[Rcpp-devel] R Session Sometimes Aborts
Dirk Eddelbuettel
edd at debian.org
Mon Dec 13 19:29:32 CET 2021
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
| _______________________________________________
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--
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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