Merge branch 'adaMala' into adaMala_debug

Author: vandenman

DESCRIPTION

@@ -22,7 +22,7 @@ URL: https://maartenmarsman.github.io/bgms/
 BugReports: https://github.com/MaartenMarsman/bgms/issues
 Imports: Rcpp (>= 1.0.7), RcppParallel, Rdpack, methods, coda, dqrng
 RdMacros: Rdpack
-LinkingTo: Rcpp, RcppProgress, RcppArmadillo, RcppParallel, dqrng
+LinkingTo: Rcpp, RcppProgress, RcppArmadillo, RcppParallel, dqrng, BH
 RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10)

src/bgmCompare_parallel.cpp

@@ -1,14 +1,11 @@
 // [[Rcpp::depends(RcppParallel, RcppArmadillo, dqrng)]]
 #include <RcppParallel.h>
 #include <RcppArmadillo.h>
-#include <dqrng.h>
-#include <dqrng_generator.h>
-#include <xoshiro.h>
+#include "bgmCompare_sampler.h"
 #include <tbb/global_control.h>
 #include <vector>
 #include <string>
-#include "sampler_output.h"
-#include "bgmCompare_sampler.h"
+#include "rng_utils.h"
 
 using namespace Rcpp;
 using namespace RcppParallel;
@@ -60,7 +57,7 @@ struct GibbsCompareChainRunner : public Worker {
   const arma::mat& inclusion_probability_master;
 
   // RNG seeds
-  const std::vector<uint64_t>& chain_seeds;
+  const std::vector<SafeRNG>& chain_rngs;
 
   // output
   std::vector<ChainResultCompare>& results;
@@ -96,7 +93,7 @@ struct GibbsCompareChainRunner : public Worker {
     const arma::imat& group_indices,
     const arma::imat& interaction_index_matrix,
     const arma::mat& inclusion_probability_master,
-    const std::vector<uint64_t>& chain_seeds,
+    const std::vector<SafeRNG>& chain_rngs,
     std::vector<ChainResultCompare>& results
   ) :
     observations(observations),
@@ -129,7 +126,7 @@ struct GibbsCompareChainRunner : public Worker {
     group_indices(group_indices),
     interaction_index_matrix(interaction_index_matrix),
     inclusion_probability_master(inclusion_probability_master),
-    chain_seeds(chain_seeds),
+    chain_rngs(chain_rngs),
     results(results)
   {}
 
@@ -140,7 +137,8 @@ struct GibbsCompareChainRunner : public Worker {
       out.error = false;
 
       try {
-        dqrng::xoshiro256plus rng(chain_seeds[i]);
+        // per-chain RNG
+        SafeRNG rng(chain_rngs[i]);
 
         // make per-chain copies
         std::vector<arma::imat> num_obs_categories = num_obs_categories_master;
@@ -242,12 +240,12 @@ Rcpp::List run_bgmCompare_parallel(
   std::vector<ChainResultCompare> results(num_chains);
 
   // per-chain seeds
-  std::vector<uint64_t> chain_seeds(num_chains);
-  dqrng::xoshiro256plus seeder;
+  std::vector<SafeRNG> chain_rngs(num_chains);
   for (int c = 0; c < num_chains; ++c) {
-    chain_seeds[c] = seeder();
+    chain_rngs[c] = SafeRNG(/*seed +*/ c); // TODO: this needs a seed passed by the user!
   }
 
+
   GibbsCompareChainRunner worker(
       observations, num_groups,
       num_obs_categories, sufficient_blume_capel, sufficient_pairwise,
@@ -257,7 +255,7 @@ Rcpp::List run_bgmCompare_parallel(
       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, chain_seeds, results
+      inclusion_probability, chain_rngs, results
   );
 
   {

src/bgmCompare_sampler.cpp

@@ -64,7 +64,7 @@ List impute_missing_data_for_graphical_model(
     const arma::imat& missing_data_indices,
     const arma::uvec& is_ordinal_variable,
     const arma::ivec& baseline_category,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   const int num_variables = observations.n_cols;
   const int num_missings = missing_data_indices.n_rows;
@@ -235,7 +235,7 @@ double find_reasonable_initial_step_size(
     const double main_alpha,
     const double main_beta,
     const double target_acceptance,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::vec theta = vectorize_model_parameters(
     main_effects, pairwise_effects, inclusion_indicator, main_effect_indices,
@@ -351,7 +351,7 @@ SamplerResult update_parameters_with_nuts(
     HMCAdaptationController& adapt,
     const bool learn_mass_matrix,
     const bool selection,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::vec current_state = vectorize_model_parameters(
     main_effects, pairwise_effects, inclusion_indicator,
@@ -614,7 +614,7 @@ void gibbs_update_step_for_graphical_model_parameters (
     const int num_groups,
     const arma::imat group_indices,
     double difference_scale,
-    dqrng::xoshiro256plus& rng,
+    SafeRNG& rng,
     arma::mat& inclusion_probability
 ) {
 
