fix hot starts for h5py archiving

erdc · Sep 24, 2017 · c8467b4 · c8467b4
1 parent b40d88b
commit c8467b4
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Showing 2 changed files with 14 additions and 8 deletions.
diff --git a/proteus/FemTools.py b/proteus/FemTools.py
@@ -3623,7 +3623,16 @@ def readFunctionXdmf(self,ar,u,tCount=0):
                 del array
             else:
                 if ar.has_h5py:
-                    u.dof[:]=ar.hdfFile["/"+u.name+"_p"+`ar.comm.rank()`+"_t"+str(tCount)]
+                    if ar.global_sync:
+                        #this is known to be slow but it scales with
+                        #respect to memory (as opposed to the faster
+                        #approach of pulling in the entire array)
+                        permute = np.argsort(self.mesh.globalMesh.nodeNumbering_subdomain2global)
+                        u.dof[permute] = ar.hdfFile["/"+u.name+"_t"+str(tCount)][self.mesh.globalMesh.nodeNumbering_subdomain2global[permute].tolist()]
+                        #faster way
+                        #u.dof[:] = ar.hdfFile["/"+u.name+"_t"+str(tCount)].value[self.mesh.globalMesh.nodeNumbering_subdomain2global]                        
+                    else:
+                        u.dof[:]=ar.hdfFile["/"+u.name+"_p"+`ar.comm.rank()`+"_t"+str(tCount)]
                 else:
                     u.dof[:]=ar.hdfFile.getNode("/",u.name+str(tCount))
         else:

diff --git a/proteus/NumericalSolution.py b/proteus/NumericalSolution.py
@@ -273,12 +273,9 @@ def __init__(self,so,pList,nList,sList,opts,simFlagsList=None):
                     if comm.isMaster() and p.genMesh:
                         tmesh.readFromPolyFile(p.domain.polyfile)
                         tmesh.writeToFile(p.domain.polyfile)
-                        logEvent("Converting to Proteus Mesh")
-                        mesh=tmesh.convertToProteusMesh(verbose=1)
                     comm.barrier()
-                    if p.genMesh:
-                        mesh = MeshTools.TriangularMesh()
-                        mesh.generateFromTriangleFiles(filebase=p.domain.polyfile,base=1)
+                    mesh = MeshTools.TriangularMesh()
+                    mesh.generateFromTriangleFiles(filebase=p.domain.polyfile,base=1)
                     mlMesh = MeshTools.MultilevelTriangularMesh(0,0,0,skipInit=True,
                                                                 nLayersOfOverlap=n.nLayersOfOverlapForParallel,
                                                                 parallelPartitioningType=n.parallelPartitioningType)
@@ -1147,7 +1144,7 @@ def calculateSolution(self,runName):
             if self.opts.hotStart:
                 logEvent("Setting initial conditions from hot start file for "+p.name)
                 tCount = int(self.ar[index].tree.getroot()[-1][-1][-1][0].attrib['Name'])
-                self.ar[index].n_datasets = tCount+1
+                self.ar[index].n_datasets = tCount + 1
                 time = float(self.ar[index].tree.getroot()[-1][-1][-1][0].attrib['Value'])
                 if len(self.ar[index].tree.getroot()[-1][-1]) > 1:
                     dt = time - float(self.ar[index].tree.getroot()[-1][-1][-2][0].attrib['Value'])
@@ -1162,7 +1159,7 @@ def calculateSolution(self,runName):
                         lm.timeIntegration.tLast = time
                         lm.timeIntegration.t = time
                         lm.timeIntegration.dt = dt
-                self.tCount = tCount+1
+                self.tCount = tCount
             elif p.initialConditions is not None:
                 logEvent("Setting initial conditions for "+p.name)
                 m.setInitialConditions(p.initialConditions,self.tnList[0])