umappp 0.1.6 → 0.2.1

data/vendor/umappp/optimize_layout.hpp

@@ -5,6 +5,10 @@
 #include <limits>
 #include <algorithm>
 #include <cmath>
+#ifndef UMAPPP_NO_PARALLEL_OPTIMIZATION
+#include <thread>
+#include <atomic>
+#endif
 
 #include "NeighborList.hpp"
 #include "aarand/aarand.hpp"
@@ -85,94 +89,9 @@ Float clamp(Float input) {
     return std::min(std::max(input, min_gradient), max_gradient);
 }
 
-template<bool batch, typename Float, class Setup, class Rng> 
-void optimize_sample(
-    size_t i,
-    int ndim,
-    Float* embedding,
-    Float* buffer,
-    Setup& setup,
-    Float a,
-    Float b,
-    Float gamma,
-    Float alpha,
-    Rng& rng,
-    Float epoch
-) {
-    const auto& head = setup.head;
-    const auto& tail = setup.tail;
-    const auto& epochs_per_sample = setup.epochs_per_sample;
-    auto& epoch_of_next_sample = setup.epoch_of_next_sample;
-    auto& epoch_of_next_negative_sample = setup.epoch_of_next_negative_sample;
-   
-    const size_t num_obs = head.size(); 
-    const Float negative_sample_rate = setup.negative_sample_rate;
-
-    size_t start = (i == 0 ? 0 : setup.head[i-1]), end = setup.head[i];
-    Float* left = embedding + i * ndim;
-
-    for (size_t j = start; j < end; ++j) {
-        if (epoch_of_next_sample[j] > epoch) {
-            continue;
-        }
-
-        Float* right = embedding + tail[j] * ndim;
-        Float dist2 = quick_squared_distance(left, right, ndim);
-        const Float pd2b = std::pow(dist2, b);
-        const Float grad_coef = (-2 * a * b * pd2b) / (dist2 * (a * pd2b + 1.0));
-        {
-            Float* lcopy = left;
-            Float* rcopy = right;
-
-            for (int d = 0; d < ndim; ++d, ++lcopy, ++rcopy) {
-                Float gradient = alpha * clamp(grad_coef * (*lcopy - *rcopy));
-                if constexpr(!batch) {
-                    *lcopy += gradient;
-                    *rcopy -= gradient;
-                } else {
-                    // Doubling as we'll assume symmetry from the same
-                    // force applied by the right node. This allows us to
-                    // avoid worrying about accounting for modifications to
-                    // the right node.
-                    buffer[d] += 2 * gradient;
-                }
-            }
-        }
-
-        // Here, we divide by epochs_per_negative_sample, defined as epochs_per_sample[j] / negative_sample_rate.
-        const size_t num_neg_samples = (epoch - epoch_of_next_negative_sample[j]) * negative_sample_rate / epochs_per_sample[j];
-
-        for (size_t p = 0; p < num_neg_samples; ++p) {
-            size_t sampled = aarand::discrete_uniform(rng, num_obs); 
-            if (sampled == i) {
-                continue;
-            }
-
-            Float* right = embedding + sampled * ndim;
-            Float dist2 = quick_squared_distance(left, right, ndim);
-            const Float grad_coef = 2 * gamma * b / ((0.001 + dist2) * (a * std::pow(dist2, b) + 1.0));
-            {
-                Float* lcopy = left;
-                const Float* rcopy = right;
-                for (int d = 0; d < ndim; ++d, ++lcopy, ++rcopy) {
-                    Float gradient = alpha * clamp(grad_coef * (*lcopy - *rcopy));
-                    if constexpr(!batch) {
-                        *lcopy += gradient;
-                    } else {
-                        buffer[d] += gradient;
-                    }
-                }
-            }
-        }
-
-        epoch_of_next_sample[j] += epochs_per_sample[j];
-
-        // The update to epoch_of_next_negative_sample involves adding
-        // num_neg_samples * epochs_per_negative_sample, which eventually boils
-        // down to setting epoch_of_next_negative_sample to 'n'.
-        epoch_of_next_negative_sample[j] = epoch;
-    }
-}
+/*****************************************************
+ ***************** Serial code ***********************
+ *****************************************************/
 
