Merge pull request #59 from GPUEngineering/feature/58-serialise-binary

Serialisation: text and binary

Author: alphaville

CHANGELOG.md

@@ -5,14 +5,29 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+<!-- ---------------------
+      v1.6.0
+     --------------------- -->
+## v1.6.0 - 2-12-2024
+
+### Added
+
+- Method `saveToFile` becomes `DTensor<T>::saveToFile(std::string pathToFile, Serialisation ser)`, i.e., the user can 
+  choose whether to save the file as a text (ASCII) file, or a binary one
+
+### Changed
+
+ - Method `parseFromTextFile` renamed to `parseFromFile` (supports text and binary formats)
+
+
 <!-- ---------------------
       v1.5.2
      --------------------- -->
 ## v1.5.2 - 1-12-2024
 
 ### Fixed
 
-- Quick bug bix in `DTensor::parseFromTextFile` (passing storage mode to `vectorFromFile`)
+- Quick bug bix in `DTensor::parseFromTextFile` (passing storage mode to `vectorFromTextFile`)
 
 
 <!-- ---------------------
@@ -23,7 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - Set precision in `DTensor::saveToFile` properly
-- `DTensor<T>::parseFromTextFile` throws `std::invalid_argument` if `T` is unsupported
+- `DTensor<T>::parseFromFile` throws `std::invalid_argument` if `T` is unsupported
 
 <!-- ---------------------
       v1.5.0

README.md

@@ -248,7 +248,8 @@ The `DTensor` `B` will be overwritten with the solution.
 
 ### 1.8. Saving and loading tensors
 
-Tensor data can be stored in simple text files which have the following structure
+Tensor data can be stored in simple text files or binary files. 
+The text-based format has the following structure
 
 ```text
 number_of_rows
@@ -259,13 +260,20 @@ data (one entry per line)
 
 To save a tensor in a file, simply call `DTensor::saveToFile(filename)`.
 
-To load a tensor from a file, the static function `DTensor<T>::parseFromTextFile(filename)` can be used. For example:
+If the file extension is `.bt` (binary tensor), the data will be stored in binary format.
+The structure of the binary encoding is similar to that of the text encoding:
+the first three `uint64_t`-sized positions correspond to the number of rows, columns
+and matrices, followed by the elements of the tensor.
+
+To load a tensor from a file, the static function `DTensor<T>::parseFromFile(filename)` can be used. For example:
 
