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lme4/RcppEigen gcc-UBSAN issues #794

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lme4/RcppEigen gcc-UBSAN issues#794
@bbolker

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@bbolker
bbolker
opened on Jun 3, 2024

On 2024-06-03 8:58 a.m., Prof Brian Ripley wrote:

On 03/06/2024 09:44, Kurt Hornik wrote:

Prof Brian Ripley writes:

Ben/Dirk,

This seems from code in lme4 using RcppEigen ... pls have a look.

(Must be caused by recent changes in R-devel, but we do not yet know
which one ...)

Looks like it is r86629 (as are a score of recent similar errors): I am
running checks with that reverted.

Best
-k

Dear maintainer,
Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_lme4.html.

Please correct before 2024-06-17 to safely retain your package on CRAN.

commit r86629 does say it turns on stricter type checking so ... ??

From https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/lme4/lme4-Ex.Rout:

(seems deep within the Eigen code itself: any chance that this is actually an upstream problem? Also, I find it a little surprising that it gets triggered exactly once in the entire test suite ... possibly Nelder-Mead related?

fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
> system.time(
+   tpr  <- profile(fm01ML, optimizer="Nelder_Mead", which="beta_")
+ )## fast; as only *one* beta parameter is profiled over -> 0.09s (2022)
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:193:18: runtime error: reference binding to misaligned address 0x000000000001 for type 'const double', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f80ce648e19 in Eigen::internal::blas_data_mapper<double const, long, 0, 0, 1>::operator()(long, long) const /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:193
    #1 0x7f80ce648e19 in Eigen::internal::const_blas_data_mapper<double, long, 0>::getSubMapper(long, long) const /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/util/BlasUtil.h:394
    #2 0x7f80ce648e19 in Eigen::internal::general_matrix_matrix_triangular_product<long, double, 1, false, double, 0, false, 0, 1, 2, 0>::run(long, long, double const*, long, double const*, long, double*, long, long, double const&, Eigen::internal::level3_blocking<double, double>&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h:100
    #3 0x7f80ce5da77d in Eigen::selfadjoint_product_selector<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> >, Eigen::Transpose<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> > const>, 2, false>::run(Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> >&, Eigen::Transpose<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> > const> const&, double const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointProduct.h:113
    #4 0x7f80ce5da77d in Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> >, 2u>& Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> >, 2u>::rankUpdate<Eigen::Transpose<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> > const> >(Eigen::MatrixBase<Eigen::Transpose<Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1>, 0, Eigen::Stride<0, 0> > const> > const&, double const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/products/SelfadjointProduct.h:126
    #5 0x7f80ce5da77d in lme4::merPredD::merPredD(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/predModule.cpp:55
    #6 0x7f80ce3e2e49 in merPredDCreate /data/gannet/ripley/R/packages/tests-gcc-SAN/lme4/src/external.cpp:679
    #7 0x58e66f in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:832
    #8 0x596807 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437
    #9 0x68ff04 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1265
    #10 0x69d2f7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #11 0x68f918 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #12 0x6996cb in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3009
    #13 0x68f918 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #14 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #15 0x6970a8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #16 0x68f4ed in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #17 0x68f4ed in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #18 0x6996cb in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3009
    #19 0x68f918 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #20 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #21 0x6970a8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #22 0x64e5b4 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #23 0x64e5b4 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8111
    #24 0x68e662 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #25 0x68eeda in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #26 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #27 0x697a13 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2571
    #28 0x7f80e20af967 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1151
    #29 0x74de37 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1344
    #30 0x664a68 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8075
    #31 0x68e662 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68eeda in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x6970a8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698d18 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x747190 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x7481a9 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:508
    #38 0x748d6f in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f339 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e662 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68eeda in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x6970a8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f4ed in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f4ed in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d2f7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68f918 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x690c09 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #49 0x690c09 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:954
    #50 0x69121f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5856
    #51 0x6558ae in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7870
    #52 0x68e662 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #53 0x68eeda in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #54 0x694c3e in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #55 0x6970a8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #56 0x68f4ed in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #57 0x68f4ed in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #58 0x714a9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:262
    #59 0x715111 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314
    #60 0x715254 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1216
    #61 0x7152a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1223
    #62 0x41b7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #63 0x7f80e1e2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #64 0x7f80e1e295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #65 0x41e034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41e034) (BuildId: 712ed179b4b313b62b0c70c49da020a03ce27c58)

   user  system elapsed 
  1.891   0.115   2.189

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