@@ -680,7 +680,7 @@ SamplerOutput run_gibbs_sampler_for_bgmCompare(
     const arma::imat& group_indices,//new
     const arma::imat& interaction_index_matrix,//new
     arma::mat inclusion_probability,//new
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   // --- Setup: dimensions and storage structures
   const int num_variables = observations.n_cols;

src/bgmCompare_sampler.h

@@ -1,10 +1,10 @@
 #pragma once
-#include <dqrng.h>
-#include <xoshiro.h>
 #include <RcppArmadillo.h>
 #include "sampler_output.h"
 
-SamplerOutput run_gibbs_sampler_for_bgmCompare(
+struct SafeRNG;
+
+Rcpp::List run_gibbs_sampler_for_bgmCompare(
     int chain_id,
     arma::imat observations,
     const int num_groups,
@@ -36,5 +36,5 @@ SamplerOutput run_gibbs_sampler_for_bgmCompare(
     const arma::imat& group_indices,
     const arma::imat& interaction_index_matrix,
     arma::mat inclusion_probability,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 );

src/bgm_helper.h

@@ -50,7 +50,7 @@ inline void initialise_graph(
     const arma::mat& incl_prob,
     arma::mat&  rest,
     const arma::imat& X,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   int V = indicator.n_rows;
   for (int i = 0; i < V-1; ++i) {

src/bgm_parallel.cpp

@@ -1,29 +1,18 @@
 // [[Rcpp::depends(RcppParallel, RcppArmadillo, dqrng)]]
 #include <RcppParallel.h>
 #include <RcppArmadillo.h>
-#include <dqrng.h>
-#include <xoshiro.h>
 #include "bgm_sampler.h"
 #include <tbb/global_control.h>
 #include <vector>
 #include <string>
+#include "rng_utils.h"
 
 using namespace Rcpp;
 using namespace RcppParallel;
 
 // -----------------------------------------------------------------------------
 // Wrapper to silence Clang warning
 // -----------------------------------------------------------------------------
-struct SafeRNG {
-  dqrng::xoshiro256plus eng;
-
-  SafeRNG() : eng() {}
-  SafeRNG(const dqrng::xoshiro256plus& other) : eng(other) {}
-  SafeRNG& operator=(const dqrng::xoshiro256plus& other) {
-    eng = other;
-    return *this;
-  }
-};
 
 // -----------------------------------------------------------------------------
 // Result struct
@@ -146,7 +135,7 @@ struct GibbsChainRunner : public Worker {
       out.error = false;
 
       try {
-        dqrng::xoshiro256plus rng = chain_rngs[i].eng;
+        SafeRNG rng = chain_rngs[i];
 
         Rcpp::List result = run_gibbs_sampler_for_bgm(
           out.chain_id,
@@ -237,11 +226,8 @@ Rcpp::List run_bgm_parallel(
 
   // Prepare one independent RNG per chain via jump()
   std::vector<SafeRNG> chain_rngs(num_chains);
-  chain_rngs[0].eng = dqrng::xoshiro256plus(seed);
-
-  for (int c = 1; c < num_chains; ++c) {
-    chain_rngs[c].eng = chain_rngs[c-1].eng;
-    chain_rngs[c].eng.jump();
+  for (int c = 0; c < num_chains; ++c) {
+    chain_rngs[c] = SafeRNG(seed + c);
   }
 