 template<typename Float, class Setup, class Rng>
 void optimize_layout(
@@ -192,20 +111,254 @@ void optimize_layout(
     if (epoch_limit> 0) {
         limit_epochs = std::min(epoch_limit, num_epochs);
     }
-
+    
+    const size_t num_obs = setup.head.size(); 
     for (; n < limit_epochs; ++n) {
         const Float epoch = n;
         const Float alpha = initial_alpha * (1.0 - epoch / num_epochs);
-        for (size_t i = 0; i < setup.head.size(); ++i) {
-            optimize_sample<false>(i, ndim, embedding, static_cast<Float*>(NULL), setup, a, b, gamma, alpha, rng, epoch);
+
+        for (size_t i = 0; i < num_obs; ++i) {
+            size_t start = (i == 0 ? 0 : setup.head[i-1]), end = setup.head[i];
+            Float* left = embedding + i * ndim;
+
+            for (size_t j = start; j < end; ++j) {
+                if (setup.epoch_of_next_sample[j] > epoch) {
+                    continue;
+                }
+
+                {
+                    Float* right = embedding + setup.tail[j] * ndim;
+                    Float dist2 = quick_squared_distance(left, right, ndim);
+                    const Float pd2b = std::pow(dist2, b);
+                    const Float grad_coef = (-2 * a * b * pd2b) / (dist2 * (a * pd2b + 1.0));
+
+                    Float* lcopy = left;
+                    for (int d = 0; d < ndim; ++d, ++lcopy, ++right) {
+                        Float gradient = alpha * clamp(grad_coef * (*lcopy - *right));
+                        *lcopy += gradient;
+                        *right -= gradient;
+                    }
+                }
+
+                // Remember that 'epochs_per_negative_sample' is defined as 'epochs_per_sample[j] / negative_sample_rate'.
+                // We just use it inline below rather than defining a new variable and suffering floating-point round-off.
+                const size_t num_neg_samples = (epoch - setup.epoch_of_next_negative_sample[j]) * 
+                    setup.negative_sample_rate / setup.epochs_per_sample[j]; // i.e., 1/epochs_per_negative_sample.
+
+                for (size_t p = 0; p < num_neg_samples; ++p) {
+                    size_t sampled = aarand::discrete_uniform(rng, num_obs);
+                    if (sampled == i) {
+                        continue;
+                    }
+
+                    const Float* right = embedding + sampled * ndim;
+                    Float dist2 = quick_squared_distance(left, right, ndim);
+                    const Float grad_coef = 2 * gamma * b / ((0.001 + dist2) * (a * std::pow(dist2, b) + 1.0));
+
+                    Float* lcopy = left;
+                    for (int d = 0; d < ndim; ++d, ++lcopy, ++right) {
+                        *lcopy += alpha * clamp(grad_coef * (*lcopy - *right));
+                    }
+                }
+
+                setup.epoch_of_next_sample[j] += setup.epochs_per_sample[j];
+
+                // The update to 'epoch_of_next_negative_sample' involves adding
+                // 'num_neg_samples * epochs_per_negative_sample', which eventually boils
+                // down to setting epoch_of_next_negative_sample to 'epoch'.
+                setup.epoch_of_next_negative_sample[j] = epoch;
+            }
         }
     }
 
