Merge branch 'ngcore' into 'master'

Add Table and HashTable from NGSolve

See merge request jschoeberl/netgen!225

libsrc/core/CMakeLists.txt

@@ -7,6 +7,7 @@ add_library(ngcore SHARED
   flags.cpp
   paje_trace.cpp
   profiler.cpp
+  table.cpp
   taskmanager.cpp
   utils.cpp
   )
@@ -59,7 +60,7 @@ target_link_libraries(ngcore PUBLIC netgen_mpi PRIVATE ${CMAKE_THREAD_LIBS_INIT}
 install(FILES ngcore.hpp archive.hpp type_traits.hpp version.hpp ngcore_api.hpp logging.hpp
   exception.hpp symboltable.hpp paje_trace.hpp utils.hpp profiler.hpp mpi_wrapper.hpp
   array.hpp taskmanager.hpp concurrentqueue.h localheap.hpp python_ngcore.hpp flags.hpp
-  xbool.hpp signal.hpp bitarray.hpp
+  xbool.hpp signal.hpp bitarray.hpp table.hpp hashtable.hpp
   DESTINATION ${NG_INSTALL_DIR_INCLUDE}/core COMPONENT netgen_devel)
 
 if(ENABLE_CPP_CORE_GUIDELINES_CHECK)

libsrc/core/ngcore.hpp

@@ -6,12 +6,14 @@
 #include "bitarray.hpp"
 #include "exception.hpp"
 #include "flags.hpp"
+#include "hashtable.hpp"
 #include "localheap.hpp"
 #include "logging.hpp"
 #include "mpi_wrapper.hpp"
 #include "profiler.hpp"
 #include "signal.hpp"
 #include "symboltable.hpp"
+#include "table.hpp"
 #include "taskmanager.hpp"
 #include "version.hpp"
 #include "xbool.hpp"

