Merge lp:~jobh/cbc.block/fenics-1.0-updates into lp:~cbc.block/cbc.block/kent

[Joachim Haga]

Changes here and there, to support fenics-1.0 and trilinos-8.4. (And a few other small things)

[lp:~jobh/cbc.block/fenics-1.0-updates]

91. By Kent-Andre Mardal on 2011-11-07

merge with jobh

=== modified file 'block/algebraic/trilinos/Epetra.py'
--- block/algebraic/trilinos/Epetra.py	2011-08-09 10:59:22 +0000
+++ block/algebraic/trilinos/Epetra.py	2011-11-04 21:09:23 +0000
@@ -25,17 +25,10 @@
         except AttributeError:
             return NotImplemented
 
-        try:
-            x = self.create_vec()
-            if len(x) != len(b):
-                raise RuntimeError, \
-                    'incompatible dimensions for %s matvec, %d != %d'%(self.__class__.__name__,len(x),len(b))
-        except TypeError:
-            # FIXME: This implies an unnecessary vector copy, and can be
-            # removed when dolfin.EpetraVector is changed to accept BlockMap
-            # instead of just Map (patch posted at https://bugs.launchpad.net/dolfin/+bug/735785)
-            from dolfin import Vector
-            x = Vector(b)
+        x = self.create_vec()
+        if len(x) != len(b):
+            raise RuntimeError, \
+                'incompatible dimensions for %s matvec, %d != %d'%(self.__class__.__name__,len(x),len(b))
 
         x.down_cast().vec().Multiply(1.0, self.v, b_vec, 0.0)
         return x
@@ -291,14 +284,14 @@
     from dolfin import EpetraMatrix
     rowmap = vec.down_cast().vec().Map()
     graph = Epetra.CrsGraph(Epetra.Copy, rowmap, 1)
-    indices = numpy.array([0])
+    indices = numpy.array([0], dtype=numpy.int32)
     for row in rowmap.MyGlobalElements():
         indices[0] = row
         graph.InsertGlobalIndices(row, indices)
     graph.FillComplete()
 
     matrix = EpetraMatrix(graph)
-    indices = numpy.array(rowmap.MyGlobalElements(), dtype='I')
+    indices = numpy.array(rowmap.MyGlobalElements(), dtype=numpy.uint32)
     if val == 0:
         matrix.zero(indices)
     else:

=== modified file 'demo/biot.py'
--- demo/biot.py	2011-05-08 04:38:28 +0000
+++ demo/biot.py	2011-11-04 21:09:23 +0000
@@ -108,7 +108,7 @@
 h = mesh.hmin()
 fluid_source_domain = compile_subdomains('{min}<x[0] && x[0]<{max} && {min}<x[1] && x[1]<{max}'
                                          .format(min=c-h, max=c+h))
-topload_source      = Expression("-sin(2*t*pi)*sin(x[0]*pi/2)/3")
+topload_source      = Expression("-sin(2*t*pi)*sin(x[0]*pi/2)/3", t=0)
 
 bc_u_bedrock        = DirichletBC(V,            [0]*dim,        boundary.bottom)
 bc_u_topload        = DirichletBC(V.sub(dim-1), topload_source, boundary.top)

=== modified file 'demo/navierstokes.py'
--- demo/navierstokes.py	2011-08-09 11:22:44 +0000
+++ demo/navierstokes.py	2011-11-04 21:09:23 +0000
@@ -11,6 +11,7 @@
 # PyTrilinos.
 import scipy
 import PyTrilinos
+import os
 
 from dolfin import *
 from block import *
@@ -20,8 +21,9 @@
 dolfin.set_log_level(15)
 
 # Load mesh and subdomains
-mesh = Mesh("dolfin-2.xml.gz")
-sub_domains = MeshFunction("uint", mesh, "subdomains.xml.gz")
+path = os.path.join(os.path.dirname(__file__), '')
+mesh = Mesh(path+"dolfin-2.xml.gz")
+sub_domains = MeshFunction("uint", mesh, path+"subdomains.xml.gz")
 
 # Define function spaces
 V = VectorFunctionSpace(mesh, "CG", 2)

=== modified file 'demo/regression-test.sh'
--- demo/regression-test.sh	2011-08-09 11:22:44 +0000
+++ demo/regression-test.sh	2011-11-04 21:09:23 +0000
@@ -1,13 +1,27 @@
-#!/bin/sh
+#!/bin/bash
+
+# Script that runs all cbc.block demos and exits if anything goes wrong. If
+# this script finishes successfully, we are reasonably confident that there are
+# no api-related breakages (and other types of error will often lead to a lack
+# of convergence, so in practice they may be apparent too).
+
 set -e
 export DOLFIN_NOPLOT=1
 
-if which parallel >/dev/null 2>/dev/null; then
-    parallel -j +0 --halt-on-error=2 -n 1 python ::: *.py
+cd ${0%/*}
+demos=$(find . -name \*.py)
+
+if which parallel &>/dev/null; then
+    parallel -j +0 --halt-on-error=2 -v -n 1 python ::: $demos
 else
-    echo *.py | xargs -n 1 python
+    for demo in $demos; do
+	echo python $demo
+	python $demo
+    done
 fi
 
-# hodge8 is the only one that runs in parallel, since it doesn't use Dirichlet BCs.
+# Only demos that don't use symmetric Dirichlet BCs can run in parallel
 mpirun -np 3 python fenics-book/hodge.py N=4
 mpirun -np 3 python parallelmixedpoisson.py
+
+ps -o etime,cputime $$

=== modified file 'demo/stokes.py'
--- demo/stokes.py	2011-04-26 11:51:16 +0000
+++ demo/stokes.py	2011-11-04 21:09:23 +0000
@@ -28,11 +28,14 @@
 from block.iterative import *
 from block.algebraic.trilinos import *
 
+import os
+
 dolfin.set_log_level(15)
 
 # Load mesh and subdomains
-mesh = Mesh("dolfin-2.xml.gz")
-sub_domains = MeshFunction("uint", mesh, "subdomains.xml.gz")
+path = os.path.join(os.path.dirname(__file__), '')
+mesh = Mesh(path+"dolfin-2.xml.gz")
+sub_domains = MeshFunction("uint", mesh, path+"subdomains.xml.gz")
 
 # Define function spaces
 V = VectorFunctionSpace(mesh, "CG", 2)

=== modified file 'demo/subdomains.xml.gz'
Binary files demo/subdomains.xml.gz	2011-04-26 11:12:12 +0000 and demo/subdomains.xml.gz	2011-11-04 21:09:23 +0000 differ