     return;
 }
 
-template<typename Float, class Setup, class SeedFunction, class EngineFunction>
-inline void optimize_layout_batched(
+/*****************************************************
+ **************** Parallel code **********************
+ *****************************************************/
+
+#ifndef UMAPPP_NO_PARALLEL_OPTIMIZATION
+template<class Float, class Setup>
+struct BusyWaiterThread {
+public:
+    std::vector<size_t> selections;
+    std::vector<unsigned char> skips;
+    size_t observation;
+    Float alpha;
+
+private:
+    int ndim;
+    Float* embedding;
+    const Setup* setup;
+    Float a;
+    Float b;
+    Float gamma;
+
+    std::vector<Float> self_modified;
+
+private:
+    std::thread pool;
+    std::atomic<bool> ready = false;
+    bool finished = false;
+    bool active = false;
+
+public:
+    void run() {
+        ready.store(true, std::memory_order_release);
+    }
+
+    void wait() {
+        while (ready.load(std::memory_order_acquire)) {
+            ;
+        }
+    }
+
+    void migrate_parameters(BusyWaiterThread& src) {
+        selections.swap(src.selections);
+        skips.swap(src.skips);
+        alpha = src.alpha;
+        observation = src.observation;
+    }
+
+    void transfer_coordinates() {
+        std::copy(self_modified.begin(), self_modified.end(), embedding + observation * ndim);
+    }
+
+public:
+    void run_direct() {
+        auto seIt = selections.begin();
+        auto skIt = skips.begin();
+        const size_t i = observation;
+        const size_t start = (i == 0 ? 0 : setup->head[i-1]), end = setup->head[i];
+
+        // Copying it over into a thread-local buffer to avoid false sharing.
+        // We don't bother doing this for the neighbors, though, as it's 
+        // tedious to make sure that the modified values are available during negative sampling.
+        // (This isn't a problem for the self, as the self cannot be its own negative sample.)
+        {
+            const Float* left = embedding + i * ndim;
+            std::copy(left, left + ndim, self_modified.data());
+        }
+
+        for (size_t j = start; j < end; ++j) {
+            if (*(skIt++)) {
+                continue;
+            }
+
+            {
+                Float* left = self_modified.data();
+                Float* right = embedding + setup->tail[j] * ndim;
+
+                Float dist2 = quick_squared_distance(left, right, ndim);
+                const Float pd2b = std::pow(dist2, b);
+                const Float grad_coef = (-2 * a * b * pd2b) / (dist2 * (a * pd2b + 1.0));
+
+                for (int d = 0; d < ndim; ++d, ++left, ++right) {
+                    Float gradient = alpha * clamp(grad_coef * (*left - *right));
+                    *left += gradient;
+                    *right -= gradient;
+                }
+            }
+
+            while (seIt != selections.end() && *seIt != -1) {
+                Float* left = self_modified.data();
+                const Float* right = embedding + (*seIt) * ndim;
+
+                Float dist2 = quick_squared_distance(left, right, ndim);
+                const Float grad_coef = 2 * gamma * b / ((0.001 + dist2) * (a * std::pow(dist2, b) + 1.0));
+
+                for (int d = 0; d < ndim; ++d, ++left, ++right) {
+                    *left += alpha * clamp(grad_coef * (*left - *right));
+                }
+                ++seIt;
+            }
+            ++seIt; // get past the -1.
+        }
+    }
+
+private:
+    void loop() {
+        while (true) {
+            while (!ready.load(std::memory_order_acquire)) {
+                ;
+            }
+            if (finished) {
+                break;
+            }
+            run_direct();
+            ready.store(false, std::memory_order_release);
+        }
+    }
+
+public:
+    BusyWaiterThread() {}
+
+    BusyWaiterThread(int ndim_, Float* embedding_, Setup& setup_, Float a_, Float b_, Float gamma_) : 
+        ndim(ndim_),
+        embedding(embedding_),
+        setup(&setup_),
+        a(a_), 
+        b(b_),
+        gamma(gamma_),
+        self_modified(ndim)
+    {}
+
+    void start() {
+        active = true;
+        pool = std::thread(&BusyWaiterThread::loop, this);
+    }
+
+public:
+    ~BusyWaiterThread() {
+        if (active) {
+            finished = true;
+            ready.store(true, std::memory_order_release);
+            pool.join();
+        }
+    }
+
+    BusyWaiterThread(BusyWaiterThread&&) = default;
+    BusyWaiterThread& operator=(BusyWaiterThread&&) = default;
+
+    BusyWaiterThread(const BusyWaiterThread& src) :
+        selections(src.selections),
+        skips(src.skips),
+        observation(src.observation),
+
+        ndim(src.ndim),
+        embedding(src.embedding),
+        setup(src.setup),
+        a(src.a), 
+        b(src.b),
+        gamma(src.gamma),
+        alpha(src.alpha),
+
+        self_modified(src.self_modified)
+    {}
+
+    BusyWaiterThread& operator=(const BusyWaiterThread& src) {
+        selections = src.selections;
+        skips = src.skips;
+        observation = src.observation;
+
+        ndim = src.ndim;
+        embedding = src.embedding;
+        setup = src.setup;
+        a = src.a; 
+        b = src.b;
+        gamma = src.gamma;
+        alpha = src.alpha;
+
+        self_modified = src.self_modified;
+    }
+};
+#endif
+
+//#define PRINT false
+
+template<typename Float, class Setup, class Rng>
+void optimize_layout_parallel(
     int ndim,
     Float* embedding, 
     Setup& setup,
@@ -213,71 +366,195 @@ inline void optimize_layout_batched(
     Float b, 
     Float gamma,
     Float initial_alpha,
-    SeedFunction seeder,
-    EngineFunction creator,
+    Rng& rng,
     int epoch_limit,
     int nthreads
 ) {
+#ifndef UMAPPP_NO_PARALLEL_OPTIMIZATION
     auto& n = setup.current_epoch;
     auto num_epochs = setup.total_epochs;
     auto limit_epochs = num_epochs;
-    if (epoch_limit > 0) {
+    if (epoch_limit> 0) {
         limit_epochs = std::min(epoch_limit, num_epochs);
     }
 
