Fixes post review with Peter: a) Correct bug in isRegularShape - detect 3d matrix where 1st slice is 2x2 and second slice is 2x1; b) Synchronisation of EigenResizeCounter done by checking we're the OMP primary thread; c) Move definition of EigenResizeCounter to new file, BaseIO.cc

Grid/serialisation/BaseIO.cc

@@ -0,0 +1,35 @@
+/*************************************************************************************
+
+Grid physics library, www.github.com/paboyle/Grid
+
+Source file: ./lib/serialisation/BaseIO.h
+
+Copyright (C) 2015
+
+Author: Michael Marshall <michael.marshall@ed.ac.uk>
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+See the full license in the file "LICENSE" in the top level distribution directory
+*************************************************************************************/
+/*  END LEGAL */
+
+#include <Grid/GridCore.h>
+
+NAMESPACE_BEGIN(Grid)
+
+std::uint64_t EigenIO::EigenResizeCounter(0);
+
+NAMESPACE_END(Grid)

Grid/serialisation/BaseIO.h

@@ -9,6 +9,7 @@
 Author: Antonin Portelli <antonin.portelli@me.com>
 Author: Peter Boyle <paboyle@ph.ed.ac.uk>
 Author: Guido Cossu <guido.cossu@ed.ac.uk>
+Author: Michael Marshall <michael.marshall@ed.ac.uk>
 
     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -114,7 +115,7 @@ namespace Grid {
 
     // Counter for resized EigenTensors (poor man's substitute for allocator)
     // Defined in BinaryIO.cc
-    extern std::atomic_uint64_t EigenResizeCounter;
+    extern std::uint64_t EigenResizeCounter;
   }
 
   // Abstract writer/reader classes ////////////////////////////////////////////
@@ -502,11 +503,14 @@ namespace Grid {
   typename std::enable_if<EigenIO::is_tensor_variable<ETensor>::value, void>::type
   Reader<T>::Reshape(ETensor &t, const std::array<typename ETensor::Index, ETensor::NumDimensions> &dims )
   {
-    typename ETensor::Index before = t.size();
+#ifdef GRID_OMP
+    // The memory counter is the reason this must be done from the primary thread
+    assert(omp_in_parallel()==0 && "Deserialisation which resizes Eigen tensor must happen from primary thread");
+#endif
+    EigenIO::EigenResizeCounter -= static_cast<uint64_t>(t.size()) * sizeof(typename ETensor::Scalar);
     //t.reshape( dims );
     t.resize( dims );
-    uint64_t diff = static_cast<uint64_t>(( t.size() - before ) * sizeof(typename ETensor::Scalar));
+    EigenIO::EigenResizeCounter += static_cast<uint64_t>(t.size()) * sizeof(typename ETensor::Scalar);
-    EigenIO::EigenResizeCounter.fetch_add(diff, std::memory_order_relaxed);
   }
 
   template <typename T>

Grid/serialisation/BinaryIO.cc

@@ -30,9 +30,6 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
 
 NAMESPACE_BEGIN(Grid);
 
-// Declared in BaseIO.h
-std::atomic_uint64_t EigenIO::EigenResizeCounter(0);
-
 // Writer implementation ///////////////////////////////////////////////////////
 BinaryWriter::BinaryWriter(const std::string &fileName)
 : file_(fileName, std::ios::binary|std::ios::out)

Grid/serialisation/Hdf5IO.cc

@@ -1,3 +1,34 @@
+/*************************************************************************************
+ 
+ Grid physics library, www.github.com/paboyle/Grid
+ 
+ Source file: ./Grid/serialisation/VectorUtils.h
+ 
+ Copyright (C) 2015
+ 
+ Author: Antonin Portelli <antonin.portelli@me.com>
+ Author: Peter Boyle <paboyle@ed.ac.uk>
+ Author: Guido Cossu <guido.cossu@ed.ac.uk>
+ Author: Michael Marshall <michael.marshall@ed.ac.uk>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ 
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ 
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ 
+ See the full license in the file "LICENSE" in the top level distribution directory
+ *************************************************************************************/
+/*  END LEGAL */
+
 #include <Grid/Grid.h>
 
 using namespace Grid;

Grid/serialisation/Hdf5IO.h

@@ -1,3 +1,34 @@
+/*************************************************************************************
+ 
+ Grid physics library, www.github.com/paboyle/Grid
+ 
+ Source file: ./Grid/serialisation/VectorUtils.h
+ 
+ Copyright (C) 2015
+ 
+ Author: Peter Boyle <paboyle@ed.ac.uk>
+ Author: Antonin Portelli <antonin.portelli@me.com>
+ Author: Guido Cossu <guido.cossu@ed.ac.uk>
+ Author: Michael Marshall <michael.marshall@ed.ac.uk>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ 
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ 
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ 
+ See the full license in the file "LICENSE" in the top level distribution directory
+ *************************************************************************************/
+/*  END LEGAL */
+
 #ifndef GRID_SERIALISATION_HDF5_H
 #define GRID_SERIALISATION_HDF5_H
 

Grid/serialisation/VectorUtils.h

@@ -9,7 +9,8 @@
  Author: Antonin Portelli <antonin.portelli@me.com>
  Author: Peter Boyle <paboyle@ph.ed.ac.uk>
  Author: paboyle <paboyle@ph.ed.ac.uk>
- 
+ Author: Michael Marshall <michael.marshall@ed.ac.uk>
+
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
@@ -500,17 +501,56 @@ namespace Grid {
   }
 
   // In general, scalar types are considered "flattenable" (regularly shaped)
+  template <typename T>
+  bool isRegularShapeHelper(const std::vector<T> &, std::vector<std::size_t> &, int, bool)
+  {
+    return true;
+  }
+
+  template <typename T>
+  bool isRegularShapeHelper(const std::vector<std::vector<T>> &v, std::vector<std::size_t> &Dims, int Depth, bool bFirst)
+  {
+    if( bFirst)
+    {
+      assert( Dims.size() == Depth     && "Bug: Delete this message after testing" );
+      Dims.push_back(v[0].size());
+      if (!Dims[Depth])
+        return false;
+    }
+    else
+    {
+      assert( Dims.size() >= Depth + 1 && "Bug: Delete this message after testing" );
+    }
+    for (std::size_t i = 0; i < v.size(); ++i)
+    {
+      if (v[i].size() != Dims[Depth] || !isRegularShapeHelper(v[i], Dims, Depth + 1, bFirst && i==0))
+      {
+        return false;
+      }
+    }
+    return true;
+  }
+
   template <typename T>
   bool isRegularShape(const T &t) { return true; }
 
+  template <typename T>
+  bool isRegularShape(const std::vector<T> &v) { return !v.empty(); }
+
   // Return non-zero if all dimensions of this std::vector<std::vector<T>> are regularly shaped
   template <typename T>
   bool isRegularShape(const std::vector<std::vector<T>> &v)
   {
+    if (v.empty() || v[0].empty())
+      return false;
     // Make sure all of my rows are the same size
-    for (std::size_t i = 0; i < v.size(); ++i)
+    std::vector<std::size_t> Dims;
+    Dims.reserve(is_flattenable<T>::vecRank);
+    Dims.push_back(v.size());
+    Dims.push_back(v[0].size());
+    for (std::size_t i = 0; i < Dims[0]; ++i)
     {
-      if (v[i].size() != v[0].size() || !isRegularShape(v[i]))
+      if (v[i].size() != Dims[1] || !isRegularShapeHelper(v[i], Dims, 2, i==0))
       {
         return false;
       }