Merge branch 'sort' into development

src/Makefile

@@ -69,10 +69,12 @@ nonhydro_x: nonhydro_sw.o TArray.o T_util.o Parformer.o Splits.o Par_util.o Spli
 derek_x: derek.o TArray.o T_util.o Parformer.o ESolver.o Timestep.o Splits.o Par_util.o Split_reader.o gmres.o gmres_1d_solver.o gmres_2d_solver.o grad.o multigrid.o 
 	$(LD) $(LDFLAGS) -o $@ $^ $(LDLIBS)
 
-cases/%.x: cases/%.o cases/%.src.o TArray.o T_util.o Parformer.o ESolver.o Timestep.o NSIntegrator.o BaseCase.o Science.o Splits.o Par_util.o Split_reader.o gmres.o gmres_1d_solver.o gmres_2d_solver.o grad.o multigrid.o Options.o
+cases/%.x: cases/%.o cases/%.src.o TArray.o T_util.o Parformer.o ESolver.o Timestep.o NSIntegrator.o BaseCase.o \
+           Science.o Splits.o Par_util.o Split_reader.o gmres.o gmres_1d_solver.o gmres_2d_solver.o grad.o multigrid.o Options.o Sorter.o
 	$(LD) $(LDFLAGS) -o $@ $^ $(LDLIBS)
 
-cases/%_x: cases/%.o cases/%.src.o TArray.o T_util.o Parformer.o ESolver.o Timestep.o NSIntegrator.o BaseCase.o Science.o Splits.o Par_util.o Split_reader.o gmres.o gmres_1d_solver.o gmres_2d_solver.o grad.o multigrid.o Options.o
+cases/%_x: cases/%.o cases/%.src.o TArray.o T_util.o Parformer.o ESolver.o Timestep.o NSIntegrator.o BaseCase.o \
+           Science.o Splits.o Par_util.o Split_reader.o gmres.o gmres_1d_solver.o gmres_2d_solver.o grad.o multigrid.o Options.o Sorter.o
 	$(LD) $(LDFLAGS) -o $@ $^ $(LDLIBS)
 