     const size_t num_obs = setup.head.size(); 
-    std::vector<decltype(seeder())> seeds(num_obs);
-    std::vector<Float> replace_buffer(num_obs * ndim);
-    Float* replacement = replace_buffer.data();
-    bool using_replacement = false;
+    std::vector<int> last_touched(num_obs);
+    std::vector<unsigned char> touch_type(num_obs);
+
+    // We run some things directly in this main thread to avoid excessive busy-waiting.
+    BusyWaiterThread<Float, Setup> staging(ndim, embedding, setup, a, b, gamma);
+
+    int nthreadsm1 = nthreads - 1;
+    std::vector<BusyWaiterThread<Float, Setup> > pool;
+    pool.reserve(nthreadsm1);
+    for (int t = 0; t < nthreadsm1; ++t) {
+        pool.emplace_back(ndim, embedding, setup, a, b, gamma);
+        pool.back().start();
+    }
+
+    std::vector<int> jobs_in_progress;
 
     for (; n < limit_epochs; ++n) {
         const Float epoch = n;
         const Float alpha = initial_alpha * (1.0 - epoch / num_epochs);
 
-        // Fill the seeds.
-        for (auto& s : seeds) {
-            s = seeder();
-        }
+        int base_iteration = 0;
+        std::fill(last_touched.begin(), last_touched.end(), -1);
+
+        size_t i = 0;
+        while (i < num_obs) {
+            bool is_clear = true;
+//            if (PRINT) { std::cout << "size is " << jobs_in_progress.size() << std::endl; }
+
+            for (int t = jobs_in_progress.size(); t < nthreads && i < num_obs; ++t) {
+                staging.alpha = alpha;
+                staging.observation = i;
+
+                // Tapping the RNG here in the serial section.
+                auto& selections = staging.selections;
+                selections.clear();
+                auto& skips = staging.skips;
+                skips.clear();
+
+                const int self_iteration = i;
+                constexpr unsigned char READONLY = 0;
+                constexpr unsigned char WRITE = 1;
+
+                {
+                    auto& touched = last_touched[i];
+                    auto& ttype = touch_type[i];
+//                    if (PRINT) { std::cout << "SELF: " << i << ": " << touched << " (" << ttype << ")" << std::endl; }
+                    if (touched >= base_iteration) {
+                        is_clear = false;
+//                        if (PRINT) { std::cout << "=== FAILED! ===" << std::endl; }
+                    }
+                    touched = self_iteration;
+                    ttype = WRITE;
+                }
 
