(squash) begin implementing yalta plan

Merge branch 'master' into yalta

still need a dummy apfArray.h

move apf::Array to vas::Array

    fun fact. every single one of our source
    files was getting assert() from an
    unnecessary #include in apfArray.h

moving the instrumented malloc into noto

changing pcu_memory.c to pcu_buffer.c

moving pcu_protect into reel.c

    this actually depended on opening
    parallel files for the traces...
    I now have them all going to stderr...
    We'll see how much worse that is

moving thread functionality into reel.c

adding vas and reel headers to PCU HEADERS

actually remove pcu_common.h

break up the MIN/MAX macros, remove pcu_common.h

update mds_smb.c to use reel_fail

moving ceil/floor_log2 into pcu_coll.c

    it is the only user of those functions,
    they are not so common

removing now-unneeded includes

moving pcu_fail into reel.c

moving pcu_malloc and friends into vas_malloc.c

apf/CMakeLists.txt

@@ -16,6 +16,7 @@ if(NOT BUILD_IN_TRILINOS)
   find_package(gmi PATHS ${CMAKE_BINARY_DIR})
   set(APF_INCLUDE_DIRS
     ${CMAKE_CURRENT_SOURCE_DIR}
+    ${CMAKE_CURRENT_SOURCE_DIR}/vas
     ${PCU_INCLUDE_DIRS}
     ${GMI_INCLUDE_DIRS})
   set(DEP_LIBS ${PCU_LIBS} ${GMI_LIBS})
@@ -78,7 +79,9 @@ set(APF_HEADERS
   apfNumbering.h
   apfPartition.h
   apfConvert.h
-  apfGeometry.h)
+  apfGeometry.h
+  vas/vasArray.h
+)
 
 if(BUILD_IN_TRILINOS)
 # THIS IS WHERE TRIBITS GETS HEADERS

apf/apf.cc

@@ -19,6 +19,7 @@
 #include "apfUserData.h"
 #include <cstdio>
 #include <cstdlib>
+#include <cassert>
 
 namespace apf {
 

apf/apfAdjReorder.cc

@@ -11,6 +11,7 @@
 #include "apfShape.h"
 
 #include <list>
+#include <cassert>
 
 namespace apf {
 

apf/apfArray.h

@@ -1,54 +1,19 @@
 /*
- * Copyright 2011 Scientific Computation Research Center
+ * Copyright 2015 Scientific Computation Research Center
  *
  * This work is open source software, licensed under the terms of the
  * BSD license as described in the LICENSE file in the top-level directory.
  */
 
-#ifndef APFARRAY_H
-#define APFARRAY_H
+#ifndef APF_ARRAY_H
+#define APF_ARRAY_H
 
-/** \file apfArray.h
-    \brief APF compile-time size array */
-
-#include <cstddef>
-#include <cassert>
+#include <vasArray.h>
 
 namespace apf {
 
-/** \brief an array of N items of type T */
 template <class T, std::size_t N>
-class Array
-{
-  public:
-    /** \brief type::size for convenience */
-    enum { size = N };
-    /** \brief constructor: no default values */
-    Array() {}
-    /** \brief copy constructor */
-    Array(Array<T,N> const& other) {copy(other);}
-    /** \brief element destruction already automatic */
-    ~Array() {}
-    /** \brief copy array contents.
-      \details this is one of the advantages
-      of apf::Array over C arrays: they are
-      copy-constructible and assignable */
-    Array<T,N>& operator=(Array<T,N> const& other)
-    {
-      copy(other);
-      return *this;
-    }
-    /** \brief mutable index operator */
-    T& operator[](std::size_t i) {return elements[i];}
-    /** \brief immutable index operator */
-    T const& operator[](std::size_t i) const {return elements[i];}
-  protected:
-    void copy(Array<T,N> const& other)
-    {
-      for (std::size_t i=0; i < N; ++i)
-        elements[i] = other.elements[i];
-    }
-    T elements[N];
+class Array : public vas::Array<T, N> {
 };
 
