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Fix for stack imbalance bgmCompare parallel #54

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Merged
vandenman merged 6 commits into from
Sep 10, 2025
Merged

Fix for stack imbalance bgmCompare parallel #54

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669768a
Fix for stack imbalance bgmCompare parallel
MaartenMarsman Sep 10, 2025
d00ae6c
ensure header and source have the same definition
vandenman Sep 10, 2025
4144345
Merge pull request #53 from vandenman/fix_adaMala_debug
vandenman Sep 10, 2025
028ed9e
Merge branch 'adaMala' into adaMala_debug
vandenman Sep 10, 2025
f089795
fix compilation
vandenman Sep 10, 2025
779c83b
fix runtime errors
vandenman Sep 10, 2025
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ S3method(print,summary.bgms)
S3method(summary,bgms)
export(bgm)
export(bgmCompare)
export(bgmCompare2)
export(extract_arguments)
export(extract_category_thresholds.bgms)
export(extract_edge_indicators)
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4 changes: 2 additions & 2 deletions R/RcppExports.R
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@@ -1,8 +1,8 @@
# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

run_bgmCompare_parallel <- function(observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads) {
.Call(`_bgms_run_bgmCompare_parallel`, observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads)
run_bgmCompare_parallel <- function(observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed) {
.Call(`_bgms_run_bgmCompare_parallel`, observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed)
}

run_bgm_parallel <- function(observations, num_categories, interaction_scale, edge_prior, inclusion_probability, beta_bernoulli_alpha, beta_bernoulli_beta, dirichlet_alpha, lambda, interaction_index_matrix, iter, burnin, num_obs_categories, sufficient_blume_capel, threshold_alpha, threshold_beta, na_impute, missing_index, is_ordinal_variable, reference_category, edge_selection, update_method, pairwise_effect_indices, target_accept, sufficient_pairwise, hmc_num_leapfrogs, nuts_max_depth, learn_mass_matrix, num_chains, nThreads, seed) {
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38 changes: 4 additions & 34 deletions R/bgmCompare2.R
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Expand Up @@ -196,7 +196,7 @@ bgmCompare2 = function(
stop("Argument 'seed' must be a non-negative integer or vector of non-negative integers.")
}
# Force to integer type
seed <- as.integer(seed)
seed = as.integer(seed)
dqrng::dqset.seed(seed)
}

Expand Down Expand Up @@ -225,44 +225,14 @@ bgmCompare2 = function(
nuts_max_depth = nuts_max_depth,
learn_mass_matrix = learn_mass_matrix,
projection = projection,
group_membership = sorted_group - 1, ######################################
group_membership = sorted_group - 1,
group_indices = group_indices,
interaction_index_matrix = Index,
inclusion_probability = model$inclusion_probability_difference,
num_chains = chains, nThreads = cores
num_chains = chains, nThreads = cores,
seed = seed
)

# out = run_gibbs_sampler_for_bgmCompare(
# chain_id = 1,
# observations = observations,
# num_groups = num_groups,
# num_obs_categories = num_obs_categories,
# sufficient_blume_capel = sufficient_blume_capel,
# sufficient_pairwise = sufficient_pairwise,
# num_categories = num_categories[, 1],
# main_alpha = threshold_alpha,
# main_beta = threshold_beta,
# pairwise_scale = interaction_scale,
# difference_scale = difference_scale,
# difference_selection_alpha = beta_bernoulli_alpha,
# difference_selection_beta = beta_bernoulli_beta,
# difference_prior = model$difference_prior, iter = iter, burnin = burnin,
# na_impute = na_impute, missing_data_indices = missing_index,
# is_ordinal_variable = ordinal_variable,
# baseline_category = reference_category,
# difference_selection = difference_selection,
# main_effect_indices = main_effect_indices,
# pairwise_effect_indices = pairwise_effect_indices,
# target_accept = target_accept,
# nuts_max_depth = nuts_max_depth,
# learn_mass_matrix = learn_mass_matrix,
# projection = projection,
# group_membership = sorted_group - 1, ######################################
# group_indices = group_indices,
# interaction_index_matrix = Index,
# inclusion_probability = model$inclusion_probability_difference)


