Help debug rstan UBSAN warnings in CRAN package multinma

dmphillippo · January 26, 2024, 9:52am

Hi all,

I’m the developer of the multinma R package, which uses rstan to fit a suite of models for network meta-analysis.

After pushing an update to CRAN this week, I now get failures in gcc-UBSAN additional tests run by CRAN.

Can anyone help me to solve this? I have until 2024-02-08 until my package is threatened with removal. I’ve tried investigating as much as I can (see below), but this is all beyond me!

The full log is here. The first (of many) warnings looks like this:

log output

/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:852:18: runtime error: reference binding to misaligned address 0x63100028148c for type 'struct Scalar', which requires 8 byte alignment
0x63100028148c: note: pointer points here
  a0 cb 8f 2d dd 7f 00 00  93 5b 47 76 f3 0a 00 c0  65 c6 8e 5d a0 64 71 40  a0 cb 8f 2d dd 7f 00 00
              ^ 
    #0 0x7fdd297a5cf8 in Eigen::internal::mapbase_evaluator<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >::coeffRef(long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:852
    #1 0x7fdd297a5cf8 in Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> > >, Eigen::internal::evaluator<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> >, 0>::assignCoeff(long) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:637
    #2 0x7fdd297a5cf8 in Eigen::internal::dense_assignment_loop<Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> > >, Eigen::internal::evaluator<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> >, 0>, 1, 0>::run(Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> > >, Eigen::internal::evaluator<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> >, 0>&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:497
    #3 0x7fdd297a5cf8 in void Eigen::internal::call_dense_assignment_loop<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > >(Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:741
    #4 0x7fdd297a5cf8 in Eigen::internal::Assignment<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> >, Eigen::internal::Dense2Dense, void>::run(Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:879
    #5 0x7fdd297a5cf8 in void Eigen::internal::call_assignment_no_alias<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > >(Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:836
    #6 0x7fdd297a5cf8 in void Eigen::internal::call_assignment<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > >(Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&, Eigen::internal::assign_op<stan::math::var_value<double, void>, stan::math::var_value<double, void> > const&, Eigen::internal::enable_if<!Eigen::internal::evaluator_assume_aliasing<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::internal::evaluator_traits<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >::Shape>::value, void*>::type) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:804
    #7 0x7fdd297a5cf8 in void Eigen::internal::call_assignment<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >(Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:782
    #8 0x7fdd297a5cf8 in Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >& Eigen::MatrixBase<Eigen::Map<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> > >::operator=<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >(Eigen::DenseBase<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> > const&) /data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Core/Assign.h:66
    #9 0x7fdd297a5cf8 in stan::math::arena_matrix<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >& stan::math::arena_matrix<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >::operator=<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >(Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&) /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/rev/core/arena_matrix.hpp:128
    #10 0x7fdd297a5cf8 in stan::math::arena_matrix<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> >::arena_matrix<Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, (void*)0>(Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&) /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/rev/core/arena_matrix.hpp:73
    #11 0x7fdd29c3eaa3 in auto stan::math::csr_matrix_times_vector<Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, (void*)0>(int, int, Eigen::Map<Eigen::Matrix<double, -1, 1, 0, -1, 1>, 0, Eigen::Stride<0, 0> > const&, std::vector<int, std::allocator<int> > const&, std::vector<int, std::allocator<int> > const&, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1> const&) /data/gannet/ripley/R/test-dev/StanHeaders/include/stan/math/rev/fun/csr_matrix_times_vector.hpp:119
    #12 0x7fdd294ae606 in stan::scalar_type<std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >, void>::type model_binomial_1par_namespace::model_binomial_1par::log_prob_impl<true, true, std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >, std::vector<int, std::allocator<int> >, (void*)0, (void*)0>(std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >&, std::vector<int, std::allocator<int> >&, std::ostream*) const /data/gannet/ripley/R/packages/tests-gcc-SAN/multinma/src/stanExports_binomial_1par.h:1925
    #13 0x7fdd294c6f7f in stan::math::var_value<double, void> model_binomial_1par_namespace::model_binomial_1par::log_prob<true, true, stan::math::var_value<double, void> >(std::vector<stan::math::var_value<double, void>, std::allocator<stan::math::var_value<double, void> > >&, std::vector<int, std::allocator<int> >&, std::ostream*) const /data/gannet/ripley/R/packages/tests-gcc-SAN/multinma/src/stanExports_binomial_1par.h:4144
    #14 0x7fdd294c6f7f in double stan::model::log_prob_grad<true, true, model_binomial_1par_namespace::model_binomial_1par>(model_binomial_1par_namespace::model_binomial_1par const&, std::vector<double, std::allocator<double> >&, std::vector<int, std::allocator<int> >&, std::vector<double, std::allocator<double> >&, std::ostream*) /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40
    #15 0x7fdd29e75c78 in std::vector<double, std::allocator<double> > stan::services::util::initialize<true, model_binomial_1par_namespace::model_binomial_1par, stan::io::var_context, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> > >(model_binomial_1par_namespace::model_binomial_1par&, stan::io::var_context const&, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> >&, double, bool, stan::callbacks::logger&, stan::callbacks::writer&) /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/util/initialize.hpp:167
    #16 0x7fdd2a08265b in int stan::services::diagnose::diagnose<model_binomial_1par_namespace::model_binomial_1par>(model_binomial_1par_namespace::model_binomial_1par&, stan::io::var_context const&, unsigned int, unsigned int, double, double, double, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) /data/gannet/ripley/R/test-dev/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49
    #17 0x7fdd2a08265b in command<model_binomial_1par_namespace::model_binomial_1par, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> > > /data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:481
    #18 0x7fdd2a090ccb in rstan::stan_fit<model_binomial_1par_namespace::model_binomial_1par, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> > >::call_sampler(SEXPREC*) /data/gannet/ripley/R/test-dev/rstan/include/rstan/stan_fit.hpp:1215
    #19 0x7fdd294d9f4f in Rcpp::CppMethod1<rstan::stan_fit<model_binomial_1par_namespace::model_binomial_1par, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> > >, SEXPREC*, SEXPREC*>::operator()(rstan::stan_fit<model_binomial_1par_namespace::model_binomial_1par, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> > >*, SEXPREC**) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/Module_generated_CppMethod.h:111
    #20 0x7fdd29ed7802 in Rcpp::class_<rstan::stan_fit<model_binomial_1par_namespace::model_binomial_1par, boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014u, 0u, 2147483563u>, boost::random::linear_congruential_engine<unsigned int, 40692u, 0u, 2147483399u> > > >::invoke_notvoid(SEXPREC*, SEXPREC*, SEXPREC**, int) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:234
    #21 0x7fdd67a12caf in CppMethod__invoke_notvoid(SEXPREC*) /tmp/RtmpULoquA/R.INSTALL23bbf97285e75/Rcpp/src/module.cpp:220
    #22 0x57baab in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:576
    #23 0x685b24 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1248
    << #24 to #279 are similar references to eval.c >>

