Changeset 23231 for issm/trunk-jpl/src/m

Timestamp:

09/08/18 13:03:10 (7 years ago)

Author:

kruegern

Message:

NEW: added Dakota/QMU Chaco tests (234,235,413,414,417,444), minor bug fixes, left out 418 due to unresolved memory issues

Location:

issm/trunk-jpl/src/m

Files:

• modules/Chaco.py (modified) (1 diff)
• modules/Scotch.py (modified) (1 diff)
• partition/partitioner.py (modified) (2 diffs)
• qmu/dakota_in_write.py (modified) (1 diff)
• qmu/dakota_out_parse.py (modified) (1 diff)
• qmu/process_qmu_response_data.m (modified) (1 diff)

issm/trunk-jpl/src/m/modules/Chaco.py

@@ -5 +5 @@
 
    Usage:
-      [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal);
+      assgn = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal);
 
    A:                   Input adjacency matrix

issm/trunk-jpl/src/m/modules/Scotch.py

@@ -2 +2 @@
 
 def Scotch(*varargin):
-'''SCOTCH - Scotch partitioner
+        '''SCOTCH - Scotch partitioner
 
    Usage:

issm/trunk-jpl/src/m/partition/partitioner.py

@@ -3 +3 @@
 import MatlabFuncs as m
 from adjacency import *
-#from Chaco import *
+from Chaco import *
 #from Scotch import *
-#from MeshPartition import *
+from MeshPartition import *
 from project3d import *
+from mesh2d import *
 
 def partitioner(md,*varargin):
@@ -60 +61 @@
 
         if m.strcmpi(package,'chaco'):
-                raise RuntimeError('Chaco is not currently supported for this function')
+                #raise RuntimeError('Chaco is not currently supported for this function')
 
                 #  default method (from chaco.m)
-                #method=np.array([1,1,0,0,1,1,50,0,.001,7654321]).reshape(-1,1)
-                #method[0]=3    #  global method (3=inertial (geometric))
-                #method[2]=0    #  vertex weights (0=off, 1=on)
+                method=np.array([1,1,0,0,1,1,50,0,.001,7654321])
+                method[0]=3    #  global method (3=inertial (geometric))
+                method[2]=0    #  vertex weights (0=off, 1=on)
 
                 #specify bisection
-                #method[5]=options.getfieldvalue('section')#  ndims (1=bisection, 2=quadrisection, 3=octasection)
+                method[5]=options.getfieldvalue('section')#  ndims (1=bisection, 2=quadrisection, 3=octasection)
 
                 #are we using weights? 
-                #if m.strcmpi(options.getfieldvalue('weighting'),'on'):
-                        #weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight))
-                        #method[2]=1
-                #else:
-                        #weights=[]
+                if m.strcmpi(options.getfieldvalue('weighting'),'on'):
+                        weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight))
+                        method[2]=1
+                else:
+                        weights=[]
         
+                method = method.reshape(-1,1)   # transpose to 1x10 instead of 10
+
                 #  partition into nparts
-                #if isinstance(md.mesh,mesh2d):
-                        #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,[]).T+1 #index partitions from 1 up. like metis.
-                #else:
-                        #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,md.mesh.z,method,npart,[]).T+1 #index partitions from 1 up. like metis.
-        
+                if isinstance(md.mesh,mesh2d):
+                        part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis.
+                else:
+                        part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,md.mesh.z,method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis.
         
         elif m.strcmpi(package,'scotch'):

issm/trunk-jpl/src/m/qmu/dakota_in_write.py

@@ -62 +62 @@
         filei2=fullfile(pathstr,name+ext)
 
-        print 'Opening Dakota input file \''+filei2 + '\''
+        print 'Opening Dakota input file \''+filei2 + '\'.'
         try:
                 with open(filei2,'w+') as fidi:

issm/trunk-jpl/src/m/qmu/dakota_out_parse.py

@@ -241 +241 @@
         dmax95 =prctile_issm(data,95,0)
 
+        # Note: the following line may cause the following warning
+        #       (should not crash or invalidate results) when one of
+        #       the inputs does not change with respect to the
+        #       other/s causing an internal divide-by-zero error
+
+        #/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py:3163:
+        #       RuntimeWarning: invalid value encountered in true_divide
+        #       c /= stddev[:,None]
+
+        #       (and/or the same but with "c /= stddev[None, :]")
+
         dcorrel=np.corrcoef(data.T)
 

issm/trunk-jpl/src/m/qmu/process_qmu_response_data.m

@@ -43 +43 @@
         %ok, process the domains named in qmu_mass_flux_profiles,  to build a list of segments (MatArray)
         md.qmu.mass_flux_segments=cell(num_mass_flux,1);
-        md.qmu.mass_flux_segments
         for i=1:num_mass_flux,
                 md.qmu.mass_flux_segments{i}=MeshProfileIntersection(md.mesh.elements,md.mesh.x,md.mesh.y,[md.qmu.mass_flux_profile_directory '/' md.qmu.mass_flux_profiles{i}]);
         end
-        md.qmu.mass_flux_segments
 end