 ```c++
-auto z = DTensor<double>::parseFromTextFile("path/to/my.dtensor")
+auto z = DTensor<double>::parseFromFile("path/to/my.dtensor")
 ```
 
-If necessary, you can provide a second argument to `parseFromTextFile` to specify the order in which the data are stored (the `StorageMode`). 
+If necessary, you can provide a second argument to `parseFromFile` to specify the order in which the data are stored (the `StorageMode`).
+
+Soon we will release a Python API for reading and serialising (numpy) arrays to `.bt` files.  
 
 ## 2. Cholesky factorisation and system solution
 

include/tensor.cuh

@@ -169,6 +169,7 @@ enum StorageMode {
     defaultMajor = columnMajor
 };
 
+
 /**
  * This library uses tensors to store and manipulate data on a GPU device.
  * A tensor has three axes: [rows (m) x columns (n) x matrices (k)].
@@ -256,13 +257,16 @@ public:
      *
      * This static function reads data from a text file, creates a DTensor and uploads the data to the device.
      *
+     * The data may be stored in a text file or a binary file. Binary files must have the extension .bt.
+     *
      * @param path_to_file path to file as string
      * @param mode storage mode (default: StorageMode::defaultMajor)
      * @return instance of DTensor
      *
      * @throws std::invalid_argument if the file is not found
      */
-    static DTensor<T> parseFromTextFile(std::string path_to_file, StorageMode mode = StorageMode::defaultMajor);
+    static DTensor<T> parseFromFile(std::string path_to_file,
+                                    StorageMode mode = StorageMode::defaultMajor);
 
     /**
     * Constructs a DTensor object.
@@ -504,7 +508,12 @@ public:
     /**
      * Saves the current instance of DTensor to a (text) file
      *
-     * @param pathToFile
+     * If the file extension is .bt, the data will be stored in a binary file.
+     * Writing to and reading from a binary file is significantly faster and
+     * the generated binary files tend to have a smaller size (about 40% of the
+     * size of text files for data of type double and float).
+     *
+     * @param pathToFile path to file
      */
     void saveToFile(std::string pathToFile);
 
@@ -595,7 +604,7 @@ struct data_t {
 };
 
 template<typename T>
-data_t<T> vectorFromFile(std::string path_to_file) {
+data_t<T> vectorFromTextFile(std::string path_to_file) {
     data_t<T> dataStruct;
     std::ifstream file;
     file.open(path_to_file, std::ios::in);
@@ -641,24 +650,70 @@ data_t<T> vectorFromFile(std::string path_to_file) {
 }
 
 template<typename T>
-DTensor<T> DTensor<T>::parseFromTextFile(std::string path_to_file,
-                                         StorageMode mode) {
-    auto parsedData = vectorFromFile<T>(path_to_file);
+data_t<T> vectorFromBinaryFile(std::string path_to_file) {
+    data_t<T> dataStruct;
+    /* Read from binary file */
+    std::ifstream inFile;
+    inFile.open(path_to_file, std::ios::binary);
+    inFile.read(reinterpret_cast<char *>(&(dataStruct.numRows)), sizeof(uint64_t));
+    inFile.read(reinterpret_cast<char *>(&(dataStruct.numCols)), sizeof(uint64_t));
+    inFile.read(reinterpret_cast<char *>(&(dataStruct.numMats)), sizeof(uint64_t));
+    uint64_t numElements = dataStruct.numRows * dataStruct.numCols * dataStruct.numMats;
+    std::vector<T> vecDataFromFile(numElements);
+    for (size_t i = 0; i < numElements; i++) {
+        T el;
+        inFile.read(reinterpret_cast<char *>(&el), sizeof(T));
+        vecDataFromFile[i] = el;
+    }
+    inFile.close();
+    dataStruct.data = vecDataFromFile;
+    return dataStruct;
+}
+
+template<typename T>
+DTensor<T> DTensor<T>::parseFromFile(std::string path_to_file,
+                                     StorageMode mode) {
+    // Figure out file extension
+    size_t pathToFileLength = path_to_file.length() ;
+    std::string fileNameExtension = path_to_file.substr(pathToFileLength-3);
+    typedef data_t<T> (*PARSER)(std::string);
+    PARSER parser = (fileNameExtension == ".bt")  ? vectorFromBinaryFile<T> : vectorFromTextFile<T>;
+    auto parsedData = parser(path_to_file);
     DTensor<T> tensorFromData(parsedData.data, parsedData.numRows, parsedData.numCols, parsedData.numMats, mode);
     return tensorFromData;
 }
 
 template<typename T>
 void DTensor<T>::saveToFile(std::string pathToFile) {
