Merge branch 'develop' of https://github.com/paboyle/Grid into develop

lib/algorithms/iterative/BlockConjugateGradient.h

@@ -87,15 +87,22 @@ void ThinQRfact (Eigen::MatrixXcd &m_rr,
   ////////////////////////////////////////////////////////////////////////////////////////////////////
   sliceInnerProductMatrix(m_rr,R,R,Orthog);
 
-  ////////////////////////////////////////////////////////////////////////////////////////////////////
+  // Force manifest hermitian to avoid rounding related
-  // Cholesky from Eigen
+  m_rr = 0.5*(m_rr+m_rr.adjoint());
-  // There exists a ldlt that is documented as more stable
-  ////////////////////////////////////////////////////////////////////////////////////////////////////
-  Eigen::MatrixXcd L    = m_rr.llt().matrixL(); 
 
+#if 0
+  std::cout << " Calling Cholesky  ldlt on m_rr "  << m_rr <<std::endl;
+  Eigen::MatrixXcd L_ldlt = m_rr.ldlt().matrixL(); 
+  std::cout << " Called Cholesky  ldlt on m_rr "  << L_ldlt <<std::endl;
+  auto  D_ldlt = m_rr.ldlt().vectorD(); 
+  std::cout << " Called Cholesky  ldlt on m_rr "  << D_ldlt <<std::endl;
+#endif
+
+  //  std::cout << " Calling Cholesky  llt on m_rr "  <<std::endl;
+  Eigen::MatrixXcd L    = m_rr.llt().matrixL(); 
+  //  std::cout << " Called Cholesky  llt on m_rr "  << L <<std::endl;
   C    = L.adjoint();
   Cinv = C.inverse();
-
   ////////////////////////////////////////////////////////////////////////////////////////////////////
   // Q = R C^{-1}
   //
@@ -103,7 +110,6 @@ void ThinQRfact (Eigen::MatrixXcd &m_rr,
   //
   // NB maddMatrix conventions are Right multiplication X[j] a[j,i] already
   ////////////////////////////////////////////////////////////////////////////////////////////////////
-  // FIXME:: make a sliceMulMatrix to avoid zero vector
   sliceMulMatrix(Q,Cinv,R,Orthog);
 }
 ////////////////////////////////////////////////////////////////////////////////////////////////////

lib/allocator/AlignedAllocator.cc

@@ -1,7 +1,5 @@
-
-
-
 #include <Grid/GridCore.h>
+#include <fcntl.h>
 
 namespace Grid {
 
@@ -63,4 +61,37 @@ void *PointerCache::Lookup(size_t bytes) {
   return NULL;
 }
 
+
+void check_huge_pages(void *Buf,uint64_t BYTES)
+{
+#ifdef __linux__
+  int fd = open("/proc/self/pagemap", O_RDONLY);
+  assert(fd >= 0);
+  const int page_size = 4096;
+  uint64_t virt_pfn = (uint64_t)Buf / page_size;
+  off_t offset = sizeof(uint64_t) * virt_pfn;
+  uint64_t npages = (BYTES + page_size-1) / page_size;
+  uint64_t pagedata[npages];
+  uint64_t ret = lseek(fd, offset, SEEK_SET);
+  assert(ret == offset);
+  ret = ::read(fd, pagedata, sizeof(uint64_t)*npages);
+  assert(ret == sizeof(uint64_t) * npages);
+  int nhugepages = npages / 512;
+  int n4ktotal, nnothuge;
+  n4ktotal = 0;
+  nnothuge = 0;
+  for (int i = 0; i < nhugepages; ++i) {
+    uint64_t baseaddr = (pagedata[i*512] & 0x7fffffffffffffULL) * page_size;
+    for (int j = 0; j < 512; ++j) {
+      uint64_t pageaddr = (pagedata[i*512+j] & 0x7fffffffffffffULL) * page_size;
+      ++n4ktotal;
+      if (pageaddr != baseaddr + j * page_size)
+	++nnothuge;
+      }
+  }
+  int rank = CartesianCommunicator::RankWorld();
+  printf("rank %d Allocated %d 4k pages, %d not in huge pages\n", rank, n4ktotal, nnothuge);
+#endif
+}
+
 }

lib/allocator/AlignedAllocator.h

@@ -64,6 +64,8 @@ namespace Grid {
 
   };
 