libsrc/core/table.cpp

@@ -0,0 +1,177 @@
+/**************************************************************************/
+/* File:   table.cpp                                                      */
+/* Author: Joachim Schoeberl                                              */
+/* Date:   25. Mar. 2000                                                  */
+/**************************************************************************/
+
+/*
+   Abstract data type Table
+*/
+
+#include "table.hpp"
+
+namespace ngcore
+{
+  template <typename TI>
+  size_t * TablePrefixSum2 (FlatArray<TI> entrysize)
+  {
+    size_t size  = entrysize.Size();
+    size_t * index = new size_t[size+1];
+
+    Array<size_t> partial_sums(TaskManager::GetNumThreads()+1);
+    partial_sums[0] = 0;
+    ParallelJob
+      ([&] (TaskInfo ti)
+       {
+         IntRange r = IntRange(size).Split(ti.task_nr, ti.ntasks);
+         size_t mysum = 0;
+         for (size_t i : r)
+           mysum += entrysize[i];
+         partial_sums[ti.task_nr+1] = mysum;
+       });
+
+    for (size_t i = 1; i < partial_sums.Size(); i++)
+      partial_sums[i] += partial_sums[i-1];
+
+    ParallelJob
+      ([&] (TaskInfo ti)
+       {
+         IntRange r = IntRange(size).Split(ti.task_nr, ti.ntasks);
+         size_t mysum = partial_sums[ti.task_nr];
+         for (size_t i : r)
+           {
+             index[i] = mysum;
+             mysum += entrysize[i];
+           }
+       });
+    index[size] = partial_sums.Last();
+
+    return index;
+  }
+
+  NGCORE_API size_t * TablePrefixSum32 (FlatArray<unsigned int> entrysize)
+  { return TablePrefixSum2 (entrysize); }
+  NGCORE_API size_t * TablePrefixSum64 (FlatArray<size_t> entrysize)
+  { return TablePrefixSum2 (entrysize); }
+
+
+  BaseDynamicTable :: BaseDynamicTable (int size)
+    : data(size)
+  {
+    for (int i = 0; i < size; i++)
+      {
+	data[i].maxsize = 0;
+	data[i].size = 0;
+	data[i].col = NULL;
+      }
+    oneblock = NULL;
+  }
+
+  BaseDynamicTable :: BaseDynamicTable (const Array<int> & entrysizes, int elemsize)
+    : data(entrysizes.Size())
+  {
+    int cnt = 0;
+    int n = entrysizes.Size();
+
+    for (int i = 0; i < n; i++)
+      cnt += entrysizes[i];
+    oneblock = new char[elemsize * cnt];
+
+    cnt = 0;
+    for (int i = 0; i < n; i++)
+      {
+	data[i].maxsize = entrysizes[i];
+	data[i].size = 0;
+
+	data[i].col = &oneblock[elemsize * cnt];
+	cnt += entrysizes[i];
+      }
+  }
+
+
+  BaseDynamicTable :: ~BaseDynamicTable ()
+  {
+    if (oneblock)
+      delete [] oneblock;
+    else
+      for (int i = 0; i < data.Size(); i++)
+	delete [] static_cast<char*> (data[i].col);
+  }
+
+  void BaseDynamicTable :: SetSize (int size)
+  {
+    for (int i = 0; i < data.Size(); i++)
+      delete [] static_cast<char*> (data[i].col);
+
+    data.SetSize(size);
+    for (int i = 0; i < size; i++)
+      {
+	data[i].maxsize = 0;
+	data[i].size = 0;
+	data[i].col = NULL;
+      }
+  }
+
+  void BaseDynamicTable :: IncSize (int i, int elsize)
+  {
+    if (i < 0 || i >= data.Size())
+      {
+        std::cerr << "BaseDynamicTable::Inc: Out of range, i = " << i << ", size = " << data.Size() << std::endl;
+	return;
+      }
+
+    linestruct & line = data[i];
+
+    if (line.size == line.maxsize)
+      {
+	void * p = new char [(2*line.maxsize+5) * elsize];
+
+	memcpy (p, line.col, line.maxsize * elsize);
+	delete [] static_cast<char*> (line.col);
+	line.col = p;
+	line.maxsize = 2*line.maxsize+5;
+      }
+
+    line.size++;
+  }
+
+  void BaseDynamicTable :: DecSize (int i)
+  {
+    if (i < 0 || i >= data.Size())
+      {
+        std::cerr << "BaseDynamicTable::Dec: Out of range" << std::endl;
+	return;
+      }
+
+    linestruct & line = data[i];
+
+    if (line.size == 0)
+      {
+        std::cerr << "BaseDynamicTable::Dec: EntrySize < 0" << std::endl;
+	return;
+      }
+
+    line.size--;
+  }
+
+  void FilteredTableCreator::Add (size_t blocknr, int data)
+  {
+    if (!takedofs||takedofs->Test(data))
+      TableCreator<int>::Add(blocknr,data);
+  }
+
+  void FilteredTableCreator::Add (size_t blocknr, IntRange range)
+  {
+    for (size_t i=range.First(); i<range.Next();i++)
+      if (!takedofs||takedofs->Test(i))
+	TableCreator<int>::Add(blocknr,i);
+  }  
+  
+  void FilteredTableCreator::Add (size_t blocknr, FlatArray<int> dofs)
+  {
+    for (size_t i = 0; i < dofs.Size(); i++)
+      if (!takedofs||takedofs->Test(dofs[i]))
+	TableCreator<int>::Add(blocknr,dofs[i]);
+  }  
+
+} // namespace ngcore