 }

apf/apfBoundaryToElementXi.cc

@@ -1,6 +1,7 @@
 #include "apf.h"
 #include "apfMesh.h"
 #include "apfShape.h"
+#include <cassert>
 
 namespace apf {
 

apf/apfConvert.cc

@@ -5,6 +5,7 @@
 #include "apfMesh2.h"
 #include "apfShape.h"
 #include <map>
+#include <cassert>
 
 namespace apf {
 

apf/apfFieldData.cc

@@ -1,6 +1,7 @@
 #include <PCU.h>
 #include "apfFieldData.h"
 #include "apfShape.h"
+#include <cassert>
 
 namespace apf {
 

apf/apfGradientByVolume.cc

@@ -1,5 +1,6 @@
 #include <apfCavityOp.h>
 #include <apf.h>
+#include <cassert>
 
 namespace apf {
 

apf/apfMesh.cc

@@ -12,6 +12,7 @@
 #include "apfNumbering.h"
 #include "apfTagData.h"
 #include <gmi.h>
+#include <cassert>
 
 namespace apf {
 

apf/apfMigrate.cc

@@ -9,6 +9,7 @@
 #include "apfMesh2.h"
 #include "apfCavityOp.h"
 #include "apf.h"
+#include <cassert>
 
 namespace apf {
 

apf/apfNumbering.cc

@@ -12,6 +12,7 @@
 #include "apfMesh.h"
 #include "apfShape.h"
 #include "apfTagData.h"
+#include <cassert>
 
 namespace apf {
 

apf/apfShape.cc

@@ -10,6 +10,7 @@
 #include "apfIntegrate.h"
 #include "apfVector.h"
 #include "apfMatrix.h"
+#include <cassert>
 
 namespace apf {
 

apf/apfVerify.cc

@@ -4,6 +4,7 @@
 #include <gmi.h>
 #include <sstream>
 #include <apfGeometry.h>
+#include <cassert>
 
 namespace apf {
 

apf/apfVtk.cc

@@ -13,6 +13,7 @@
 #include "apfFieldData.h"
 #include <sstream>
 #include <fstream>
+#include <cassert>
 
 namespace apf {
 

apf/vas/vasArray.h

@@ -0,0 +1,55 @@
+/*
+ * Copyright 2011 Scientific Computation Research Center
+ *
+ * This work is open source software, licensed under the terms of the
+ * BSD license as described in the LICENSE file in the top-level directory.
+ */
+
+#ifndef VAS_ARRAY_H
+#define VAS_ARRAY_H
+
+/** \file vasArray.h
+    \brief compile-time size array */
+
+#include <cstddef>
+
+namespace vas {
+
+/** \brief an array of N items of type T */
+template <class T, std::size_t N>
+class Array
+{
+  public:
+    /** \brief type::size for convenience */
+    enum { size = N };
+    /** \brief constructor: no default values */
+    Array() {}
+    /** \brief copy constructor */
+    Array(Array<T,N> const& other) {copy(other);}
+    /** \brief element destruction already automatic */
+    ~Array() {}
+    /** \brief copy array contents.
+      \details this is one of the advantages
+      of vas::Array over C arrays: they are
+      copy-constructible and assignable */
+    Array<T,N>& operator=(Array<T,N> const& other)
+    {
+      copy(other);
+      return *this;
+    }
+    /** \brief mutable index operator */
+    T& operator[](std::size_t i) {return elements[i];}
+    /** \brief immutable index operator */
+    T const& operator[](std::size_t i) const {return elements[i];}
+  protected:
+    void copy(Array<T,N> const& other)
+    {
+      for (std::size_t i=0; i < N; ++i)
+        elements[i] = other.elements[i];
+    }
+    T elements[N];
+};
+
+}
+
+#endif

crv/crvBezierPoints.cc

@@ -7,6 +7,7 @@
 
 #include "crvBezier.h"
 #include "crvTables.h"
+#include <cassert>
 
 namespace crv {
 

crv/crvCurveMesh.cc

@@ -9,6 +9,7 @@
  *******************************************************************************/
 #include "crv.h"
 #include "crvSnap.h"
+#include <cassert>
 