+  void check_huge_pages(void *Buf,uint64_t BYTES);
+
 ////////////////////////////////////////////////////////////////////
 // A lattice of something, but assume the something is SIMDized.
 ////////////////////////////////////////////////////////////////////

lib/serialisation/BaseIO.h

@@ -86,7 +86,7 @@ namespace Grid {
                                       or element<T>::is_number;
   };
   
-  // Vector flatening utility class ////////////////////////////////////////////
+  // Vector flattening utility class ////////////////////////////////////////////
   // Class to flatten a multidimensional std::vector
   template <typename V>
   class Flatten

lib/serialisation/JSON_IO.cc

@@ -42,6 +42,7 @@ JSONWriter::~JSONWriter(void)
 
   // write prettified JSON to file
   std::ofstream os(fileName_);
+  //std::cout << "JSONWriter::~JSONWriter" << std::endl;
   os << std::setw(2) << json::parse(ss_.str()) << std::endl;
 }
 
@@ -56,6 +57,7 @@ void JSONWriter::push(const string &s)
 
 void JSONWriter::pop(void)
 {
+  //std::cout << "JSONWriter::pop" << std::endl;
   delete_comma();
   ss_ << "},";
 }
@@ -67,20 +69,22 @@ void JSONWriter::delete_comma()
   ss_.str(dlast);
 }
 
+
 // here we are hitting a g++ bug (Bug 56480)
 // compiles fine with clang
 // have to wrap in the Grid namespace
 // annoying, but necessary for TravisCI
 namespace Grid
 {
-  template<>
+  void JSONWriter::writeDefault(const std::string &s,	const std::string &x)
-  void JSONWriter::writeDefault(const std::string &s,
-				const std::string &x)
   {
+    //std::cout << "JSONWriter::writeDefault(string) : " << s <<  std::endl;
+    std::ostringstream os;
+    os << std::boolalpha << x;
     if (s.size())
-      ss_ << "\""<< s << "\" : \"" << x << "\" ," ; 
+      ss_ << "\""<< s << "\" : \"" << os.str() << "\" ," ;
     else
-      ss_ << "\"" << x << "\" ," ;
+     ss_ << os.str() << " ," ;
   }
 }// namespace Grid 
 
@@ -138,6 +142,7 @@ void JSONReader::pop(void)
 
 bool JSONReader::nextElement(const std::string &s)
 {
+  // Work in progress
   // JSON dictionaries do not support multiple names 
   // Same name objects must be packed in vectors
   ++it_;

lib/serialisation/JSON_IO.h

@@ -58,10 +58,15 @@ namespace Grid
     void writeDefault(const std::string &s, const std::complex<U> &x);
     template <typename U>
     void writeDefault(const std::string &s, const std::vector<U> &x);
+    template <typename U, typename P>
+    void writeDefault(const std::string &s, const std::pair<U,P> &x);
 
     template<std::size_t N>
     void writeDefault(const std::string &s, const char(&x)[N]);
 
+    void writeDefault(const std::string &s, const std::string &x);
+
+
   private:
     void delete_comma();
     std::string         fileName_;
@@ -82,6 +87,8 @@ namespace Grid
     void readDefault(const std::string &s, std::complex<U> &output);
     template <typename U>
     void readDefault(const std::string &s, std::vector<U> &output);
+    template <typename U, typename P>
+    void readDefault(const std::string &s, std::pair<U,P> &output);
   private:
     json                jobject_; // main object
     json                jcur_;  // current json object
@@ -106,7 +113,7 @@ namespace Grid
   template <typename U>
   void JSONWriter::writeDefault(const std::string &s, const U &x)
   {
-    //std::cout << "JSONReader::writeDefault(U) : " << s <<  std::endl;
+    //std::cout << "JSONWriter::writeDefault(U) : " << s <<  " " << x <<std::endl;
     std::ostringstream os;
     os << std::boolalpha << x;
     if (s.size())
@@ -118,7 +125,7 @@ namespace Grid
   template <typename U>
   void JSONWriter::writeDefault(const std::string &s, const std::complex<U> &x)
   {
-    //std::cout << "JSONReader::writeDefault(complex) : " << s <<  std::endl;
+    //std::cout << "JSONWriter::writeDefault(complex) : " << s <<  " " << x <<  std::endl;
     std::ostringstream os;
     os << "["<< std::boolalpha << x.real() << ", " << x.imag() << "]";
     if (s.size())
@@ -127,10 +134,22 @@ namespace Grid
      ss_ << os.str() << " ," ;
   }
 
