[Rcpp-devel] R Session Sometimes Aborts
Alex Ilich
alexilich93 at gmail.com
Mon Dec 13 21:43:34 CET 2021
Thanks for digging into this for me. If focal_val is 16, then this is an
out of bounds error as the matrix is 16x16 and the maximum index can be 15.
What I'm confused about is that focal_val comes from the data which has
been transformed to be restricted to integers in the range of 0-15 (0 -
n_levels-1). This is explicitly checked for in the glcm_textures2 function
with the line " if((terra::global(r, fun = max) > (n_levels-1)) |
(terra::global(r, fun = min) < 0)){stop("Error: raster must have values
between 0 and n_levels-1")}". Additionally, if I start with numbers in 0-15
and don't do any transformation (quantization="none"), I still run into
this issue (see code below).
Thanks,
Alex
library(terra)
library(raster)
library(GLCMTextures)
r1b<- terra::rast(volcano)
set.seed(5)
values(r1b)<- sample(0:15, size = ncell(r1b), replace = TRUE) # Replace
values with random integers from 0-15
r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = "none",
shift=c(0,1)) #Often leads to Rsession Aborted
On Mon, Dec 13, 2021 at 3:12 PM Bill Dunlap <williamwdunlap at gmail.com>
wrote:
> In this example vgdb shows that valgrind's first complaint is at
> (gdb) where 5
> #0 0x000000001c1ada01 in C_make_glcm (x=..., n_levels=16, shift=...,
> na_opt=...) at glcm_cpp_functions.cpp:73
> #1 0x000000001c1b2238 in C_glcm_textures_helper2 (x=..., w2=...,
> n_levels=16, shift=..., na_opt=..., ni=1, nw=21)
> at glcm_cpp_functions.cpp:218
> #2 0x000000001c1a098e in _GLCMTextures_C_glcm_textures_helper2
> (xSEXP=0x19023168, w2SEXP=0x92cbde8,
> n_levelsSEXP=0xa3138d8, shiftSEXP=0x92cc468, na_optSEXP=0xa313398,
> niSEXP=0xb655560, nwSEXP=0x1aeec7d0)
> at RcppExports.cpp:94
> #3 0x00000000001f6b02 in R_doDotCall (
> ofun=0x1c1a0732 <_GLCMTextures_C_glcm_textures_helper2(SEXP, SEXP,
> SEXP, SEXP, SEXP, SEXP, SEXP)>, nargs=7,
> cargs=0x1ffeff6830, call=0x15ed3c88) at
> /mnt/c/R/R-svn/trunk/src/main/dotcode.c:622
> #4 0x00000000002637ca in bcEval (body=0x15ed4078, rho=0x19023210,
> useCache=TRUE)
> at /mnt/c/R/R-svn/trunk/src/main/eval.c:7695
>
> Line 73 is
> GLCM(neighbor_val,focal_val) = GLCM(neighbor_val,focal_val)+1;
> where GLCM is a 16 x 16 IntegerMatrix and focal_val is 16:
> (gdb) print neighbor_val
> $1 = 9
> (gdb) print focal_val
> $2 = 16
> (gdb) print i
> $3 = 2
> (gdb) print j
> $4 = 1
>
> -Bill
>
> On Mon, Dec 13, 2021 at 11:37 AM Bill Dunlap <williamwdunlap at gmail.com>
> wrote:
>
>> Thanks, I hadn't noticed the --use-valgrind option to check.
>>
>> I often run R under valgrind with the command line:
>> $ R --quiet --no-save --debugger=valgrind
>> --debugger-args="--track-origins=yes --vgdb=full --vgdb-error=0"
>> then in another window start a debugger process with
>> $ gdb RHOME/bin/exec/R
>> ...
>> (gdb) target remote | vgdb
>> (gdb) cont
>> You may need to supply a complete path to vgdb, valgrind's interface to
>> gdb.
>> Then gdb will set breakpoints where valgrind reports memory misuse and
>> you can inspect variables, etc., where an error occurs.
>> You can check for memory leaks from gdb with
>> (gdb) monitor leak_check full
>>
>> -Bill
>>
>>
>> On Mon, Dec 13, 2021 at 10:29 AM Dirk Eddelbuettel <edd at debian.org>
>> wrote:
>>
>>>
>>> On 13 December 2021 at 09:15, Bill Dunlap wrote:
>>> | I ran your example under valgrind on Linux (Ubuntu 20.04)
>>>
>>> Excellent call, as usual! Thanks for doing that.
>>>
>>> R actually makes is so easy to run with valgrind by calling
>>>
>>> R CMD check --use-valgrind somePkg_1.2-3.tar.gz
>>>
>>> that I started to add it to some CI setups.
>>>
>>> Dirk
>>>
>>> | 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
>>> | _______________________________________________
>>> | 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
>>> --
>>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>>
>> _______________________________________________
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