 namespace crv {
 

crv/crvVtk.cc

@@ -11,6 +11,7 @@
 #include "apfFieldData.h"
 #include <sstream>
 #include <fstream>
+#include <cassert>
 
 namespace crv {
 

dsp/dspGraphDistance.cc

@@ -1,5 +1,6 @@
 #include "dspGraphDistance.h"
 #include <PCU.h>
+#include <cassert>
 
 namespace dsp {
 

ma/maAdapt.cc

@@ -18,6 +18,7 @@
 #include "maLayer.h"
 #include <apf.h>
 #include <cfloat>
+#include <cassert>
 #include <stdarg.h>
 
 namespace ma {

ma/maCoarsen.cc

@@ -12,6 +12,7 @@
 #include "maAdapt.h"
 #include "maCollapse.h"
 #include "maOperator.h"
+#include <cassert>
 
 namespace ma {
 

ma/maCollapse.cc

@@ -11,6 +11,7 @@
 #include "maAdapt.h"
 #include "maShape.h"
 #include <apfCavityOp.h>
+#include <cassert>
 
 namespace ma {
 

ma/maDoubleSplitCollapse.cc

@@ -10,6 +10,7 @@
 #include "maDoubleSplitCollapse.h"
 #include "maAdapt.h"
 #include "maShape.h"
+#include <cassert>
 
 namespace ma {
 

ma/maEdgeSwap.cc

@@ -12,6 +12,7 @@
 #include "maShape.h"
 #include "maShapeHandler.h"
 #include <cstdio>
+#include <cassert>
 
 namespace ma {
 

ma/maInput.cc

@@ -10,6 +10,7 @@
 #include "maInput.h"
 #include <apfShape.h>
 #include <cstdio>
+#include <cassert>
 
 namespace ma {
 

ma/maLayer.cc

@@ -4,6 +4,7 @@
 #include "maRefine.h"
 #include "maShape.h"
 #include <sstream>
+#include <cassert>
 
 namespace ma {
 

ma/maLayerCoarsen.cc

@@ -5,6 +5,7 @@
 #include "maCoarsen.h"
 #include "maCrawler.h"
 #include "maLayerCollapse.h"
+#include <cassert>
 
 /* see maCoarsen.cc for the unstructured equivalent. */
 namespace ma {

ma/maLayerCollapse.cc

@@ -3,6 +3,7 @@
 #include "maShape.h"
 
 #include <cstdio>
+#include <cassert>
 
 namespace ma {
 

ma/maLayerRefine.cc

@@ -2,6 +2,7 @@
 #include "maCrawler.h"
 #include "maRefine.h"
 #include "maLayer.h"
+#include <cassert>
 
 namespace ma {
 

ma/maLayerSnap.cc

@@ -3,6 +3,7 @@
 #include "maLayer.h"
 #include "maSnap.h"
 #include "maShape.h"
+#include <cassert>
 
 namespace ma {
 

ma/maLayerTemplates.cc

@@ -6,6 +6,7 @@
 
 #include <cstdio>
 #include <sstream>
+#include <cassert>
 
 namespace ma {
 

ma/maMesh.cc

@@ -12,6 +12,7 @@
 #include "maTables.h"
 #include <algorithm>
 #include <cfloat>
+#include <cassert>
 #include <apf.h>
 
 namespace ma {

ma/maQuality.cc

@@ -9,6 +9,7 @@
 *******************************************************************************/
 
 #include <cfloat>
+#include <cassert>
 #include "maMesh.h"
 #include "maSize.h"
 #include "maAdapt.h"

ma/maRefine.cc

@@ -19,6 +19,7 @@
 #include "maSnap.h"
 #include "maLayer.h"
 #include <apf.h>
+#include <cassert>
 
 namespace ma {
 

ma/maShape.cc

@@ -16,6 +16,7 @@
 #include "maDoubleSplitCollapse.h"
 #include "maShortEdgeRemover.h"
 #include "maShapeHandler.h"
+#include <cassert>
 
 namespace ma {
 

ma/maShapeHandler.cc

@@ -12,6 +12,7 @@
 #include "maShape.h"
 #include "maAdapt.h"
 #include <apfShape.h>
+#include <cassert>
 
 namespace ma {