+  template <typename U, typename P>
+  void JSONWriter::writeDefault(const std::string &s, const std::pair<U,P> &x)
+  {
+    //std::cout << "JSONWriter::writeDefault(pair) : " << s <<  " " << x <<  std::endl;
+    std::ostringstream os;
+    os << "["<< std::boolalpha << "\""<< x.first << "\" , \"" << x.second << "\" ]";
+    if (s.size())
+      ss_ << "\""<< s << "\" : " << os.str() << " ," ;
+    else
+     ss_ << os.str() << " ," ;
+  }
+
   template <typename U>
   void JSONWriter::writeDefault(const std::string &s, const std::vector<U> &x)
   {
-    //std::cout << "JSONReader::writeDefault(vec U) : " << s <<  std::endl;
+    //std::cout << "JSONWriter::writeDefault(vec U) : " << s <<  std::endl;
 
     if (s.size())
       ss_ << " \""<<s<<"\" : [";
@@ -146,12 +165,12 @@ namespace Grid
 
   template<std::size_t N>
   void JSONWriter::writeDefault(const std::string &s, const char(&x)[N]){
-    //std::cout << "JSONReader::writeDefault(char U) : " << s <<  std::endl;
+    //std::cout << "JSONWriter::writeDefault(char U) : " << s <<  "  " << x << std::endl;
 
     if (s.size())
-    ss_ << "\""<< s << "\" : \"" << x << "\" ," ;
+      ss_ << "\""<< s << "\" : \"" << x << "\" ," ;
     else
-    ss_ << "\"" << x << "\" ," ;
+      ss_ << "\"" << x << "\" ," ;
   }
 
   // Reader template implementation ////////////////////////////////////////////
@@ -173,11 +192,35 @@ namespace Grid
 
   }
 
+  // Reader template implementation ////////////////////////////////////////////
+  template <typename U, typename P>
+  void JSONReader::readDefault(const std::string &s, std::pair<U,P> &output)
+  {
+    U first;
+    P second;
+    json j;
+    if (s.size()){
+      //std::cout << "JSONReader::readDefault(pair) : " << s << "  |  "<< jcur_[s] << std::endl;
+      j = jcur_[s];
+    } else {
+      j = jcur_;
+    }
+    json::iterator it = j.begin();
+    jcur_ = *it;
+    read("", first);
+    it++;
+    jcur_ = *it;
+    read("", second);
+    output = std::pair<U,P>(first,second);
+  }
+
+
+
   template <typename U>
   void JSONReader::readDefault(const std::string &s, std::complex<U> &output)
   {
     U tmp1, tmp2;
-    //std::cout << "JSONReader::readDefault( complex U) : " << s << "  :  "<< jcur_ << std::endl;
+    //std::cout << "JSONReader::readDefault(complex U) : " << s << "  :  "<< jcur_ << std::endl;
     json j = jcur_;
     json::iterator it = j.begin();
     jcur_ = *it;