libsrc/core/table.hpp

@@ -0,0 +1,496 @@
+#ifndef NETGEN_CORE_TABLE_HPP
+#define NETGEN_CORE_TABLE_HPP
+
+/**************************************************************************/
+/* File:   table.hpp                                                      */
+/* Author: Joachim Schoeberl                                              */
+/* Date:   25. Mar. 2000                                                  */
+/**************************************************************************/
+
+#include <atomic>
+#include <iostream>
+
+#include "array.hpp"
+#include "bitarray.hpp"
+#include "taskmanager.hpp"
+#include "ngcore_api.hpp"
+
+namespace ngcore
+{
+
+
+template <class T>
+class FlatTable
+{
+protected:
+  /// number of rows
+  size_t size;
+  /// pointer to first in row
+  size_t * index;
+  /// array of data
+  T * data;
+
+public:
+  FlatTable() = delete;
+
+  NETGEN_INLINE FlatTable(size_t as, size_t * aindex, T * adata)
+    : size(as), index(aindex), data(adata) { ; }
+
+  /// Size of table
+  NETGEN_INLINE size_t Size() const { return size; }
+
+  /// Access entry
+  NETGEN_INLINE const FlatArray<T> operator[] (size_t i) const
+  {
+    return FlatArray<T> (index[i+1]-index[i], data+index[i]);
+  }
+
+  NETGEN_INLINE T * Data() const { return data; }
+
+  NETGEN_INLINE FlatArray<T> AsArray() const
+  {
+    return FlatArray<T> (index[size]-index[0], data+index[0]);
+  }
+
+  NETGEN_INLINE FlatArray<size_t> IndexArray() const
+  {
+    return FlatArray<size_t> (size+1, index);
+  }
+
+  /// takes range starting from position start of end-start elements
+  NETGEN_INLINE FlatTable<T> Range (size_t start, size_t end) const
+  {
+    return FlatTable<T> (end-start, index+start, data);
+  }
+
+  /// takes range starting from position start of end-start elements
+  NETGEN_INLINE FlatTable<T> Range (T_Range<size_t> range) const
+  {
+    return FlatTable<T> (range.Size(), index+range.First(), data);
+  }
+
+
+  class Iterator
+  {
+    const FlatTable & tab;
+    size_t row;
+  public:
+    Iterator (const FlatTable & _tab, size_t _row) : tab(_tab), row(_row) { ; }
+    Iterator & operator++ () { ++row; return *this; }
+    FlatArray<T> operator* () const { return tab[row]; }
+    bool operator!= (const Iterator & it2) { return row != it2.row; }
+  };
+
+  Iterator begin() const { return Iterator(*this, 0); }
+  Iterator end() const { return Iterator(*this, size); }
+};
+
+  NGCORE_API extern size_t * TablePrefixSum32 (FlatArray<unsigned int> entrysize);
+  NGCORE_API extern size_t * TablePrefixSum64 (FlatArray<size_t> entrysize);
+
+
+  NETGEN_INLINE size_t * TablePrefixSum (FlatArray<unsigned int> entrysize)
+  { return TablePrefixSum32 (entrysize); }
+  NETGEN_INLINE size_t * TablePrefixSum (FlatArray<int> entrysize)
+  { return TablePrefixSum32 (FlatArray<unsigned> (entrysize.Size(), (unsigned int*)(int*)(entrysize.Addr(0)))); }
+  NETGEN_INLINE size_t * TablePrefixSum (FlatArray<std::atomic<int>> entrysize)
+  { return TablePrefixSum32 (FlatArray<unsigned> (entrysize.Size(), (unsigned int*)(std::atomic<int>*)entrysize.Addr(0))); }
+  NETGEN_INLINE size_t * TablePrefixSum (FlatArray<size_t> entrysize)
+  { return TablePrefixSum64 (entrysize); }
+
+
+/**
+    A compact Table container.
+    A table contains size entries of variable size.