 tests/test%.src.c: tests/test%.cpp CaseFileSource.c

src/Sorter.cpp

+// Development case for array sorting in parallel, via quickselect
+
+#include <blitz/array.h>
+#include "TArray.hpp"
+#include <mpi.h>
+#include <random/normal.h>
+#include "Par_util.hpp"
+#include <stdio.h>
+#include <unistd.h>
+#include <vector>
+#include <algorithm>
+#include <stdlib.h>
+#include <blitz/tinyvec-et.h>
+
+#include "Sorter.hpp"
+
+using std::vector;
+
+using namespace ranlib;
+
+namespace Sorter {
+
+   parsorter::parsorter(int isize, MPI_Comm incomm):
+      c(incomm), ASIZE(isize), tmparray(0) {
+         MPI_Comm_rank(MPI_COMM_WORLD,&mygrank);
+         MPI_Comm_rank(c,&myrank);
+         MPI_Comm_size(c,&nproc);
+         asizes.resize(nproc);
+         ASIZE = isize;
+
+         if (nproc > 1) {
+//            double now = MPI_Wtime();
+            MPI_Allgather(&ASIZE,1,MPI_INT,&asizes[0],1,MPI_INT,c);
+            int color = (myrank >= (nproc/2));
+            MPI_Comm_split(c,color,myrank,&nestedcomm);
+//            mpilag += MPI_Wtime()-now;
+
+            nested = new parsorter(isize,nestedcomm);
+         } else {
+            asizes[0] = ASIZE;
+            nested = 0;
+         }
+   }
+
+   parsorter::~parsorter() {
+      if (nested) delete nested;
+      if (tmparray) delete tmparray;
+      //if (nproc > 1) MPI_Comm_free(&nestedcomm);
+   }
+
+   void parsorter::sortkvpairs(vector<kvpair> * inarray, vector<kvpair> * tarray) {
+      vector<kvpair> &local = *inarray;
+
+      if (nproc == 1) {
+         //double now = MPI_Wtime();
+         std::stable_sort(local.begin(),local.end());
+         //sortlag += MPI_Wtime()-now;
+         return;
+      }
+
+      if (tarray == 0) {
+         if (tmparray == 0) tmparray = new vector<kvpair>(ASIZE);
+         tarray = tmparray;
+      } 
+      vector<kvpair> &tmp = *tarray;
+
+      // Perform a global search for the median;
+      int gtoosmall = 0; // Number of global entries confirmed to be too small
+      int gtoobig = 0; // Number of global entries confirmed to be too big
+      typedef struct {int lt; int eq;} iterstats;
+      iterstats giterstat = {0,0}, literstat = {0,0}; // Iteration statistics: number now less-than and equal-to
+
+      int gtarget = 1; // Base-one index of the target, if we had a globally-sorted array
+      for (int pp = 0; pp < (nproc/2); pp++) {
+         // We want to put the median just after the halfway-processor
+         gtarget += asizes[pp];
+      }
+
+      double gmedkey = 0; // Key of the median element
+
+      int llbound = 0; 
+      int lubound = ASIZE-1;
+
+      double lmedkey = 0.0; // Key of the local median
+      int lvalid = 0;
+
+      vector<double> allmedians(nproc);
+      double now;
+
+      for(;;) {
+
+         //gmedfindcount++;
+
+//         now = MPI_Wtime(); 
+         if (lubound >= llbound) {
+            //kvpair med = median(local,llbound,lubound);
+            kvpair med = pivotselect(local,llbound,lubound);
+            lmedkey = med.key;
+            lvalid = 1;
+         } else {
+            lmedkey = 999999;
+            lvalid = 0;
+         }
+//         MPI_Barrier(c);
+//         medlag += MPI_Wtime()-now;
+
+         /*for (int pp = 0; pp < nproc; pp++) {
+           if (myrank == pp) {
+           fprintf(stdout,"%d: Local median (%d-%d) is %f\n",mygrank,llbound,lubound,lmedkey);
+           usleep(100);
+           MPI_Barrier(c);
+           } else {
+           MPI_Barrier(c);
+           }
+           }*/
+
+         // Collect each of the candidate median values
+//         now = MPI_Wtime();
+         MPI_Allgather(&lmedkey,1,MPI_DOUBLE,&allmedians[0],1,MPI_DOUBLE,c);
+
+         // Count how many processors actually had a valid sub-array to take a median on
+         int gvalid = 0;
+         MPI_Allreduce(&lvalid,&gvalid,1,MPI_INT,MPI_SUM,c);
+//         mpilag += MPI_Wtime()-now;
+
+         // Now, we know the array contains (allvalid) good entries, with the remainder set
+         // to a very high value; that means we want to find the (allvalid)/2 element
+
+//         now = MPI_Wtime();
+         double est_pivot = median(allmedians,0,nproc-1,gvalid/2+1);
+         /*if (myrank == 0) {
+           fprintf(stdout,"Candidate median (of %d) is %f\n",gvalid,est_pivot);
+           }*/
+
+         if (lubound >= llbound) {
+            // Pivot the array about the estimated median
+            partition(local,llbound,lubound,kvpair(est_pivot),literstat.lt,literstat.eq);
+         } else {
+            literstat.lt = 0; literstat.eq = 0;
+         }
+//         partlag += MPI_Wtime()-now;
+         /*for (int pp = 0; pp < nproc; pp++) {
+           if (myrank == pp) {
+           fprintf(stdout,"%d: %d below, %d equal %d above\n",pp,literstat.lt,literstat.eq,(lubound-llbound-literstat.lt-literstat.eq+1));
+           usleep(100);
+           MPI_Barrier(c);
+           } else {
+           MPI_Barrier(c);
+           }
+           }*/
+
+         // Accumulate the local statistics to find out how many elements
+         // of the global array were less than or equal to the candidate median