# Main output handler in the wrapper function
# output = prepare_output_bgmCompare2(
# out = out, ...
Expand Down
11 changes: 7 additions & 4 deletions R/function_input_utils.R
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Expand Up @@ -737,8 +737,10 @@ check_compare2_model = function(
if(difference_inclusion_probability >= 1)
stop("The inclusion probability for differences cannot equal or exceed the value one.")

inclusion_probability_difference = inclusion_probability_difference +
difference_probability
inclusion_probability_difference = matrix(difference_probability,
nrow = ncol(x),
ncol = ncol(x))

} else {
if(!inherits(difference_probability, what = "matrix") &&
!inherits(difference_probability, what = "data.frame"))
Expand All @@ -765,8 +767,9 @@ check_compare2_model = function(
stop("One or more inclusion probabilities for differences are one or larger.")
}
} else {
inclusion_probability_difference = inclusion_probability_difference + 0.5

inclusion_probability_difference = matrix(0.5,
nrow = ncol(x),
ncol = ncol(x))
if(beta_bernoulli_alpha <= 0 || beta_bernoulli_beta <= 0)
stop("The scale parameters of the beta distribution for the differences need to be positive.")
if(!is.finite(beta_bernoulli_alpha) || !is.finite(beta_bernoulli_beta))
Expand Down
3 changes: 2 additions & 1 deletion man/bgm.Rd
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38 changes: 0 additions & 38 deletions man/summarySBM.Rd
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This file was deleted.

4 changes: 2 additions & 2 deletions src/Makevars
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@@ -1,4 +1,4 @@
CXX_STD = CXX14
CXX_STD = CXX20