-        // Input and output alternate between epochs, to avoid the need for a
-        // copy operation on the entire embedding at the end of each epoch.
-        Float* reference = (using_replacement ? replacement : embedding); 
-        Float* output = (using_replacement ? embedding : replacement);
-        using_replacement = !using_replacement;
+                const size_t start = (i == 0 ? 0 : setup.head[i-1]), end = setup.head[i];
+                for (size_t j = start; j < end; ++j) {
+                    bool skip = setup.epoch_of_next_sample[j] > epoch;
+                    skips.push_back(skip);
+                    if (skip) {
+                        continue;
+                    }
 
-#ifndef UMAPPP_CUSTOM_PARALLEL
-        #pragma omp parallel num_threads(nthreads)
-        {
-            std::vector<Float> buffer(ndim);
-            #pragma omp for
-            for (size_t i = 0; i < setup.head.size(); ++i) {
-#else
-        UMAPPP_CUSTOM_PARALLEL(setup.head.size(), [&](size_t first, size_t last) -> void {
-            std::vector<Float> buffer(ndim);
-            for (size_t i = first; i < last; ++i) {
-#endif
+                    {
+                        auto neighbor = setup.tail[j];
+                        auto& touched = last_touched[neighbor];
+                        auto& ttype = touch_type[neighbor];
+//                        if (PRINT) { std::cout << "\tNEIGHBOR: " << neighbor << ": " << touched << " (" << ttype << ")" << std::endl; }
+                        if (touched >= base_iteration) {
+                            if (touched != self_iteration) {
+                                is_clear = false;
+//                                if (PRINT) { std::cout << "=== FAILED! ===" << std::endl; }
+                            }
+                        }
+                        touched = self_iteration;
+                        ttype = WRITE;
+                    }
+
+                    const size_t num_neg_samples = (epoch - setup.epoch_of_next_negative_sample[j]) * 
+                        setup.negative_sample_rate / setup.epochs_per_sample[j]; 
+
+                    for (size_t p = 0; p < num_neg_samples; ++p) {
+                        size_t sampled = aarand::discrete_uniform(rng, num_obs);
+                        if (sampled == i) {
+                            continue;
+                        }
+                        selections.push_back(sampled);
+
+                        auto& touched = last_touched[sampled];
+                        auto& ttype = touch_type[sampled];
+//                        if (PRINT) { std::cout << "\t\tSAMPLED: " << sampled << ": " << touched << " (" << ttype << ")" << std::endl; }
+                        if (touched >= base_iteration) { 
+                            if (touched != self_iteration) {
+                                if (ttype == WRITE) {
+                                    is_clear = false;
+//                                    if (PRINT) { std::cout << "=== FAILED! ===" << std::endl; }
+                                }
+                            }
+                        } else {
+                            // Only updating if it wasn't touched by a previous thread in this
+                            // round of thread iterations.
+                            ttype = READONLY;
+                            touched = self_iteration;
+                        }
+                    }
+
+                    selections.push_back(-1);
 
-                size_t shift = i * ndim;
-                std::copy(reference + shift, reference + shift + ndim, buffer.data());
-                auto rng = creator(seeds[i]);
-                optimize_sample<true>(i, ndim, reference, buffer.data(), setup, a, b, gamma, alpha, rng, epoch);
-                std::copy(buffer.begin(), buffer.end(), output + shift);
+                    setup.epoch_of_next_sample[j] += setup.epochs_per_sample[j];
+                    setup.epoch_of_next_negative_sample[j] = epoch;
+                }
 