+//         now = MPI_Wtime();
+         MPI_Allreduce(&literstat,&giterstat,2,MPI_INT,MPI_SUM,c);
+//         mpilag += MPI_Wtime()-now;
+
+         /*if (myrank == 0) {
+           fprintf(stdout,"Global: %d below, %d equal (+%d/%d)\n",giterstat.lt,giterstat.eq,gtoosmall,gtarget);
+           }*/
+
+
+         if (gtoosmall + giterstat.lt + giterstat.eq < gtarget) {
+            // Candidate median was too small, so update bounds to exclude values
+            // less than or equal to the candidate
+            gtoosmall += giterstat.lt + giterstat.eq;
+            llbound += literstat.lt + literstat.eq;
+
+            /*if (myrank == 0) {
+              fprintf(stdout,"Candidate median too small (%d)\n",gtoosmall);
+              }*/
+         } else if (gtoosmall + giterstat.lt >= gtarget) {
+            // Candidate median was too large, so update bounds to exclude
+            // values greater than or equal to the candidate
+            lubound = llbound + literstat.lt - 1;
+            /*if (myrank == 0) {
+              fprintf(stdout,"Candidate median too large\n");
+              }*/
+         } else {
+            gtoosmall += giterstat.lt;
+            llbound += literstat.lt;
+            /*if (myrank == 0) {
+              fprintf(stdout,"Candidate median is just right\n");
+              }*/
+            break;
+         }
+
+
+      }
+
+      // Now, accumulate per-processor stats on how many entries are lower than and equal to
+      // the global median
+
+      literstat.lt = llbound;
+      iterstats procstats[nproc]; 
+
+//      now = MPI_Wtime();
+      MPI_Allgather(&literstat,2,MPI_INT,procstats,2,MPI_INT,c);
+
+      // Number of at-median entries that are distributed with below-median entries
+      // for even-splitting purposes
+      int medbelow = gtarget - gtoosmall - 1;
+
+      /*if (myrank == 0) {
+        fprintf(stdout,"%d median entries to reclassify as less-than\n",medbelow);
+        }*/
+      for (int pp = 0; pp < nproc; pp++) {
+         if (procstats[pp].eq >= medbelow) {
+            procstats[pp].eq -= medbelow;
+            procstats[pp].lt += medbelow;
+            medbelow = 0;
+            break;
+         } else if (procstats[pp].eq > 0) {
+            medbelow -= procstats[pp].eq;
+            procstats[pp].lt += procstats[pp].eq;
+            procstats[pp].eq = 0;
+         }
+      }
+
+
+
+      int receivefrom[nproc];
+      int sendto[nproc];
+      for (int ii = 0; ii < nproc; ii++) {
+         receivefrom[ii] = 0;
+         sendto[ii] = 0;
+      }
+      // Bottom-half of processors 
+      if (myrank < nproc/2) {
+
+         // Calculate receive-counts from the top half
+         int fillbefore = 0; // Number of spots that must be filled before this processor's allotment
+         int fillme = ASIZE-procstats[myrank].lt; // number of spots that must be filled here
+         //recfrom[myrank] = procstats[myrank].lt;
+         //sendto[myrank] = procstats[myrank].lt;
+         for (int pp = 0; pp < myrank; pp++) {
+            fillbefore += (asizes[pp]-procstats[pp].lt);
+         }
+         for (int pp = nproc/2; pp < nproc; pp++) {
+            int sendfromhere = procstats[pp].lt; // Number of entries available at this processor
+            fillbefore -= sendfromhere;
+            if (fillbefore < 0) {
+               if (-fillbefore > fillme) {
+                  receivefrom[pp] = fillme;
+                  // If the array size does not change, sends and receives are symmetric
+                  sendto[pp] = receivefrom[pp];
+                  break;
+               } else {
+                  receivefrom[pp] = -fillbefore;
+                  sendto[pp] = receivefrom[pp];
+                  fillme -= (-fillbefore);
+                  fillbefore = 0;
+               }
+            }
+         }
+      } else {
+         int fillbefore = 0;
+         int fillme = procstats[myrank].lt;
+         for (int pp = nproc/2; pp < myrank; pp++) {
+            fillbefore += procstats[pp].lt;
+         }
+         for (int pp = 0; pp < nproc/2; pp++) {
+            int sendfromhere = asizes[pp]-procstats[pp].lt;
+            fillbefore -= sendfromhere;
+            if (fillbefore < 0) {
+               if (-fillbefore > fillme) {
+                  receivefrom[pp] = fillme;
+                  sendto[pp] = receivefrom[pp];
+                  break;
+               } else {
+                  receivefrom[pp] = -fillbefore;
+                  sendto[pp] = receivefrom[pp];
+                  fillme -= (-fillbefore);
+                  fillbefore = 0;
+               }
+            }
+         }
+      }
+
+      // Print array
+      /*for (int pp = 0; pp < nproc; pp++) {
+        if (myrank == pp) {
+      //fprintf(stdout,"%d: %d+%d+%d\n",pp,literstat.lt,literstat.eq,ASIZE-(literstat.lt+literstat.eq));
+      fprintf(stdout,"%3d: ",mygrank);
+      for (int qq = 0; qq < nproc; qq++) {
+      fprintf(stdout,"%3d ",receivefrom[qq]);
+      }
+      fprintf(stdout,"\n");
+      usleep(100);
+      MPI_Barrier(c);
+      } else {
+      MPI_Barrier(c);
+      }