   GibbsChainRunner worker(

src/bgm_sampler.cpp

@@ -50,7 +50,7 @@ void impute_missing_values_for_graphical_model (
     const arma::uvec& is_ordinal_variable,
     const arma::ivec& reference_category,
     arma::imat& sufficient_pairwise,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   const int num_variables = observations.n_cols;
   const int num_missings = missing_index.n_rows;
@@ -193,7 +193,7 @@ double find_reasonable_initial_step_size(
     const double interaction_scale,
     const double target_acceptance,
     const arma::imat& sufficient_pairwise,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::vec theta = vectorize_model_parameters(
     main_effects, pairwise_effects, inclusion_indicator,
@@ -278,7 +278,7 @@ void update_main_effects_with_metropolis (
     arma::mat& proposal_sd_main,
     RWMAdaptationController& adapter,
     const int iteration,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   const int num_vars = observations.n_cols;
   arma::umat index_mask_main = arma::ones<arma::umat>(proposal_sd_main.n_rows, proposal_sd_main.n_cols);
@@ -381,7 +381,7 @@ void update_pairwise_effects_with_metropolis (
     const arma::ivec& reference_category,
     const int iteration,
     const arma::imat& sufficient_pairwise,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::mat accept_prob_pairwise = arma::zeros<arma::mat>(num_variables, num_variables);
   arma::umat index_mask_pairwise = arma::zeros<arma::umat>(num_variables, num_variables);
@@ -478,7 +478,7 @@ void update_parameters_with_hmc(
     HMCAdaptationController& adapt,
     const bool learn_mass_matrix,
     const bool selection,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::vec current_state = vectorize_model_parameters(
     main_effects, pairwise_effects, inclusion_indicator,
@@ -587,7 +587,7 @@ SamplerResult update_parameters_with_nuts(
     HMCAdaptationController& adapt,
     const bool learn_mass_matrix,
     const bool selection,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   arma::vec current_state = vectorize_model_parameters(
     main_effects, pairwise_effects, inclusion_indicator,
@@ -668,7 +668,7 @@ void tune_pairwise_proposal_sd(
     const arma::imat& sufficient_pairwise,
     int iteration,
     const WarmupSchedule& sched,
-    dqrng::xoshiro256plus& rng,
+    SafeRNG& rng,
     double target_accept = 0.44,
     double rm_decay = 0.75
 )
@@ -762,7 +762,7 @@ void update_indicator_interaction_pair_with_metropolis (
     const arma::uvec& is_ordinal_variable,
     const arma::ivec& reference_category,
     const arma::imat& sufficient_pairwise,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   for (int cntr = 0; cntr < num_interactions; cntr++) {
     const int variable1 = index(cntr, 1);
@@ -912,7 +912,7 @@ void gibbs_update_step_for_graphical_model_parameters (
     arma::ivec& treedepth_samples,
     arma::ivec& divergent_samples,
     arma::vec& energy_samples,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
 
   // Step 0: Initialise random graph structure when edge_selection = TRUE
@@ -1071,7 +1071,7 @@ Rcpp::List run_gibbs_sampler_for_bgm(
     const int hmc_num_leapfrogs,
     const int nuts_max_depth,
     const bool learn_mass_matrix,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 ) {
   // --- Setup: dimensions and storage structures
   const int num_variables = observations.n_cols;
@@ -1176,8 +1176,8 @@ Rcpp::List run_gibbs_sampler_for_bgm(
   for (int iteration = 0; iteration < total_iter; iteration++) {
     if (iteration % print_every == 0) {
       tbb::mutex::scoped_lock lock(get_print_mutex());
-      //Rcpp::Rcout
       std::cout
+      // Rcpp::Rcout
       << "[bgm] chain " << chain_id
       << " iteration " << iteration
       << " / " << total_iter

src/bgm_sampler.h

@@ -1,8 +1,9 @@
 #pragma once
-#include <dqrng.h>
-#include <xoshiro.h>
 #include <RcppArmadillo.h>
 
+// forward declaration
+struct SafeRNG;
+
 Rcpp::List run_gibbs_sampler_for_bgm(
     int chain_id,
     arma::imat observations,
@@ -33,5 +34,5 @@ Rcpp::List run_gibbs_sampler_for_bgm(
     const int hmc_num_leapfrogs,
     const int nuts_max_depth,
     const bool learn_mass_matrix,
-    dqrng::xoshiro256plus& rng
+    SafeRNG& rng
 );

src/gibbs_functions_edge_prior.cpp

@@ -33,7 +33,7 @@ arma::uvec table_cpp(arma::uvec x) {
 arma::mat add_row_col_block_prob_matrix(arma::mat X,
                                             double beta_alpha,
                                             double beta_beta,
-                                            dqrng::xoshiro256plus& rng) {
+                                            SafeRNG& rng) {
   arma::uword dim = X.n_rows;
   arma::mat Y(dim+1,dim+1,arma::fill::zeros);
 
@@ -159,7 +159,7 @@ inline void update_sumG(double &sumG,
 // Sample the cluster assignment in sample_block_allocations_mfm_sbm()
 // ----------------------------------------------------------------------------|
 arma::uword sample_cluster(arma::vec cluster_prob,
-                           dqrng::xoshiro256plus& rng) {
+                           SafeRNG& rng) {
   arma::vec cum_prob = arma::cumsum(cluster_prob);
   double u = runif(rng) * arma::max(cum_prob);
 
@@ -182,7 +182,7 @@ arma::uvec block_allocations_mfm_sbm(arma::uvec cluster_assign,
                                         arma::uword dirichlet_alpha,
                                         double beta_bernoulli_alpha,
                                         double beta_bernoulli_beta,
-                                        dqrng::xoshiro256plus& rng) {
+                                        SafeRNG& rng) {
   arma::uword old;
   arma::uword cluster;
   arma::uword no_clusters;
@@ -320,7 +320,7 @@ arma::mat block_probs_mfm_sbm(arma::uvec cluster_assign,
                                   arma::uword no_variables,
                                   double beta_bernoulli_alpha,
                                   double beta_bernoulli_beta,
-                                  dqrng::xoshiro256plus& rng) {
+                                  SafeRNG& rng) {
 
   arma::uvec cluster_size = table_cpp(cluster_assign);
   arma::uword no_clusters = cluster_size.n_elem;