-#ifndef UMAPPP_CUSTOM_PARALLEL
+                if (!is_clear) {
+                    // As we only updated the access for 'sampled' to READONLY
+                    // if they weren't touched by another thread, we need to go
+                    // through and manually update them now that the next round
+                    // of thread_iterations will use 'self_iteration' as the
+                    // 'base_iteration'. This ensures that the flags are properly
+                    // set for the next round, under the expectation that the
+                    // pending thread becomes the first thread.
+                    for (auto s : selections) {
+                        if (s != -1) {
+                            auto& touched = last_touched[s];
+                            if (touched != self_iteration) {
+                                touched = self_iteration;
+                                touch_type[s] = READONLY;
+                            }
+                        }
+                    }
+                    break;
+                } 
+
+                // Submitting if it's not the final job, otherwise just running it directly.
+                // This avoids a busy-wait on the main thread that uses up an extra CPU.
+                if (t < nthreadsm1) {
+                    const int thread_index = i % nthreadsm1;
+                    pool[thread_index].migrate_parameters(staging);
+                    pool[thread_index].run();
+                    jobs_in_progress.push_back(thread_index);
+                } else {
+                    staging.run_direct();
+                    staging.transfer_coordinates();
+                }
+
+                ++i;
             }
-        }
-#else
+
+            // Waiting for all the jobs that were submitted.
+            for (auto job : jobs_in_progress) {
+                pool[job].wait();
+                pool[job].transfer_coordinates();
             }
-        }, nthreads);
-#endif
-    }
+            jobs_in_progress.clear();
 
-    if (using_replacement) {
-        std::copy(replace_buffer.begin(), replace_buffer.end(), embedding);
+//            if (PRINT) { std::cout << "###################### OK ##########################" << std::endl; }
+
+            base_iteration = i;
+            if (!is_clear) {
+                const int thread_index = i % nthreadsm1;
+                pool[thread_index].migrate_parameters(staging);
+                pool[thread_index].run();
+                jobs_in_progress.push_back(thread_index);
+                ++i;
+            }
+        }
+
+        for (auto job : jobs_in_progress) {
+            pool[job].wait();
+            pool[job].transfer_coordinates();
+        }
+        jobs_in_progress.clear();
     }
 
     return;
+#else
+    throw std::runtime_error("umappp was not compiled with support for parallel optimization");
+#endif
 }
 
 }

data/vendor/umappp/spectral_init.hpp

@@ -101,7 +101,10 @@ bool normalized_laplacian(const NeighborList<Float>& edges, int ndim, Float* Y,
      * correspond to the smallest 'ndim + 1' eigenvalues from the original
      * matrix. This is obvious when we realize that the eigenvectors of A are
      * the same as the eigenvectors of (xI - A), but the order of eigenvalues
-     * is reversed because of the negation.
+     * is reversed because of the negation. Then, out of the 'ndim + 1' largest
+     * eigenvalues, we remove the largest one, because that corresponds to the
+     * smallest eigenvalue of zero in the original matrix - leaving us with
+     * eigenvectors for the 'ndim' smallest positive eigenvalues.
      *
      * Initially motivated by comments at yixuan/spectra#126 but I misread the
      * equations so this approach (while correct) is not what is described in

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: umappp
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.2.1
 platform: ruby
 authors:
 - kojix2
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-11-16 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -28,16 +27,16 @@ dependencies:
   name: rice
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: 4.5.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: 4.5.0
 description: Umappp wrapper for Ruby
 email:
 - 2xijok@gmail.com
@@ -443,7 +442,6 @@ homepage: https://github.com/kojix2/ruby-umappp
 licenses:
 - BSD-2-Clause
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -458,8 +456,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
-signing_key: 
+rubygems_version: 3.6.7
 specification_version: 4
 summary: Umap for Ruby
 test_files: []