lib/simd/Grid_neon.h

@@ -82,11 +82,11 @@ namespace Optimization {
       double tmp[2]={a,b};
       return vld1q_f64(tmp);
     }
-    //Real double // N:tbc
+    //Real double
     inline float64x2_t operator()(double a){
       return vdupq_n_f64(a);
     }
-    //Integer // N:tbc
+    //Integer
     inline uint32x4_t operator()(Integer a){
       return vdupq_n_u32(a);
     }
@@ -124,33 +124,32 @@ namespace Optimization {
   // Nils: Vset untested; not used currently in Grid at all;
   // git commit 4a8c4ccfba1d05159348d21a9698028ea847e77b
   struct Vset{
-    // Complex float // N:ok
+    // Complex float
     inline float32x4_t operator()(Grid::ComplexF *a){
       float tmp[4]={a[1].imag(),a[1].real(),a[0].imag(),a[0].real()};
       return vld1q_f32(tmp);
     }
-    // Complex double // N:ok
+    // Complex double
     inline float64x2_t operator()(Grid::ComplexD *a){
       double tmp[2]={a[0].imag(),a[0].real()};
       return vld1q_f64(tmp);
     }
-    // Real float // N:ok
+    // Real float
     inline float32x4_t operator()(float *a){
       float tmp[4]={a[3],a[2],a[1],a[0]};
       return vld1q_f32(tmp);
     }
-    // Real double // N:ok
+    // Real double
     inline float64x2_t operator()(double *a){
       double tmp[2]={a[1],a[0]};
       return vld1q_f64(tmp);
     }
-    // Integer // N:ok
+    // Integer
     inline uint32x4_t operator()(Integer *a){
       return vld1q_dup_u32(a);
     }
   };
 
-  // N:leaving as is
   template <typename Out_type, typename In_type>
   struct Reduce{
     //Need templated class to overload output type
@@ -249,9 +248,9 @@ namespace Optimization {
       return vfmaq_f32(r4, r0, a); //  ar*br-ai*bi ai*br+ar*bi ...
 
       // no fma, use mul and add
-      //float32x4_t r5;
+      // float32x4_t r5;
-      //r5 = vmulq_f32(r0, a);
+      // r5 = vmulq_f32(r0, a);
-      //return vaddq_f32(r4, r5);
+      // return vaddq_f32(r4, r5);
     }
     // Complex double
     inline float64x2_t operator()(float64x2_t a, float64x2_t b){
@@ -272,9 +271,9 @@ namespace Optimization {
       return vfmaq_f64(r4, r0, a); //  ar*br-ai*bi ai*br+ar*bi
 
       // no fma, use mul and add
-      //float64x2_t r5;
+      // float64x2_t r5;
-      //r5 = vmulq_f64(r0, a);
+      // r5 = vmulq_f64(r0, a);
-      //return vaddq_f64(r4, r5);
+      // return vaddq_f64(r4, r5);
     }
   };
 
@@ -421,11 +420,6 @@ namespace Optimization {
       }
     }
 
-// working, but no restriction on n
-//    template<int n> static inline float32x4_t tRotate(float32x4_t in){ return vextq_f32(in,in,n); };
-//    template<int n> static inline float64x2_t tRotate(float64x2_t in){ return vextq_f64(in,in,n); };
-
-// restriction on n
     template<int n> static inline float32x4_t tRotate(float32x4_t in){ return vextq_f32(in,in,n%4); };
     template<int n> static inline float64x2_t tRotate(float64x2_t in){ return vextq_f64(in,in,n%2); };
 
@@ -441,7 +435,7 @@ namespace Optimization {
       sb = vcvt_high_f32_f16(h);
       // there is no direct conversion from lower float32x4_t to float64x2_t
       // vextq_f16 not supported by clang 3.8 / 4.0 / arm clang
-      //float16x8_t h1 = vextq_f16(h, h, 4); // correct, but not supported by clang
+      // float16x8_t h1 = vextq_f16(h, h, 4); // correct, but not supported by clang
       // workaround for clang
       uint32x4_t h1u = reinterpret_cast<uint32x4_t>(h);
       float16x8_t h1 = reinterpret_cast<float16x8_t>(vextq_u32(h1u, h1u, 2));
@@ -547,7 +541,7 @@ namespace Optimization {
 