## Pull in the include-paths for RcppParallel
PKG_CPPFLAGS = \
Expand All @@ -11,4 +11,4 @@ PKG_CPPFLAGS = \
PKG_LIBS = \
$(shell "${R_HOME}/bin/Rscript" -e "cat(RcppParallel::LdFlags())") \
-Wl,-rpath,$(shell "${R_HOME}/bin/Rscript" -e "cat(system.file('lib',package='RcppParallel'))") \
$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
41 changes: 21 additions & 20 deletions src/RcppExports.cpp
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Expand Up @@ -12,44 +12,45 @@ Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// run_bgmCompare_parallel
Rcpp::List run_bgmCompare_parallel(const arma::imat& observations, const int num_groups, const std::vector<arma::imat>& num_obs_categories, const std::vector<arma::imat>& sufficient_blume_capel, const std::vector<arma::mat>& sufficient_pairwise, const arma::ivec& num_categories, const double main_alpha, const double main_beta, const double pairwise_scale, const double difference_scale, const double difference_selection_alpha, const double difference_selection_beta, const std::string& difference_prior, const int iter, const int burnin, const bool na_impute, const arma::imat& missing_data_indices, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, const bool difference_selection, const arma::imat& main_effect_indices, const arma::imat& pairwise_effect_indices, const double target_accept, const int nuts_max_depth, const bool learn_mass_matrix, const arma::mat& projection, const arma::ivec& group_membership, const arma::imat& group_indices, const arma::imat& interaction_index_matrix, const arma::mat& inclusion_probability, const int num_chains, const int nThreads);
RcppExport SEXP _bgms_run_bgmCompare_parallel(SEXP observationsSEXP, SEXP num_groupsSEXP, SEXP num_obs_categoriesSEXP, SEXP sufficient_blume_capelSEXP, SEXP sufficient_pairwiseSEXP, SEXP num_categoriesSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP pairwise_scaleSEXP, SEXP difference_scaleSEXP, SEXP difference_selection_alphaSEXP, SEXP difference_selection_betaSEXP, SEXP difference_priorSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP na_imputeSEXP, SEXP missing_data_indicesSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP difference_selectionSEXP, SEXP main_effect_indicesSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP projectionSEXP, SEXP group_membershipSEXP, SEXP group_indicesSEXP, SEXP interaction_index_matrixSEXP, SEXP inclusion_probabilitySEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP) {
Rcpp::List run_bgmCompare_parallel(const arma::imat& observations, int num_groups, const std::vector<arma::imat>& num_obs_categories, const std::vector<arma::imat>& sufficient_blume_capel, const std::vector<arma::mat>& sufficient_pairwise, const arma::ivec& num_categories, double main_alpha, double main_beta, double pairwise_scale, double difference_scale, double difference_selection_alpha, double difference_selection_beta, const std::string& difference_prior, int iter, int burnin, bool na_impute, const arma::imat& missing_data_indices, const arma::uvec& is_ordinal_variable, const arma::ivec& baseline_category, bool difference_selection, const arma::imat& main_effect_indices, const arma::imat& pairwise_effect_indices, double target_accept, int nuts_max_depth, bool learn_mass_matrix, const arma::mat& projection, const arma::ivec& group_membership, const arma::imat& group_indices, const arma::imat& interaction_index_matrix, const arma::mat& inclusion_probability, int num_chains, int nThreads, int seed);
RcppExport SEXP _bgms_run_bgmCompare_parallel(SEXP observationsSEXP, SEXP num_groupsSEXP, SEXP num_obs_categoriesSEXP, SEXP sufficient_blume_capelSEXP, SEXP sufficient_pairwiseSEXP, SEXP num_categoriesSEXP, SEXP main_alphaSEXP, SEXP main_betaSEXP, SEXP pairwise_scaleSEXP, SEXP difference_scaleSEXP, SEXP difference_selection_alphaSEXP, SEXP difference_selection_betaSEXP, SEXP difference_priorSEXP, SEXP iterSEXP, SEXP burninSEXP, SEXP na_imputeSEXP, SEXP missing_data_indicesSEXP, SEXP is_ordinal_variableSEXP, SEXP baseline_categorySEXP, SEXP difference_selectionSEXP, SEXP main_effect_indicesSEXP, SEXP pairwise_effect_indicesSEXP, SEXP target_acceptSEXP, SEXP nuts_max_depthSEXP, SEXP learn_mass_matrixSEXP, SEXP projectionSEXP, SEXP group_membershipSEXP, SEXP group_indicesSEXP, SEXP interaction_index_matrixSEXP, SEXP inclusion_probabilitySEXP, SEXP num_chainsSEXP, SEXP nThreadsSEXP, SEXP seedSEXP) {
BEGIN_RCPP
Rcpp::RObject rcpp_result_gen;
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< const arma::imat& >::type observations(observationsSEXP);
Rcpp::traits::input_parameter< const int >::type num_groups(num_groupsSEXP);
Rcpp::traits::input_parameter< int >::type num_groups(num_groupsSEXP);
Rcpp::traits::input_parameter< const std::vector<arma::imat>& >::type num_obs_categories(num_obs_categoriesSEXP);
Rcpp::traits::input_parameter< const std::vector<arma::imat>& >::type sufficient_blume_capel(sufficient_blume_capelSEXP);
Rcpp::traits::input_parameter< const std::vector<arma::mat>& >::type sufficient_pairwise(sufficient_pairwiseSEXP);