-    std::ofstream file(pathToFile);
-    file << numRows() << std::endl << numCols() << std::endl << numMats() << std::endl;
-    std::vector<T> myData(numEl()); download(myData);
-    if constexpr (std::is_floating_point<T>::value) {
-        file << std::setprecision(std::numeric_limits<T>::max_digits10);
-    }
-    for(const T& el : myData) file << el << std::endl;
+    std::vector<T> myData(numEl());
+    download(myData);
+
+    // Figure out file extension
+    size_t pathToFileLength = pathToFile.length() ;
+    std::string fileNameExtension = pathToFile.substr(pathToFileLength-3);
+    // If the extension is .bt...
+     if (fileNameExtension == ".bt") {
+        uint64_t nr = (uint64_t) numRows(),
+                nc = (uint64_t) numCols(),
+                nm = (uint64_t) numMats();
+        std::ofstream outFile;
+        outFile.open(pathToFile, std::ios::binary);
+        outFile.write(reinterpret_cast<const char *>(&nr), sizeof(uint64_t));
+        outFile.write(reinterpret_cast<const char *>(&nc), sizeof(uint64_t));
+        outFile.write(reinterpret_cast<const char *>(&nm), sizeof(uint64_t));
+        for (const T &el: myData) outFile.write(reinterpret_cast<const char *>(&el), sizeof(T));
+        outFile.close();
+    } else {
+         std::ofstream file(pathToFile);
+         file << numRows() << std::endl << numCols() << std::endl << numMats() << std::endl;
+         if constexpr (std::is_floating_point<T>::value) {
+             file << std::setprecision(std::numeric_limits<T>::max_digits10);
+         }
+         for (const T &el: myData) file << el << std::endl;
+     }
 }
 
+
 template<typename T>
 void DTensor<T>::reshape(size_t newNumRows, size_t newNumCols, size_t newNumMats) {
     if (m_numRows == newNumRows && m_numCols == newNumCols && m_numMats == newNumMats) return;

main.cu

@@ -6,9 +6,15 @@
 
 
 int main() {
-    auto z = DTensor<size_t>::parseFromTextFile("../test/data/my.dtensor",
-                                                StorageMode::rowMajor);
-    std::cout << z;
-    z.saveToFile("hohoho.dtensor");
+    /* Write to binary file */
+    auto r = DTensor<double>::createRandomTensor(3, 6, 4, -1, 1);
+    std::string fName = "tensor.bt"; // binary tensor file extension: .bt
+    r.saveToFile(fName);
+
+    /* Parse binary file */
+    auto recov = DTensor<double>::parseFromFile(fName);
+    auto err = r - recov;
+    std::cout << "max error : " << err.maxAbs();
+
     return 0;
 }

test/testTensor.cu

@@ -117,7 +117,7 @@ TEST_F(TensorTest, randomTensorCreation) {
 }
 
 /* ---------------------------------------
- * Save to file and parse
+ * Save to file and parse (text)
  * --------------------------------------- */
 
 TEMPLATE_WITH_TYPE_T
@@ -128,7 +128,7 @@ void parseTensorFromFile() {
         auto r = DTensor<T>::createRandomTensor(nR, nC, nM, -1, 1);
         std::string fName = "myTest.dtensor";
         r.saveToFile(fName);
-        auto a = DTensor<T>::parseFromTextFile(fName);
+        auto a = DTensor<T>::parseFromFile(fName);
         EXPECT_EQ(nR, a.numRows());
         EXPECT_EQ(nC, a.numCols());
         EXPECT_EQ(nM, a.numMats());
@@ -148,7 +148,31 @@ TEST_F(TensorTest, parseTensorUnsupportedDataType) {
     auto r = DTensor<double>::createRandomTensor(nR, nC, nM, -1, 1);
     std::string fName = "myTest.dtensor";
     r.saveToFile(fName);
-    EXPECT_THROW(DTensor<char>::parseFromTextFile(fName), std::invalid_argument);
+    EXPECT_THROW(DTensor<char>::parseFromFile(fName), std::invalid_argument);
+}
+
+/* ---------------------------------------
+ * Save to file and parse (binary)
+ * --------------------------------------- */
+
+TEMPLATE_WITH_TYPE_T
+void parseTensorFromFileBinary() {
+    size_t nR = 20, nC = 40, nM = 6;
+    auto r = DTensor<T>::createRandomTensor(nR, nC, nM, -1, 1);
+    std::string fName = "myTest.bt";
+    r.saveToFile(fName);
+    auto a = DTensor<T>::parseFromFile(fName);
+    EXPECT_EQ(nR, a.numRows());
+    EXPECT_EQ(nC, a.numCols());
+    EXPECT_EQ(nM, a.numMats());
+    auto diff = a - r;
+    T err = diff.maxAbs();
+    EXPECT_LT(err, 2 * std::numeric_limits<T>::epsilon());
+}
+
+TEST_F(TensorTest, parseTensorFromFileBinary) {
+    parseTensorFromFileBinary<float>();
+    parseTensorFromFileBinary<double>();
 }
 
 /* ---------------------------------------