+    The entry sizes must be known at construction.
+*/
+template <class T>
+class Table : public FlatTable<T>
+{
+protected:
+
+  using FlatTable<T>::size;
+  using FlatTable<T>::index;
+  using FlatTable<T>::data;
+
+public:
+  ///
+  NETGEN_INLINE Table () : FlatTable<T> (0,nullptr,nullptr) { ; }
+  /// Construct table of uniform entrysize
+  NETGEN_INLINE Table (size_t asize, size_t entrysize)
+    : FlatTable<T>( asize, new size_t[asize+1], new T[asize*entrysize] )
+  {
+    for (size_t i : Range(size))
+      index[i] = i*entrysize;
+  }
+
+  /// Construct table of variable entrysize
+  template <typename TI>
+  NETGEN_INLINE Table (FlatArray<TI> entrysize)
+  : FlatTable<T> (0, nullptr, nullptr)
+  {
+    size  = entrysize.Size();
+    index = TablePrefixSum (entrysize);
+    size_t cnt = index[size];
+    data = new T[cnt];
+  }
+
+  explicit NETGEN_INLINE Table (const Table<T> & tab2)
+    : FlatTable<T>(0, nullptr, nullptr)
+  {
+    size = tab2.Size();
+
+    index = new size_t[size+1];
+    for (size_t i = 0; i <= size; i++)
+      index[i] = tab2.index[i];
+
+    size_t cnt = index[size];
+    data = new T[cnt];
+    for (size_t i = 0; i < cnt; i++)
+      data[i] = tab2.data[i];
+  }
+
+  NETGEN_INLINE Table (Table<T> && tab2)
+    : FlatTable<T>(0, nullptr, nullptr)
+  {
+    Swap (size, tab2.size);
+    Swap (index, tab2.index);
+    Swap (data, tab2.data);
+  }
+
+  NETGEN_INLINE Table & operator= (Table<T> && tab2)
+  {
+    Swap (size, tab2.size);
+    Swap (index, tab2.index);
+    Swap (data, tab2.data);
+    return *this;
+  }
+
+
+
+  /// Delete data
+  NETGEN_INLINE ~Table ()
+  {
+    delete [] data;
+    delete [] index;
+  }
+
+  /// Size of table
+  using FlatTable<T>::Size;
+
+  /// number of elements in all rows
+  NETGEN_INLINE size_t NElements() const { return index[size]; }
+
+  using FlatTable<T>::operator[];
+};
+
+
+/// Print table
+template <class T>
+inline ostream & operator<< (ostream & s, const Table<T> & table)
+{
+  for (auto i : Range(table))
+    {
+      s << i << ":";
+      for (auto el : table[i])
+	s << " " << el;
+      s << "\n";
+    }
+  s << std::flush;
+  return s;
+}
+
+
+
+
+template <class T>
+  class TableCreator
+  {
+  protected:
+    int mode;    // 1 .. cnt, 2 .. cnt entries, 3 .. fill table
+    std::atomic<size_t> nd;
+    Array<std::atomic<int>> cnt;
+    Table<T> table;
+  public:
+    TableCreator()
+    { nd = 0; mode = 1; }
+    TableCreator (size_t acnt)
+    { nd = acnt; SetMode(2); }
+
+    Table<T> MoveTable()
+    {
+      return std::move(table);
+    }
+
+    bool Done () { return mode > 3; }
+    void operator++(int) { SetMode (mode+1); }
+
+    int GetMode () const { return mode; }
+    void SetMode (int amode)
+    {
+      mode = amode;
+      if (mode == 2)
+	{
+	  // cnt.SetSize(nd);  // atomic has no copy
+          cnt = Array<std::atomic<int>> (nd);
+          for (auto & ci : cnt) ci.store (0, std::memory_order_relaxed);
+	}
+      if (mode == 3)
+	{
+          table = Table<T> (cnt);
+          // for (auto & ci : cnt) ci = 0;
+          for (auto & ci : cnt) ci.store (0, std::memory_order_relaxed);
+          // cnt = 0;
+	}
+    }
+
+    void SetSize (size_t _nd)
+    {
+      if (mode == 1)
+        nd = _nd;
+      else
+        {
+          if (nd != _nd)