+      }*/
+
+      MPI_Request sendreqs[nproc], recreqs[nproc];
+      int snum = 0, rnum = 0;
+
+      // Copy the portion of our array that's kept from local to laprt
+      if (myrank < nproc/2) {
+         // Copy the first part
+         memcpy(&tmp[0],&local[0],procstats[myrank].lt*sizeof(kvpair));
+      } else {
+         int keepnum = ASIZE-procstats[myrank].lt;
+         memcpy(&tmp[procstats[myrank].lt],&local[procstats[myrank].lt],keepnum*sizeof(kvpair));
+      }
+
+      // Rolling offset used for send/receive caluclations
+      int soffset = 0, roffset = 0;
+      if (myrank < nproc/2) {
+         soffset = procstats[myrank].lt;
+         roffset = procstats[myrank].lt;
+      }
+
+      // Build non-blocking send/receives
+      for (int pp = 0; pp < nproc; pp++) {
+         if (sendto[pp] > 0) {
+            MPI_Isend(&local[soffset],2*sendto[pp],MPI_DOUBLE,pp,0,c,&sendreqs[snum]);
+            soffset += sendto[pp];
+            snum++;
+         }
+         if (receivefrom[pp] > 0) {
+            MPI_Irecv(&tmp[roffset],2*receivefrom[pp],MPI_DOUBLE,pp,0,c,&recreqs[rnum]);
+            roffset += receivefrom[pp];
+            rnum++;
+         }
+      }
+
+      // Move the request handles to a single array
+      MPI_Request areqs[2*nproc];
+      MPI_Status astats[2*nproc];
+
+      for (int kk = 0; kk < snum; kk++) areqs[kk] = sendreqs[kk];
+      for (int kk = 0; kk < rnum; kk++) areqs[snum+kk] = recreqs[kk];
+
+      MPI_Waitall(snum+rnum,areqs,astats);
+//      mpilag += MPI_Wtime()-now;
+
+//      now = MPI_Wtime();
+      local = tmp;
+//      othlag += MPI_Wtime()-now;
+
+      nested->sortkvpairs(&local,&tmp);
+
+   }
+}// end namespace
+
+
+// Outside of namespace
+
+using blitz::Array;
+using namespace Sorter;
+
+void sortarray(Array<double,3> const &keys, Array<double,3> const &vals,
+               Array<double,3> & sortkeys, Array<double,3> & sortvals,
+               MPI_Comm c) {
+   /* Interface to sorting: take input 3D key/value arrays, sort them,
+      and return the results in 1D output sortkeys/sortvalues; the output
+      arrays are formally 3D for write_array purposes, but they will
+      be of dimension <Nx,1,1> */
+
+   // Static variables hold repeated state.  This will be double-checked
+   // against the input arrays and communicator; in most use-cases we
+   // should only call this function with a single unique array shape
+
+   static parsorter * sortobj = 0;
+   static MPI_Comm lastcomm = MPI_COMM_WORLD;
+   static TinyVector<int,3> keybase;
+   static int asize = 0, abase = 0;
+   static bool warned = false;
+   static vector<kvpair> pairs; // Array to hold key-value pairs for sorting
+   bool initialize = false;
+
+   if (!sortobj) {
+      // First call -- initialize the above static arrays
+
+      initialize = true;
+   } else if (asize != keys.numElements() || lastcomm != c || 
+              any(keybase != keys.base())) {
+      // Also initialize, but complain about it
+
+      delete sortobj;
+      if (!warned) {
+         fprintf(stderr,"WARNING: sortarray() called with multiple array shapes in a single program.\n"
+                        "         this will result in poor performance.\n");
+         warned = true;
+      }
+
+      initialize = true;
+   }
+
+   if (initialize) {
+      asize = keys.numElements();
+      pairs.resize(asize);
+      lastcomm = c;
+      keybase = keys.base();
+
+      sortobj = new parsorter(asize,lastcomm);
+
+      // Calculate the base index of our output array, since it is still
+      // a single, global 1D array.  This is accomplished via MPI_Exscan,
+      // which works like a cumulative sum exclusive of "this" element.
+
+      int myrank;
+      MPI_Comm_rank(lastcomm,&myrank);
+      
+      MPI_Exscan(&asize,&abase,1,MPI_INT,MPI_SUM,lastcomm);
+
+      if (myrank == 0) abase = 0; // This is left undefined by Exscan
+
+      // Debugging printout -- to be deleted
+      fprintf(stdout,"Proc %d: local size %d elements, local base %d\n",myrank,asize,abase);
+   } 
+
+   for (int ii = 0; ii < asize; ii++) {
+      // Copy keys and values from input array to pair-vector.  Since we're sorting this,
+      // we don't need to care about the actual index-to-data mapping for the keys/values,
+      // and we can copy in memory order
+      pairs[ii].key = keys.data()[ii];
+      pairs[ii].value = vals.data()[ii];
+   }
+
+   // Sort
+   sortobj->sortkvpairs(&pairs);
+
+
+   // If necessary, resize and rebase the sorted arrays
+   if (sortkeys.numElements() != asize) sortkeys.resize(asize,1,1);
+   if (sortvals.numElements() != asize) sortvals.resize(asize,1,1);
+
+   // And rebase the sorted arrays if necessary
+   if (sortkeys.lbound(0) != abase) {
+      sortkeys.reindexSelf(TinyVector<int,3>(abase,0,0));
+   }
+   if (sortvals.lbound(0) != abase) {
+      sortvals.reindexSelf(TinyVector<int,3>(abase,0,0));
+   }
+
+   // Copy the sorted results to sortkeys/sortvals
+   for (int ii = 0; ii < asize; ii++) {
+      sortkeys.data()[ii] = pairs[ii].key;
+      sortvals.data()[ii] = pairs[ii].value;
+   }
+
+
+}
+
+
+
+