The other warnings are all in the same model (binomial_1par.stan), and all similar involving misaligned addresses.

I have managed to recreate the issue using the rocker/r-devel-san docker image, and tracked down the issue to this line in my tests:

expect_warning(nma(smknet, trt_effects = "random", test_grad = TRUE), paste0(m, ".+prior_intercept.+", "prior_trt.+", "prior_het.+"))

(multinma/tests/testthat/test-nma.R at 387ea9d2b0f24b1b7af8b4815f5d4c1bf541eaca · dmphillippo/multinma · GitHub)

For a minimum reproducible example, you can run

library(multinma)
smknet <- set_agd_arm(smoking, studyn, trtc, r = r, n = n, trt_ref = "No intervention")
nma(smknet, trt_effects = "random", test_grad = TRUE)

(test_grad = TRUE makes no difference, the errors happen with sampling too.)

The sanitizer errors seem to occur the first time that a random effects model (trt_effects = "random") is run within a session. Re-running the same model, the errors don’t appear.

Tracking down a little further, I wonder whether this is related to the sparse matrix representation that I am using for the random effects correlation matrix? This is set up in include/transformed_data_common.stan

// Sparse representation
vector[0] wdummy;
array[0] int vudummy;
int RE_L_nz = count_nonzero(RE_L); // Number of non-zero entries
int RE_sparse = RE_L_nz * 1.0 / num_elements(RE_L) <= 0.1; // Use sparse representation? (yes = 1)
vector[RE_sparse ? RE_L_nz : 0] RE_L_w = RE_sparse ? csr_extract_w(RE_L): wdummy; // Non-zero entries
array[RE_sparse ? RE_L_nz : 0] int RE_L_v = RE_sparse ? csr_extract_v(RE_L): vudummy; // v sparse component
array[RE_sparse ? n_delta + 1 : 0] int RE_L_u = RE_sparse ? csr_extract_u(RE_L) : vudummy; // u sparse component

(multinma/inst/stan/include/transformed_data_common.stan at 387ea9d2b0f24b1b7af8b4815f5d4c1bf541eaca · dmphillippo/multinma · GitHub)

And then applied in include/transformed_parameters_common.stan to construct the random effects

// -- RE deltas --
// Avoid evaluating tau[1] when no RE (u_delta is zero dim in this case)
vector[n_delta] f_delta =
  RE ? (
    RE_sparse ?
      tau[1] * csr_matrix_times_vector(n_delta, n_delta, RE_L_w, RE_L_v, RE_L_u, u_delta) :
      tau[1] * RE_L * u_delta
  ) : u_delta;