+            throw Exception ("cannot change size of table-creator");
+        }
+    }
+
+    void Add (size_t blocknr, const T & data)
+    {
+      switch (mode)
+	{
+	case 1:
+          {
+            size_t oldval = nd;
+            while (blocknr+1>nd) {
+              nd.compare_exchange_weak (oldval, blocknr+1);
+              oldval = nd;
+            }
+            break;
+          }
+	case 2:
+	  cnt[blocknr]++;
+	  break;
+	case 3:
+          int ci = cnt[blocknr]++;
+          table[blocknr][ci] = data;
+	  break;
+	}
+    }
+
+
+    void Add (size_t blocknr, IntRange range)
+    {
+      switch (mode)
+	{
+	case 1:
+          {
+            size_t oldval = nd;
+            while (blocknr+1>nd) {
+              nd.compare_exchange_weak (oldval, blocknr+1);
+              oldval = nd;
+            }
+            break;
+          }
+	case 2:
+	  cnt[blocknr] += range.Size();
+	  break;
+	case 3:
+          size_t ci = ( cnt[blocknr] += range.Size() ) - range.Size();
+	  for (size_t j = 0; j < range.Size(); j++)
+            table[blocknr][ci+j] = range.First()+j;
+	  break;
+	}
+    }
+
+    void Add (size_t blocknr, const FlatArray<int> & dofs)
+    {
+      switch (mode)
+	{
+	case 1:
+          {
+            size_t oldval = nd;
+            while (blocknr+1>nd) {
+              nd.compare_exchange_weak (oldval, blocknr+1);
+              oldval = nd;
+            }
+            break;
+          }
+	case 2:
+	  cnt[blocknr] += dofs.Size();
+	  break;
+	case 3:
+          size_t ci = ( cnt[blocknr] += dofs.Size() ) - dofs.Size();
+	  for (size_t j = 0; j < dofs.Size(); j++)
+            table[blocknr][ci+j] = dofs[j];
+	  break;
+	}
+    }
+  };
+
+  class NGCORE_API FilteredTableCreator : public TableCreator<int>
+  {
+  protected:
+    const BitArray* takedofs;
+  public:
+    FilteredTableCreator(const BitArray* atakedofs)
+      : TableCreator<int>(), takedofs(atakedofs) { };
+    FilteredTableCreator(int acnt, const BitArray* atakedofs)
+      : TableCreator<int>(acnt),takedofs(atakedofs) { };
+    void Add (size_t blocknr, int data);
+    void Add (size_t blocknr, IntRange range);
+    void Add (size_t blocknr, FlatArray<int> dofs);
+  };
+
+
+  /// Base class to generic DynamicTable.
+  class BaseDynamicTable
+  {
+  protected:
+
+    ///
+    struct linestruct
+    {
+      ///
+      int size;
+      ///
+      int maxsize;
+      ///
+      void * col;
+    };
+
+    ///
+    Array<linestruct> data;
+    ///
+    char * oneblock;
+
+  public:
+    ///
+    NGCORE_API BaseDynamicTable (int size);
+    ///
+    NGCORE_API BaseDynamicTable (const Array<int> & entrysizes, int elemsize);
+    ///
+    NGCORE_API ~BaseDynamicTable ();
+
+    /// Changes Size of table to size, deletes data
+    NGCORE_API void SetSize (int size);
+    ///
+    NGCORE_API void IncSize (int i, int elsize);
+
+    NGCORE_API void DecSize (int i);
+  };
+
+
+
+  /**
+      A dynamic table class.
+
+      A DynamicTable contains entries of variable size. Entry sizes can
+      be increased dynamically.
+  */
+  template <class T>
+  class DynamicTable : public BaseDynamicTable
+  {
+  public:
+    /// Creates table of size size
+    DynamicTable (int size = 0)
+      : BaseDynamicTable (size) { ; }
+
+    /// Creates table with a priori fixed entry sizes.
+    DynamicTable (const Array<int> & entrysizes)
