[Rcpp-devel] R Session Sometimes Aborts
Bill Dunlap
williamwdunlap at gmail.com
Mon Dec 13 21:11:55 CET 2021
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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