Rcpp::traits::input_parameter< const arma::ivec& >::type num_categories(num_categoriesSEXP);
Rcpp::traits::input_parameter< const double >::type main_alpha(main_alphaSEXP);
Rcpp::traits::input_parameter< const double >::type main_beta(main_betaSEXP);
Rcpp::traits::input_parameter< const double >::type pairwise_scale(pairwise_scaleSEXP);
Rcpp::traits::input_parameter< const double >::type difference_scale(difference_scaleSEXP);
Rcpp::traits::input_parameter< const double >::type difference_selection_alpha(difference_selection_alphaSEXP);
Rcpp::traits::input_parameter< const double >::type difference_selection_beta(difference_selection_betaSEXP);
Rcpp::traits::input_parameter< double >::type main_alpha(main_alphaSEXP);
Rcpp::traits::input_parameter< double >::type main_beta(main_betaSEXP);
Rcpp::traits::input_parameter< double >::type pairwise_scale(pairwise_scaleSEXP);
Rcpp::traits::input_parameter< double >::type difference_scale(difference_scaleSEXP);
Rcpp::traits::input_parameter< double >::type difference_selection_alpha(difference_selection_alphaSEXP);
Rcpp::traits::input_parameter< double >::type difference_selection_beta(difference_selection_betaSEXP);
Rcpp::traits::input_parameter< const std::string& >::type difference_prior(difference_priorSEXP);
Rcpp::traits::input_parameter< const int >::type iter(iterSEXP);
Rcpp::traits::input_parameter< const int >::type burnin(burninSEXP);
Rcpp::traits::input_parameter< const bool >::type na_impute(na_imputeSEXP);
Rcpp::traits::input_parameter< int >::type iter(iterSEXP);
Rcpp::traits::input_parameter< int >::type burnin(burninSEXP);
Rcpp::traits::input_parameter< bool >::type na_impute(na_imputeSEXP);
Rcpp::traits::input_parameter< const arma::imat& >::type missing_data_indices(missing_data_indicesSEXP);
Rcpp::traits::input_parameter< const arma::uvec& >::type is_ordinal_variable(is_ordinal_variableSEXP);
Rcpp::traits::input_parameter< const arma::ivec& >::type baseline_category(baseline_categorySEXP);
Rcpp::traits::input_parameter< const bool >::type difference_selection(difference_selectionSEXP);
Rcpp::traits::input_parameter< bool >::type difference_selection(difference_selectionSEXP);
Rcpp::traits::input_parameter< const arma::imat& >::type main_effect_indices(main_effect_indicesSEXP);
Rcpp::traits::input_parameter< const arma::imat& >::type pairwise_effect_indices(pairwise_effect_indicesSEXP);
Rcpp::traits::input_parameter< const double >::type target_accept(target_acceptSEXP);
Rcpp::traits::input_parameter< const int >::type nuts_max_depth(nuts_max_depthSEXP);
Rcpp::traits::input_parameter< const bool >::type learn_mass_matrix(learn_mass_matrixSEXP);
Rcpp::traits::input_parameter< double >::type target_accept(target_acceptSEXP);
Rcpp::traits::input_parameter< int >::type nuts_max_depth(nuts_max_depthSEXP);
Rcpp::traits::input_parameter< bool >::type learn_mass_matrix(learn_mass_matrixSEXP);
Rcpp::traits::input_parameter< const arma::mat& >::type projection(projectionSEXP);
Rcpp::traits::input_parameter< const arma::ivec& >::type group_membership(group_membershipSEXP);
Rcpp::traits::input_parameter< const arma::imat& >::type group_indices(group_indicesSEXP);
Rcpp::traits::input_parameter< const arma::imat& >::type interaction_index_matrix(interaction_index_matrixSEXP);
Rcpp::traits::input_parameter< const arma::mat& >::type inclusion_probability(inclusion_probabilitySEXP);
Rcpp::traits::input_parameter< const int >::type num_chains(num_chainsSEXP);
Rcpp::traits::input_parameter< const int >::type nThreads(nThreadsSEXP);
rcpp_result_gen = Rcpp::wrap(run_bgmCompare_parallel(observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads));
Rcpp::traits::input_parameter< int >::type num_chains(num_chainsSEXP);
Rcpp::traits::input_parameter< int >::type nThreads(nThreadsSEXP);
Rcpp::traits::input_parameter< int >::type seed(seedSEXP);
rcpp_result_gen = Rcpp::wrap(run_bgmCompare_parallel(observations, num_groups, num_obs_categories, sufficient_blume_capel, sufficient_pairwise, num_categories, main_alpha, main_beta, pairwise_scale, difference_scale, difference_selection_alpha, difference_selection_beta, difference_prior, iter, burnin, na_impute, missing_data_indices, is_ordinal_variable, baseline_category, difference_selection, main_effect_indices, pairwise_effect_indices, target_accept, nuts_max_depth, learn_mass_matrix, projection, group_membership, group_indices, interaction_index_matrix, inclusion_probability, num_chains, nThreads, seed));
return rcpp_result_gen;
END_RCPP
}
Expand Down Expand Up @@ -188,7 +189,7 @@ END_RCPP
}

static const R_CallMethodDef CallEntries[] = {
{"_bgms_run_bgmCompare_parallel", (DL_FUNC) &_bgms_run_bgmCompare_parallel, 32},
{"_bgms_run_bgmCompare_parallel", (DL_FUNC) &_bgms_run_bgmCompare_parallel, 33},
{"_bgms_run_bgm_parallel", (DL_FUNC) &_bgms_run_bgm_parallel, 31},
{"_bgms_sample_omrf_gibbs", (DL_FUNC) &_bgms_sample_omrf_gibbs, 6},
{"_bgms_sample_bcomrf_gibbs", (DL_FUNC) &_bgms_sample_bcomrf_gibbs, 8},
Expand Down
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