+      : BaseDynamicTable (entrysizes, sizeof(T)) { ; }
+
+    /// Inserts element acont into row i. Does not test if already used.
+    void Add (int i, const T & acont)
+    {
+      if (data[i].size == data[i].maxsize)
+        IncSize (i, sizeof (T));
+      else
+        data[i].size++;
+      static_cast<T*> (data[i].col) [data[i].size-1] = acont;
+    }
+
+    /// Inserts element acont into row i, iff not yet exists.
+    void AddUnique (int i, const T & cont)
+    {
+      int es = EntrySize (i);
+      int * line = const_cast<int*> (GetLine (i));
+      for (int j = 0; j < es; j++)
+        if (line[j] == cont)
+          return;
+      Add (i, cont);
+    }
+
+
+    /// Inserts element acont into row i. Does not test if already used.
+    void AddEmpty (int i)
+    {
+      IncSize (i, sizeof (T));
+    }
+
+    /** Set the nr-th element in the i-th row to acont.
+        Does not check for overflow. */
+    void Set (int i, int nr, const T & acont)
+    { static_cast<T*> (data[i].col)[nr] = acont; }
+
+
+    /** Returns the nr-th element in the i-th row.
+      Does not check for overflow. */
+    const T & Get (int i, int nr) const
+    { return static_cast<T*> (data[i].col)[nr]; }
+
+
+    /** Returns pointer to the first element in row i. */
+    const T * GetLine (int i) const
+    { return static_cast<T*> (data[i].col); }
+
+
+    /// Returns size of the table.
+    int Size () const
+    { return data.Size(); }
+
+    /// Returns size of the i-th row.
+    int EntrySize (int i) const
+    { return data[i].size; }
+
+    ///
+    void DecEntrySize (int i)
+    { DecSize(i); }
+
+    /// Access entry i
+    FlatArray<T> operator[] (int i)
+    { return FlatArray<T> (data[i].size, static_cast<T*> (data[i].col)); }
+
+    /*
+    typedef const FlatArray<T> ConstFlatArray;
+    /// Access entry i
+    ConstFlatArray operator[] (int i) const
+    { return FlatArray<T> (data[i].size, static_cast<T*> (data[i].col)); }
+    */
+    FlatArray<T> operator[] (int i) const
+    { return FlatArray<T> (data[i].size, static_cast<T*> (data[i].col)); }
+  };
+
+
+
+
+  /// Print table
+  template <class T>
+  inline ostream & operator<< (ostream & s, const DynamicTable<T> & table)
+  {
+    for (int i = 0; i < table.Size(); i++)
+      {
+        s << i << ":";
+        for (int j = 0; j < table[i].Size(); j++)
+          s << " " << table[i][j];
+        s << "\n";
+      }
+    s << std::flush;
+    return s;
+  }
+
+  typedef DynamicTable<int> IntTable;
+
+} // namespace ngcore
+
+#endif // NETGEN_CORE_TABLE_HPP

libsrc/core/utils.hpp

@@ -146,6 +146,35 @@ namespace ngcore
   template<typename T>
   using index_type = typename detail::IndexTypeHelper<T>::type;
 
+  class MyMutex
+  {
+    std::atomic<bool> m;
+  public:
+    MyMutex() { m.store(false, std::memory_order_relaxed); }
+    void lock()
+    {
+      bool should = false;
+      while (!m.compare_exchange_weak(should, true))
+        {
+          should = false;
+          _mm_pause();
+        }
+    }
+    void unlock()
+    {
+      m = false;
+    }
+  };
+
+  class MyLock
+  {
+    MyMutex & mutex;
+  public:
+    MyLock (MyMutex & amutex) : mutex(amutex) { mutex.lock(); }
+    ~MyLock () { mutex.unlock(); }
+  };
+
+
 } // namespace ngcore
 
 #endif // NETGEN_CORE_UTILS_HPP