From 3f3613c8c797a8842f4a44432e1fd9b28c62e595 Mon Sep 17 00:00:00 2001 From: Brian Kelley Date: Tue, 15 Jan 2019 14:01:36 -0500 Subject: [PATCH] Fixes #2209 - testEnumeration on 32bit systems --- .../Enumerate/EvenSamplePairs.cpp | 72 ++++++++++--------- .../ChemReactions/Enumerate/EvenSamplePairs.h | 24 +++---- 2 files changed, 51 insertions(+), 45 deletions(-) diff --git a/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp b/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp index cb4b0f184..2f3d4dc95 100644 --- a/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +++ b/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp @@ -39,34 +39,40 @@ using namespace EnumerationTypes; // Based on an implementation from a correspondance with Bernd Rohde. void EvenSamplePairsStrategy::initializeStrategy(const ChemicalReaction &, const BBS &bbs) { - size_t npos = bbs.size(); + // If we fail here, someone has a ridiculous amount of memory + PRECONDITION(m_numPermutations != EnumerationStrategyBase::EnumerationOverflow, + "Cannot represent all permutations for the even sampler"); + + boost::uint64_t npos = bbs.size(); used_count.resize(npos); std::fill(used_count.begin(), used_count.end(), 0); var_used.resize(npos); - for (size_t i = 0; i < npos; ++i) { + for (boost::uint64_t i = 0; i < npos; ++i) { var_used[i].resize(m_permutationSizes[i]); std::fill(var_used[i].begin(), var_used[i].end(), 0); } boost::uint64_t nmonomers = 0; - for (size_t i = 0; i < bbs.size(); ++i) nmonomers += m_permutationSizes[i]; + for (boost::uint64_t i = 0; i < bbs.size(); ++i) { + nmonomers += m_permutationSizes[i]; + } pair_used.resize(nmonomers); - for (size_t i = 0; i < nmonomers; ++i) { + for (boost::uint64_t i = 0; i < nmonomers; ++i) { pair_used[i].resize(nmonomers); std::fill(pair_used[i].begin(), pair_used[i].end(), 0); } pair_counts.resize(npos); - for (size_t i = 0; i < npos; i++) { + for (boost::uint64_t i = 0; i < npos; i++) { pair_counts[i].resize(npos); std::fill(pair_counts[i].begin(), pair_counts[i].end(), 0); } /* Initialize random number generator */ /* Find modulus */ - for (M = 1; M < rdcast(m_numPermutations); M = 2 * M) + for (M = 1; M < rdcast(m_numPermutations); M = 2 * M) ; /* Set factor */ a = 5; @@ -91,13 +97,13 @@ void EvenSamplePairsStrategy::initializeStrategy(const ChemicalReaction &, // This is fairly suboptimal for large collections // of building blocks and may take a while to // terminate... -bool EvenSamplePairsStrategy::try_add(size_t seed) { +bool EvenSamplePairsStrategy::try_add(boost::uint64_t seed) { const RGROUPS &digits = decode(seed); const RGROUPS &rgroups = m_permutationSizes; - size_t islack = 0; - size_t num_rgroups = m_permutationSizes.size(); + boost::uint64_t islack = 0; + boost::uint64_t num_rgroups = m_permutationSizes.size(); - for (size_t i = 0; i < num_rgroups; ++i) { + for (boost::uint64_t i = 0; i < num_rgroups; ++i) { if (var_used[i][digits[i]]) islack += var_used[i][digits[i]]; if (islack > nslack) { // add better heuristic here?? @@ -107,14 +113,14 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { } islack = 0; - size_t ioffset = 0; + boost::uint64_t ioffset = 0; // check that building block pairs get evenly sampled - for (size_t i = 0; i < num_rgroups; ++i) { - size_t joffset = 0; - for (size_t j = 0; j < num_rgroups; ++j) { + for (boost::uint64_t i = 0; i < num_rgroups; ++i) { + boost::uint64_t joffset = 0; + for (boost::uint64_t j = 0; j < num_rgroups; ++j) { if (j == i) continue; - size_t ii = digits[i] + ioffset; - size_t jj = digits[j] + joffset; + boost::uint64_t ii = digits[i] + ioffset; + boost::uint64_t jj = digits[j] + joffset; if (pair_used[ii][jj] > 0) { double numer = (double)pair_used[ii][jj]; double denom = sqrt((double)(rgroups[i]) * (double)(rgroups[j])); @@ -131,7 +137,7 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { } // keep track of bb usage - for (size_t i = 0; i < num_rgroups; ++i) { + for (boost::uint64_t i = 0; i < num_rgroups; ++i) { if (var_used[i][digits[i]] == 0) { used_count[i]++; } @@ -142,7 +148,7 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { nslack = min_nslack; used_count[i] = 0; - for (size_t j = 0; j < rgroups[i]; ++j) { + for (boost::uint64_t j = 0; j < rgroups[i]; ++j) { var_used[i][j]--; if (var_used[i][j] > 0) used_count[i]++; } @@ -151,14 +157,14 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { // keep track of BB Pair usage ioffset = 0; - for (size_t i = 0; i < num_rgroups; ioffset += rgroups[i], ++i) { - size_t joffset = 0; - for (size_t j = 0; j < num_rgroups; joffset += rgroups[j], ++j) { + for (boost::uint64_t i = 0; i < num_rgroups; ioffset += rgroups[i], ++i) { + boost::uint64_t joffset = 0; + for (boost::uint64_t j = 0; j < num_rgroups; joffset += rgroups[j], ++j) { if (j == i) { continue; } - size_t ii = digits[i] + ioffset; - size_t jj = digits[j] + joffset; + boost::uint64_t ii = digits[i] + ioffset; + boost::uint64_t jj = digits[j] + joffset; if (pair_used[ii][jj] == 0) { pair_counts[i][j]++; } @@ -168,8 +174,8 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { nslack = min_nslack; } pair_counts[i][j] = 0; - for (size_t ii = 0; ii < rgroups[i]; ++ii) { - for (size_t jj = 0; jj < rgroups[j]; ++jj) { + for (boost::uint64_t ii = 0; ii < rgroups[i]; ++ii) { + for (boost::uint64_t jj = 0; jj < rgroups[j]; ++jj) { pair_used[ioffset + ii][joffset + jj]--; if (pair_used[ioffset + ii][joffset + jj] > 0) { pair_counts[i][j]++; @@ -186,11 +192,11 @@ bool EvenSamplePairsStrategy::try_add(size_t seed) { const RGROUPS &EvenSamplePairsStrategy::next() { nslack = 0; - while (m_numPermutationsProcessed < rdcast(m_numPermutations)) { + while (m_numPermutationsProcessed < rdcast(m_numPermutations)) { bool added = false; - for (size_t l = 0; l < M; ++l) { + for (boost::uint64_t l = 0; l < M; ++l) { seed = ((seed * a + b) % M); - if (seed > rdcast(m_numPermutations)) { + if (seed > rdcast(m_numPermutations)) { rejected_period += 1; continue; } else if (selected.find(seed) != selected.end()) { @@ -216,12 +222,12 @@ const RGROUPS &EvenSamplePairsStrategy::next() { std::string EvenSamplePairsStrategy::stats() const { std::ostringstream ss; - size_t npos = m_permutationSizes.size(); + boost::uint64_t npos = m_permutationSizes.size(); const RGROUPS &nvars = m_permutationSizes; - size_t i, l, j, ii, jj, ioffset, joffset; + boost::uint64_t i, l, j, ii, jj, ioffset, joffset; ss << "#BEGIN# BBSTAT\n"; for (i = 0; i < npos; i++) { - size_t maxcount = 0; + boost::uint64_t maxcount = 0; if (nvars[i] == 1) continue; for (j = 0; j < nvars[i]; j++) if (maxcount < var_used[i][j]) maxcount = var_used[i][j]; @@ -230,7 +236,7 @@ std::string EvenSamplePairsStrategy::stats() const { ((double)m_numPermutationsProcessed / nvars[i]); for (l = 0; l <= maxcount; l++) { - size_t n = 0; + boost::uint64_t n = 0; for (j = 0; j < nvars[i]; j++) if (var_used[i][j] == l) n++; if (n > 0) ss << boost::format("\t%lu|%lu") % l % n; @@ -243,7 +249,7 @@ std::string EvenSamplePairsStrategy::stats() const { for (i = 0, ioffset = 0; i < npos; ioffset += nvars[i], i++) { if (nvars[i] == 1) continue; for (j = 0, joffset = 0; j < npos; joffset += nvars[j], j++) { - size_t maxcount = 0; + boost::uint64_t maxcount = 0; if (nvars[j] == 1) continue; if (j <= i) continue; for (ii = 0; ii < nvars[i]; ii++) diff --git a/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h b/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h index ce126644c..64219e08f 100644 --- a/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h +++ b/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.h @@ -56,16 +56,16 @@ class RDKIT_CHEMREACTIONS_EXPORT EvenSamplePairsStrategy : public EnumerationStr boost::uint64_t m_numPermutationsProcessed; std::vector used_count; - std::vector > var_used; - std::vector > pair_used; - std::vector > pair_counts; - std::set selected; + std::vector > var_used; + std::vector > pair_used; + std::vector > pair_counts; + std::set selected; - size_t seed; // last seed for permutation (starts at 0) - size_t M, a, b; // random number stuff - size_t nslack, min_nslack; - size_t rejected_period, rejected_unique; - size_t rejected_slack_condition, rejected_bb_sampling_condition; + boost::uint64_t seed; // last seed for permutation (starts at 0) + boost::uint64_t M, a, b; // random number stuff + boost::uint64_t nslack, min_nslack; + boost::uint64_t rejected_period, rejected_unique; + boost::uint64_t rejected_slack_condition, rejected_bb_sampling_condition; public: EvenSamplePairsStrategy() @@ -120,7 +120,7 @@ class RDKIT_CHEMREACTIONS_EXPORT EvenSamplePairsStrategy : public EnumerationStr EvenSamplePairsStrategy rgroups; rgroups.initialize(rxn, bbs); - for(size_t i=0; i lprops = rxn.RunReactants(rvect); ... @@ -151,7 +151,7 @@ class RDKIT_CHEMREACTIONS_EXPORT EvenSamplePairsStrategy : public EnumerationStr friend class boost::serialization::access; // decode a packed integer into an RGroup selection - const EnumerationTypes::RGROUPS &decode(size_t seed) { + const EnumerationTypes::RGROUPS &decode(boost::uint64_t seed) { for (boost::int64_t j = m_permutationSizes.size() - 1; j >= 0; j--) { m_permutation[j] = seed % m_permutationSizes[j]; seed /= m_permutationSizes[j]; @@ -159,7 +159,7 @@ class RDKIT_CHEMREACTIONS_EXPORT EvenSamplePairsStrategy : public EnumerationStr return m_permutation; } - bool try_add(size_t seed); + bool try_add(boost::uint64_t seed); public: #ifdef RDK_USE_BOOST_SERIALIZATION