OpenMP optimisations

Author: highperformancecoder

models/ecolab_model.cc

@@ -690,9 +690,14 @@ unsigned SpatialModel::migrate()
       }
 
     c.density+=delta[c.idx()];
+#ifdef _OPENMP
+#pragma omp atomic
+#endif
     totalMigration+=sum(abs(delta[c.idx()]));
 #if !defined(NDEBUG)
+#ifdef _OPENMP
 #pragma omp critical
+#endif
     ssum+=delta[c.idx()];
 #endif
     });
@@ -712,25 +717,6 @@ unsigned SpatialModel::migrate()
   MPI_Reduce(ssum.data(),s.data(),s.size(),MPI_INT,MPI_SUM,0,MPI_COMM_WORLD);
   ssum=s;
 #endif
-  if (sum(ssum==0)!=int(ssum.size()))
-    {
-      for (size_t i=0; i<ssum.size(); ++i)
-        if (ssum[i])
-          {
-            cout<<"species "<<i<<":"<<endl;
-            for (size_t idx=0; idx<size(); ++idx)
-              if (delta[idx][i])
-                {
-                  auto& c=*(*this)[idx]->as<EcolabCell>();
-                  cout<<"  delta "<<c.id<<"="<<delta[idx][i]<<" n="<<c.density[i]<<endl;
-                  for (auto& n: c)
-                    {
-                      auto& nbr=*n->as<EcolabCell>();
-                      cout<<"    nbr:"<<nbr.id<<"="<<nbr.density[i]<<endl;
-                    }
-                }                    
-          }
-    }
   if (myid()==0) assert(sum(ssum==0)==int(ssum.size()));
 #endif
   return totalMigration;

models/spatial_ecolab.py

@@ -13,7 +13,7 @@
 array_urand.seed(10+myid())
 
 # initial number of species
-nsp=30
+nsp=100
 
 ecolab.repro_min(-0.1)
 ecolab.repro_max(0.1)
@@ -28,8 +28,8 @@ def randomList(num, min, max):
 
 ecolab.species(range(nsp))
 
-numX=1
-numY=2
+numX=16
+numY=16
 ecolab.setGrid(numX,numY)
 ecolab.partitionObjects()
 
@@ -60,7 +60,7 @@ def randomList(num, min, max):
 def stepImpl():
     #ecolab.setDensitiesDevice()
     ecolab.generate(100)
-    ecolab.mutate()
+    #ecolab.mutate()
 
     epochTs=ecolab.tstep()%epoch
     if (epochTs==0):
@@ -82,17 +82,18 @@ def stepImpl():
 print(ecolab.nsp()())
 
 from timeit import timeit
-print(timeit('stepImpl()', globals=globals(), number=10))
+#print(timeit('stepImpl()', globals=globals(), number=10))
 
 def step():
-    global extinctions
+    global extinctions, migrations
     extinctions=0
     migrations=0
-    for i in range(epoch//10000):
+    for i in range(epoch//epoch):
         stepImpl()
     if myid()==0:
         nsp=len(ecolab.species)
         statusBar.configure(text=f't={ecolab.tstep()} nsp:{nsp}')
+        print(f't={ecolab.tstep()} nsp:{nsp} extinctions:{extinctions} migrations:{migrations}')
         plot('No. species',ecolab.tstep(),nsp,200*(ecolab.tstep()%epoch<0.5*epoch))
         #plot('No. species',ecolab.tstep(),nsp)
         plot('No. species by cell',ecolab.tstep(),ecolab.nsp()())