(multinma/inst/stan/include/transformed_parameters_common.stan at 387ea9d2b0f24b1b7af8b4815f5d4c1bf541eaca · dmphillippo/multinma · GitHub)

Interestingly, data that doesn’t trigger the sparse representation doesn’t see the sanitizer errors:

library(multinma)
dat <- data.frame(study = rep(LETTERS[1:9], each = 2), 
                  trt = rep(c("a", "b"), times = 9), 
                  r = 1, n = 2)
# Greater than 0.1, not sparse
mean(chol(RE_cor(dat$study, dat$trt, rep(FALSE, nrow(dat)))))
net <- set_agd_arm(dat, study, trt, r = r, n = n)
nma(net, trt_effects = "random", test_grad = TRUE)

whereas data that does trigger the sparse representation does see the sanitizer errors:

library(multinma)
dat <- data.frame(study = rep(LETTERS[1:11], each = 2), 
                  trt = rep(c("a", "b"), times = 11), 
                  r = 1, n = 2)
# Less than 0.1, sparse
mean(chol(RE_cor(dat$study, dat$trt, rep(FALSE, nrow(dat)))))
net <- set_agd_arm(dat, study, trt, r = r, n = n)
nma(net, trt_effects = "random", test_grad = TRUE)

At this point though I’m stuck; I don’t see how to resolve the sanitizer errors beyond blind trial and error. Any help would be hugely appreciated!

dmphillippo · January 26, 2024, 8:10pm

A bit more digging and I’m pretty sure this is a problem with the sparse matrices. This small model recreates the issue:

library(rstan)

mod <- "
data {
  int n;
  matrix[n, n] M;
}
transformed data {
  int nz = num_elements(csr_extract_w(M));
  vector[nz] Mw = csr_extract_w(M);
  array[nz] int Mv = csr_extract_v(M);
  array[n + 1] int Mu = csr_extract_u(M);
}
parameters {
  vector[n] x;
}
transformed parameters {
  vector[n] y = csr_matrix_times_vector(n, n, Mw, Mv, Mu, x);
}
model {
  x ~ std_normal();
}
"

stan(model_code = mod,
     data = list(
       n = 2,
       M = matrix(c(1, 0.5, 0.5, 1), nrow = 2, ncol = 2)
     ),
     test_grad = TRUE)

Commenting out the transformed parameter removes the sanitizer warnings, so this seems to be a problem with csr_matrix_times_vector().

I’ve raised an issue on the rstan repo:

github.com/stan-dev/rstan

Misaligned address sanitizer errors with `csr_matrix_times_vector()` - leading to CRAN package failing additional tests