 
   //Complex double Reduce
-  template<> // N:by Boyle
+  template<>
   inline Grid::ComplexD Reduce<Grid::ComplexD, float64x2_t>::operator()(float64x2_t in){
     u128d conv; conv.v = in;
     return Grid::ComplexD(conv.f[0],conv.f[1]);
@@ -562,9 +556,7 @@ namespace Optimization {
   //Integer Reduce
   template<>
   inline Integer Reduce<Integer, uint32x4_t>::operator()(uint32x4_t in){
-    // FIXME unimplemented
+    return vaddvq_u32(in);
-    printf("Reduce : Missing integer implementation -> FIX\n");
-    assert(0);
   }
 }
 
@@ -604,3 +596,4 @@ namespace Optimization {
   typedef Optimization::TimesI      TimesISIMD;
 
 }
+

lib/stencil/Stencil.h

@@ -400,11 +400,13 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
       if ( sshift[0] == sshift[1] ) {
 	if (splice_dim) {
 	  splicetime-=usecond();
-	  same_node = same_node && GatherSimd(source,dimension,shift,0x3,compress,face_idx);
+	  auto tmp  = GatherSimd(source,dimension,shift,0x3,compress,face_idx);
+	  same_node = same_node && tmp;
 	  splicetime+=usecond();
 	} else { 
 	  nosplicetime-=usecond();
-	  same_node = same_node && Gather(source,dimension,shift,0x3,compress,face_idx);
+	  auto tmp  = Gather(source,dimension,shift,0x3,compress,face_idx);
+	  same_node = same_node && tmp;
 	  nosplicetime+=usecond();
 	}
       } else {
@@ -412,13 +414,15 @@ class CartesianStencil { // Stencil runs along coordinate axes only; NO diagonal
 	  splicetime-=usecond();
 	  // if checkerboard is unfavourable take two passes
 	  // both with block stride loop iteration
-	  same_node = same_node && GatherSimd(source,dimension,shift,0x1,compress,face_idx);
+	  auto tmp1 =  GatherSimd(source,dimension,shift,0x1,compress,face_idx);
-	  same_node = same_node && GatherSimd(source,dimension,shift,0x2,compress,face_idx);
+	  auto tmp2 =  GatherSimd(source,dimension,shift,0x2,compress,face_idx);
+	  same_node = same_node && tmp1 && tmp2;
 	  splicetime+=usecond();
 	} else {
 	  nosplicetime-=usecond();
-	  same_node = same_node && Gather(source,dimension,shift,0x1,compress,face_idx);
+	  auto tmp1 = Gather(source,dimension,shift,0x1,compress,face_idx);
-	  same_node = same_node && Gather(source,dimension,shift,0x2,compress,face_idx);
+	  auto tmp2 = Gather(source,dimension,shift,0x2,compress,face_idx);
+	  same_node = same_node && tmp1 && tmp2;
 	  nosplicetime+=usecond();
 	}
       }

tests/IO/Test_serialisation.cc

@@ -29,7 +29,6 @@ Author: Peter Boyle <paboyle@ph.ed.ac.uk>
     /*  END LEGAL */
 #include <Grid/Grid.h>
 
-
 using namespace Grid;
 using namespace Grid::QCD;
 
@@ -151,6 +150,11 @@ int main(int argc,char **argv)
   ioTest<TextWriter, TextReader>("iotest.dat", obj, "text   (object)           ");
   ioTest<TextWriter, TextReader>("iotest.dat", vec, "text   (vector of objects)");
   ioTest<TextWriter, TextReader>("iotest.dat", pair, "text   (pair of objects)");
+  //// text
+  ioTest<JSONWriter, JSONReader>("iotest.json", obj,  "JSON   (object)           ");
+  ioTest<JSONWriter, JSONReader>("iotest.json", vec,  "JSON   (vector of objects)");
+  ioTest<JSONWriter, JSONReader>("iotest.json", pair, "JSON   (pair of objects)");
+
   //// HDF5
 #undef HAVE_HDF5
 #ifdef HAVE_HDF5
@@ -201,8 +205,10 @@ int main(int argc,char **argv)
     JSONWriter JW("bother.json");
 
