.version
> # platform x86_64-w64-mingw32
> # arch x86_64
> # os mingw32
> # system x86_64, mingw32
> # status
> # major 4
> # minor 0.4
> # year 2021
> # month 02
> # day 15
> # svn rev 80002
> # language R
> # version.string R version 4.0.4 (2021-02-15)
> # nickname Lost Library Book
>
> packageVersion("terra")
> # ‘1.5.2’
> packageVersion("raster")
> # ‘3.5.10’
> packageVersion("Rcpp")
> # ‘1.0.7’
> packageVersion("RcppArmadillo")
> # ‘0.10.7.3.0’
> _______________________________________________
> Rcpp-devel mailing list
> Rcpp-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
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