src/Sorter.hpp

+#ifndef SORTER_HPP
+#define SORTER_HPP 1
+
+namespace Sorter {
+
+   template <typename T>
+      T pivotselect(const vector<T> &arr, int lbound, int ubound);
+
+   template <typename T>
+      void partition(vector <T> &arr, int lbound, int ubound, T pivotval, int &pivotlt, int &pivoteq);
+
+   template <typename T>
+      T median(vector <T> &array, int lbound, int ubound, int idx = -1);
+
+
+   class kvpair {
+      public:
+      double key;
+      double value;
+
+      kvpair(double ikey = 0, double ival = 0):
+         key(ikey), value(ival) {
+      }
+
+      bool operator< (const kvpair & rhs) const {
+         return (key < rhs.key);
+      }
+      bool operator== (const kvpair & rhs) const {
+         return (key == rhs.key);
+      }
+      operator double() const { 
+         return key; 
+      };
+   };
+
+   class parsorter {
+      public: 
+         MPI_Comm c, nestedcomm;
+         int nproc, myrank, mygrank;
+         vector<kvpair> * tmparray;
+         vector<int> asizes;
+         int ASIZE;
+
+         parsorter * nested;
+
+         parsorter(int isize, MPI_Comm incomm);
+         ~parsorter();
+         void sortkvpairs(vector<kvpair> * inarray, vector<kvpair> * tarray = 0);
+   };
+
+
+#include "Sorter_impl.cc"
+};
+
+// Outside the namespace
+
+void sortarray(blitz::Array<double,3> const &keys, blitz::Array<double,3> const &values, 
+               blitz::Array<double,3> & sortkeys,
+               blitz::Array<double,3> & sortvals,
+               MPI_Comm c = MPI_COMM_WORLD);
+
+#endif