     // test basic type writing
+    myenum a = myenum::red;
     push(JW,"BasicTypes");
     write(JW,std::string("i16"),i16);
+    write(JW,"myenum",a);
     write(JW,"u16",u16);
     write(JW,"i32",i32);
     write(JW,"u32",u32);
@@ -213,13 +219,14 @@ int main(int argc,char **argv)
     write(JW,"b",b);
     pop(JW);
 
+
     // test serializable class writing
     myclass obj(1234); // non-trivial constructor
+    std::cout << obj << std::endl;
     std::cout << "-- serialisable class writing to 'bother.json'..." << std::endl;
     write(JW,"obj",obj);
     JW.write("obj2", obj);
 
-    std::cout << obj << std::endl;
 
     std::vector<myclass> vec;
     vec.push_back(myclass(1234));
@@ -229,6 +236,7 @@ int main(int argc,char **argv)
 
   }
 
+
   {
     JSONReader RD("bother.json");
     myclass jcopy1;
@@ -239,6 +247,7 @@ int main(int argc,char **argv)
     std::cout << jcopy1 << std::endl << jveccopy1 << std::endl;
   }
  
+
 /*
   // This is still work in progress
   {

tests/solver/Test_staggered_cg_prec.cc

@@ -0,0 +1,87 @@
+    /*************************************************************************************
+
+    Grid physics library, www.github.com/paboyle/Grid 
+
+    Source file: ./tests/Test_wilson_cg_unprec.cc
+
+    Copyright (C) 2015
+
+Author: Azusa Yamaguchi <ayamaguc@staffmail.ed.ac.uk>
+Author: Peter Boyle <paboyle@ph.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>
+#include <Grid/algorithms/iterative/BlockConjugateGradient.h>
+
+using namespace std;
+using namespace Grid;
+using namespace Grid::QCD;
+
+template<class d>
+struct scal {
+  d internal;
+};
+
+  Gamma::Algebra Gmu [] = {
+    Gamma::Algebra::GammaX,
+    Gamma::Algebra::GammaY,
+    Gamma::Algebra::GammaZ,
+    Gamma::Algebra::GammaT
+  };
+
+int main (int argc, char ** argv)
+{
+  typedef typename ImprovedStaggeredFermionR::FermionField FermionField; 
+  typedef typename ImprovedStaggeredFermionR::ComplexField ComplexField; 
+  typename ImprovedStaggeredFermionR::ImplParams params; 
+
+  Grid_init(&argc,&argv);
+
+  std::vector<int> latt_size   = GridDefaultLatt();
+  std::vector<int> simd_layout = GridDefaultSimd(Nd,vComplex::Nsimd());
+  std::vector<int> mpi_layout  = GridDefaultMpi();
+  GridCartesian               Grid(latt_size,simd_layout,mpi_layout);
+  GridRedBlackCartesian     RBGrid(latt_size,simd_layout,mpi_layout);
+
+  std::vector<int> seeds({1,2,3,4});
+  GridParallelRNG          pRNG(&Grid);  pRNG.SeedFixedIntegers(seeds);
+
+  FermionField src(&Grid); random(pRNG,src);
+  RealD nrm = norm2(src);
+  LatticeGaugeField Umu(&Grid); SU3::HotConfiguration(pRNG,Umu);
+
+  double volume=1;
+  for(int mu=0;mu<Nd;mu++){
+    volume=volume*latt_size[mu];
+  }  
+  
+  RealD mass=0.1;
+  ImprovedStaggeredFermionR Ds(Umu,Umu,Grid,RBGrid,mass);
+
+  FermionField res_o(&RBGrid); 
+  FermionField src_o(&RBGrid); 
+  pickCheckerboard(Odd,src_o,src);
+  res_o=zero;
+
+  SchurDiagMooeeOperator<ImprovedStaggeredFermionR,FermionField> HermOpEO(Ds);
+  ConjugateGradient<FermionField> CG(1.0e-8,10000);
+  CG(HermOpEO,src_o,res_o);
+
+  Grid_finalize();
+}