commit to work in parallel

HySoP/hysop/domain/topology.py

@@ -73,7 +73,7 @@ class CartesianTopology(object):
         self.mesh = LocalMesh(self.rank,
                               resolution=localResolution,
                               start=start,
-                              dom_size=self.domain.length / self.resolution,
+                              dom_size=self.domain.length / (self.resolution-1),
                               dom_origin=self.domain.origin,
                               ghosts=self.ghosts)
 
@@ -133,19 +133,28 @@ class LocalMesh(object):
         # Local resolution
         self.resolution = resolution.copy() + 2 * ghosts
         # index of the lower point (in each dir) in the global mesh
-        self.start = start
+        self.start = start # - ghosts
         # index of the upper point (in each dir), global mesh
         self.end = self.start + self.resolution - 1
         # Mesh step size
         self.size = dom_size
         # Mesh coordinates
-        coord_start = self.start * self.size + dom_origin
+        coord_start = self.start * self.size + dom_origin - ghosts* self.size
         self.origin = coord_start
-        coord_end = (self.end + 1) * self.size + dom_origin
+        coord_end = (self.end + 1) * self.size + dom_origin - ghosts* self.size
+#        print 'ghost* size' , ghosts* self.size
+#        print 'rank, resolutionx2, start, end, size',self.rank, resolution, self.resolution, self.start, self.end, self.size
+#        print 'coord_start, coord_end',coord_start, coord_end
+#        print 'taille suivant processeur', self.rank , (coord_end-coord_start)/(self.size)
+
         if self.start.size == 3:
             self.coords = np.ogrid[coord_start[0]:coord_end[0]:self.size[0],
                                    coord_start[1]:coord_end[1]:self.size[1],
                                    coord_start[2]:coord_end[2]:self.size[2]]
+#            print 'rank', rank,'iowaqfwajq', np.ogrid[coord_start[0]:coord_end[0]:self.size[0],
+#                                   coord_start[1]:coord_end[1]:self.size[1],
+#                                   coord_start[2]:coord_end[2]:self.size[2]][0].shape , coord_start[0],coord_end[0],self.size[0]
+
         elif self.start.size == 2:
             self.coords = np.ogrid[coord_start[0]:coord_end[0]:self.size[0],
                                    coord_start[1]:coord_end[1]:self.size[1]]

HySoP/hysop/operator/differentialOperator_d.py

@@ -95,10 +95,30 @@ class DifferentialOperator_d(DiscreteOperator):
 #                     self.field1[2][ind,ind,ind-1] * self.field2[2][ind,ind,ind-1]) / (2. * self.meshSize[2]) 
 
             # Ghosts synchronization
+            linenb = 0
+            if (self.topology.rank == 0):
+                time.sleep(2)
+                print 'Bligne 1', field1[:,linenb,linenb]
+                time.sleep(2)
+                print 'Bligne 2', field1[linenb,:,linenb]
+                time.sleep(2)
+                print 'Bligne 3', field1[linenb,linenb,:]
+                time.sleep(2)
+
             OpSynchronize = Synchronize(self.topology)
-#            OpSynchronize.apply(self.field2, self.field1)
-            OpSynchronize.apply(self.field2)
-            OpSynchronize.apply(self.field1)
+            OpSynchronize.apply(self.field2, self.field1)
+
+            if (self.topology.rank == 0):
+                time.sleep(2)
+                print 'Aligne 1', field1[:,linenb,linenb]
+                time.sleep(2)
+                print 'Aligne 2', field1[linenb,:,linenb]
+                time.sleep(2)
+                print 'Aligne 3', field1[linenb,linenb,:]
+                time.sleep(2)
+
+#            OpSynchronize.apply(self.field2)
+#            OpSynchronize.apply(self.field1)
 #           X components of temp and result
             temp1 = (1.0 * self.field1[0][ind0-2,ind1a:ind1b,ind2a:ind2b] * self.field2[0][ind0-2,ind1a:ind1b,ind2a:ind2b] -
                      8.0 * self.field1[0][ind0-1,ind1a:ind1b,ind2a:ind2b] * self.field2[0][ind0-1,ind1a:ind1b,ind2a:ind2b] +\
@@ -152,7 +172,7 @@ class DifferentialOperator_d(DiscreteOperator):
                      1.0 * self.field1[2][ind0a:ind0b,ind1a:ind1b,ind2+2] * self.field2[2][ind0a:ind0b,ind1a:ind1b,ind2+2]) / (12. * self.meshSize[2]) 
 
             tmp3 = np.array([temp1 + temp2 + temp3])
-            result = np.concatenate((np.array([tmp1]), np.array([tmp2]), np.array([tmp3])))
+            result = np.concatenate((np.array(tmp1), np.array(tmp2), np.array(tmp3)))
             return result
 
         elif self.choice == 'gradV':

HySoP/hysop/tools/cpu_data_transfer.py

@@ -7,7 +7,6 @@ from ..constants import *
 import numpy as np
 import mpi4py.MPI as MPI
 import time
-import sys
 
 
 class Synchronize(object):
@@ -48,6 +47,7 @@ class Synchronize(object):
 
         for f in listFields:
             self.size= f.data[0].shape
+#            print 'size array:' ,self.size,  'size topo :',  self.topo.mesh.resolution
             for i in xrange(self.topo.tabSort[:,0].shape[0]) :
 #                print 'rang, destinataire, orientation', self.topo.rank, self.topo.tabSort[i,0], self.topo.tabSort[i,1]
                 if ( self.topo.rank == self.topo.tabSort[i,0]):