src/Sorter_impl.cc

+#ifndef SORTER_HPP
+   #error "Sorter_impl.cc may only be #included in Sorter.hpp
+#endif
+
+#ifndef SORTER_IMPL_CC
+#define SORTER_IMPL_CC 1
+
+template <typename T>
+   T pivotselect(const vector<T> &arr, int lbound, int ubound) {
+   // Selects a candidate local pivot via median-of-3, using randomly-
+   // selected entries
+   int low = rand()%(1+ubound-lbound)+lbound;
+   int mid = rand()%(1+ubound-lbound)+lbound;
+   int high = rand()%(1+ubound-lbound)+lbound;
+   //T lkey = arr[lbound], mkey = arr[mid], ukey = arr[ubound];
+   T lkey = arr[low], mkey = arr[mid], ukey = arr[high];
+
+   /*int myrank;
+   MPI_Comm_rank(MPI_COMM_WORLD,&myrank);*/
+
+   T outkey;
+
+   if (lkey <= mkey) {
+      if (mkey <= ukey) outkey = mkey;
+      else outkey = ukey;
+   } else {
+      if (lkey <= ukey) outkey = lkey;
+      else outkey = ukey;
+   }
+/*   if (!myrank) {
+      fprintf(stdout,"ps: [%d] %.2f [%d] %.2f [%d] %.2f = %f\n",lbound,double(lkey),
+            mid,double(mkey),ubound,double(ukey),double(outkey));
+   }*/
+   return outkey;
+
+}
+
+template <typename T>
+   void partition(vector<T> &arr, int lbound, int ubound, T pivotval, int &pivotlt, int &pivoteq) {
+   // Partitions the array arr[] using the "Dutch National Flag" algorithm, such
+   // that the array is split into three parts, containing:
+   // *) Values strictly less than the pivot
+   // *) Values equal to the pivot
+   // *) Values strictly greater than the pivot
+
+   // Initialize output values to 0
+   pivotlt = 0; // Number of values in this array <= the pivot
+   pivoteq = 0; // Number of values strictly equal to the pivot
+
+   int lptr = lbound;
+   int mptr = lbound;
+   int hptr = ubound;
+
+   T dummy;
+
+   /*int myrank;
+   MPI_Comm_rank(MPI_COMM_WORLD,&myrank);*/
+
+   while (mptr <= hptr) {
+      // All values strictly below lptr are less than the pivot,
+      // all values >= lptr and strictly below mptr are equal to the pivot,
+      // and all values strictly greater than hptr are greater than the pivot.
+      // The values at mptr and hptr are unknown, so we work by examining mptr:
+
+      /*if (!myrank) {
+         for (int ii = lbound; ii <= ubound; ii++) {
+            char fchar;
+            if (ii == lptr) fchar = '*';
+            else if (ii == mptr) fchar = '^';
+            else if (ii == hptr) fchar = '#';
+            else fchar = ' ';
+            fprintf(stdout,"%c%+4.2f ",fchar,double(arr[ii]));
+         } fprintf(stdout,"\n");
+      }*/
+      if (arr[mptr] < pivotval) {
+         // This element belongs in the lower bucket, which expands to arr[lptr].
+         // This value was previously inside the middle bucket, so it is placed
+         // at arr[mptr] and we can increment both low and middle pointers
+         if (lptr != mptr) {
+            dummy = arr[lptr];
+            arr[lptr] = arr[mptr];
+            arr[mptr] = dummy;
+         }
+         lptr += 1; mptr += 1;
+      } else if (arr[mptr] == pivotval) {
+         // This element belongs in the middle bucket, so it does not need to move
+         mptr += 1;
+      } else { // arr[mptr] > pivotval
+         // This element belongs in the upper bucket, freeing up some room;
+         // put arr[hptr] into its proper location
+         if (pivotval > arr[hptr]) {
+            // arr[hptr] belongs in the low bucket
+            dummy = arr[hptr];
+            arr[hptr] = arr[mptr]; // put middle-pointed value in top of array
+            if (mptr != lptr) {
+               arr[mptr] = arr[lptr]; // Move first