opened 11:21AM - 26 Jan 24 UTC

dmphillippo

#### Summary: Sparse matrix arithmetic using `csr_matrix_times_vector()` seems …to trigger sanitizer "misaligned address" errors. #### Description: My package multinma that fits models using rstan has been flagged as failing [additional tests](https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/multinma/tests/testthat.Rout) in gcc-UBSAN. Closer inspection seems to point to `csr_matrix_times_vector()` as the cause. I have also opened a [thread](https://discourse.mc-stan.org/t/help-debug-rstan-ubsan-warnings-in-cran-package-multinma/33939/1) on discourse. #### Reproducible Steps: This small model recreates the sanitizer errors: ``` library(rstan) mod <- " data { int n; matrix[n, n] M; } transformed data { int nz = num_elements(csr_extract_w(M)); vector[nz] Mw = csr_extract_w(M); array[nz] int Mv = csr_extract_v(M); array[n + 1] int Mu = csr_extract_u(M); } parameters { vector[n] x; } transformed parameters { vector[n] y = csr_matrix_times_vector(n, n, Mw, Mv, Mu, x); } model { x ~ std_normal(); } " stan(model_code = mod, data = list( n = 2, M = matrix(c(1, 0.5, 0.5, 1), nrow = 2, ncol = 2) ), test_grad = TRUE) ``` Commenting out the transformed parameter removes the sanitizer warnings, so this seems to be a problem with `csr_matrix_times_vector()`. #### Current Output: <details><summary>Details</summary> <p> ``` TESTING GRADIENT FOR MODEL 'anon_model' NOW (CHAIN 1). /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:852:18: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'struct Scalar', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 00 00 00 00 b0 1b a4 f9 56 55 00 00 20 4b 9e f9 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:637:26: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 00 00 00 00 b0 1b a4 f9 56 55 00 00 20 4b 9e f9 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/functors/AssignmentFunctors.h:24:100: runtime error: store to misaligned address 0x5556fef3455c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 00 00 00 00 b0 1b a4 f9 56 55 00 00 20 4b 9e f9 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:840:18: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:549:21: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/value_of.hpp:25: runtime error: member access within misaligned address 0x5556fef3455c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/fun/value_of.hpp:25: runtime error: member access within misaligned address 0x5556fef3455c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:852:18: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'struct Scalar', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:637:26: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/var.hpp:82: runtime error: constructor call on misaligned address 0x5556fef3458c for type 'struct vari_type', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 00 00 00 00 00 00 00 00 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: constructor call on misaligned address 0x5556fef3458c for type 'struct vari_base', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 00 00 00 00 00 00 00 00 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:28: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_base', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 00 00 00 00 00 00 00 00 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 b0 3f 14 7c 5d 7f 00 00 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 d0 3f 14 7c 5d 7f 00 00 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:126: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 b8 b8 ea 3f 56 55 00 00 70 c0 9d f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/rev/core/vari.hpp:130: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_value', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 70 c0 9d f9 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 b8 b8 ea 3f 00 00 00 00 00 00 00 00 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/functors/AssignmentFunctors.h:24:100: runtime error: store to misaligned address 0x5556fef3457c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 56 55 00 00 70 c0 9d f9 56 55 00 00 70 c0 9d f9 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:840:18: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:637:26: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/functors/AssignmentFunctors.h:24:100: runtime error: load of misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:834:18: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:774:21: runtime error: reference binding to misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/eigen_plugins.h:160:41: runtime error: member access within misaligned address 0x5556fef3457c for type 'const struct var_value', which requires 8 byte alignment 0x5556fef3457c: note: pointer points here 60 bd 9d f9 8c 45 f3 fe 56 55 00 00 a4 45 f3 fe 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/eigen_plugins.h:160:46: runtime error: member access within misaligned address 0x5556fef3458c for type 'struct vari_type', which requires 8 byte alignment 0x5556fef3458c: note: pointer points here 56 55 00 00 d0 3f 14 7c 5d 7f 00 00 27 1c f4 c8 b8 b8 ea 3f 00 00 00 00 00 00 00 00 d0 3f 14 7c ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/eigen_plugins.h:160:46: runtime error: reference binding to misaligned address 0x5556fef3459c for type 'const double', which requires 8 byte alignment 0x5556fef3459c: note: pointer points here b8 b8 ea 3f 00 00 00 00 00 00 00 00 d0 3f 14 7c 5d 7f 00 00 40 bf c4 63 46 6c 9d bf 00 00 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:774:47: runtime error: reference binding to misaligned address 0x5556fef3459c for type 'const double', which requires 8 byte alignment 0x5556fef3459c: note: pointer points here b8 b8 ea 3f 00 00 00 00 00 00 00 00 d0 3f 14 7c 5d 7f 00 00 40 bf c4 63 46 6c 9d bf 00 00 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:100:67: runtime error: reference binding to misaligned address 0x5556fef3459c for type 'const double', which requires 8 byte alignment 0x5556fef3459c: note: pointer points here ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/SparseCore/SparseDenseProduct.h:100:96: runtime error: load of misaligned address 0x5556fef3459c for type 'const double', which requires 8 byte alignment 0x5556fef3459c: note: pointer points here b8 b8 ea 3f 00 00 00 00 00 00 00 00 d0 3f 14 7c 5d 7f 00 00 40 bf c4 63 46 6c 9d bf 00 00 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:852:18: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'struct Scalar', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:792:21: runtime error: reference binding to misaligned address 0x5556fef3455c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ /usr/local/lib/R/site-library/StanHeaders/include/stan/math/prim/eigen_plugins.h:160:41: runtime error: member access within misaligned address 0x5556fef3455c for type 'struct var_value', which requires 8 byte alignment 0x5556fef3455c: note: pointer points here 04 00 00 00 d0 40 f3 fe 56 55 00 00 e8 40 f3 fe 56 55 00 00 56 55 00 00 b8 da 9f f9 56 55 00 00 ^ TESTING GRADIENT FOR MODEL 'anon_model' NOW (CHAIN 2). TESTING GRADIENT FOR MODEL 'anon_model' NOW (CHAIN 3). TESTING GRADIENT FOR MODEL 'anon_model' NOW (CHAIN 4). ``` </p> </details> #### RStan Version: ``` > packageVersion("rstan") [1] ‘2.32.5’ ``` #### R Version: Issue recreated using the [rocker/r-devel-san](https://hub.docker.com/r/rocker/r-devel-san) docker container, which builds r-devel with compiler sanitizers. ``` > R.version.string [1] "R Under development (unstable) (2024-01-22 r85820)" ``` #### Operating System: Linux run in rocker/r-devel-san docker container. Issue first appeared on CRAN gcc-UBSAN test environment (also a flavour of linux).

Update: Brian is already on it with a fix! Looks like an issue with Stan Math.

Bob_Carpenter · February 6, 2024, 10:18pm

Thanks for updating yourself. I saw this go by on GitHub and our devs have been discussing a fix.

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