added an example that uses Proto

lib/mk/Make.defs.config

@@ -1,4 +1,3 @@
-# -*- Mode: Makefile;  -*-
 
 ## Set the configuration string used in filenames.
 ## `Make.rules' is the only Chombo makefile that uses this file, but
@@ -71,14 +70,15 @@ _md        := $(subst FALSE,,$(subst TRUE,md,$(MULTIDIM)))
 _pic       := $(subst FALSE,,$(subst TRUE,.pic,$(PIC)))
 _openmpcc  := $(subst FALSE,,$(subst TRUE,.OPENMPCC,$(OPENMPCC)))
 _openmpfc  := $(subst FALSE,,$(subst TRUE,.OPENMPFC,$(OPENMPFC)))
+_proto     := $(subst FALSE,,$(subst TRUE,.PROTO,$(USE_PROTO)))
 
 # configuration string for multidim executable builds -- also use as a base
 # for the other config strings
 
-newconfig := $(shell echo                     $(system)$(_obj64).$(_cxxname).$(_fname)$(_precision)$(_debug)$(_opt)$(_profile)$(_mpi)$(_openmpcc)$(_openmpfc)$(_petsc)$(_rose)$(_gpu)$(_pic)$(XTRACONFIG) | sed -e 's/ //g' -e 's/	//g')
+newconfig := $(shell echo                     $(system)$(_obj64).$(_cxxname).$(_fname)$(_precision)$(_debug)$(_opt)$(_profile)$(_mpi)$(_openmpcc)$(_openmpfc)$(_proto)$(_petsc)$(_rose)$(_gpu)$(_pic)$(XTRACONFIG) | sed -e 's/ //g' -e 's/	//g')
 
 # create a base for all of the other config strings
-baseconfig  := $(shell echo      d$(_ch)$(_md).$(system)$(_obj64).$(_cxxname).$(_fname)$(_precision)$(_debug)$(_opt)$(_profile)$(_mpi)$(_openmpcc)$(_openmpfc)$(_petsc)$(_rose)$(_gpu)$(_pic)$(XTRACONFIG) | sed -e 's/ //g' -e 's/	//g')
+baseconfig  := $(shell echo      d$(_ch)$(_md).$(system)$(_obj64).$(_cxxname).$(_fname)$(_precision)$(_debug)$(_opt)$(_profile)$(_mpi)$(_openmpcc)$(_openmpfc)$(_proto)$(_petsc)$(_rose)$(_gpu)$(_pic)$(XTRACONFIG) | sed -e 's/ //g' -e 's/	//g')
 
 #these are config strings needed by multidim builds
 1dconfig  := 1$(baseconfig)

lib/mk/Make.defs.defaults

@@ -29,6 +29,7 @@
 ##  CXXFLAGS        options for compiling C++ code
 ##  FFLAGS          options for compiling Fortran code
 ##  LDFLAGS         options for linking
+##  CXXSTD          chombo default is C++11.  Set to 14 for C++14, etc.
 ##  USE_64          if TRUE, use 64bit pointers on systems where 32bits is the default
 ##  USE_COMPLEX     if TRUE, enable the 'Complex' type
 ##                   (default is TRUE, disable only if compiler doesn't allow it)
@@ -99,8 +100,10 @@ CXXFLAGS?=
 CHFFLAGS?=
 FFLAGS?=
 LDFLAGS?=
+OUTPUT?=EXEC
 
 # Chombo optional features
+CXXSTD?=11#          # C++ 11 standard
 USE_64?=TRUE#        #64bit pointers
 USE_MT?=TRUE#         #memory tracking
 # USE_SETVAL?=TRUE#     #initialize FAB data

lib/mk/local/Make.defs.ANAG

@@ -223,6 +223,6 @@ ifneq ($(ANAG_OPENMPI_DIR),)
 endif
 
 ifeq ($(USE_PROTO),TRUE)
- XTRACPPFLAGS += -I$(PROTO_HOME)/include -DDIM=$(DIM) -DUSE_PROTO=1
+ XTRACPPFLAGS += -I$(PROTO_HOME)/include -DDIM=$(DIM) -DUSE_PROTO=1 -DPR_TURN_OFF_TIMERS=1
 endif
 

lib/mk/local/Make.defs.igor

@@ -1,15 +1,21 @@
 #it is prounouced eye-gore
 makefiles+=local/Make.defs.igor
-USE_HDF=TRUE
+PROTO_HOME=/home/dtgraves/_proto/proto
+USE_PROTO=TRUE
+OPENMPCC=TRUE
+USE_HDF=FALSE
 USE_MF=TRUE
 USE_EB=TRUE
 USE_64=TRUE
 CXX=g++
 CPP=cpp
 FC=gfortran
-HDFINCFLAGS   = -I/home/graves/_hdf5/include
-HDFLIBFLAGS   = -L/home/graves/_hdf5/lib -lhdf5 -lhdf5_hl -ldl -lz
-HDFMPIINCFLAGS= -I/home/graves/_hdf5/include
-HDFMPILIBFLAGS= -L/home/graves/_hdf5/lib -lhdf5 -lhdf5_hl -ldl -lz
+HDFINCFLAGS   = -I/home/dtgraves/_hdf5/include
+HDFLIBFLAGS   = -L/home/dtgraves/_hdf5/lib -lhdf5 -lhdf5_hl -ldl 
+HDFMPIINCFLAGS= -I/home/dtgraves/_hdf5/include
+HDFMPILIBFLAGS= -L/home/dtgraves/_hdf5/lib -lhdf5 -lhdf5_hl -ldl 
 
 
+ifeq ($(USE_PROTO),TRUE)
+ XTRACPPFLAGS += -I$(PROTO_HOME)/include -DDIM=$(DIM) -DUSE_PROTO=1 -DPR_TURN_OFF_TIMERS=1
+endif

lib/src/BoxTools/ProtoInterface.H

@@ -0,0 +1,60 @@
+#ifdef CH_LANG_CC
+/*
+ *      _______              __
+ *     / ___/ /  ___  __ _  / /  ___
+ *    / /__/ _ \/ _ \/  V \/ _ \/ _ \
+ *    \___/_//_/\___/_/_/_/_.__/\___/
+ *    Please refer to Copyright.txt, in Chombo's root directory.
+ */
+#endif
+
+#ifndef _PROTOINTERFACE_H_
+#define _PROTOINTERFACE_H_
+
+#ifdef USE_PROTO
+#include "Proto.H"
+#endif
+#include "IntVect.H"
+#include "Box.H"
+#include "BaseFab.H"
+
+
+
+#ifdef USE_PROTO
+
+
+using Proto::Point;
+using Proto::BoxData;
+using Proto::Var;
+///these functions are meant to interface with the Proto language.
+namespace ProtoCh
+{
+
+
+///get point from intvect
+  extern Point      getPoint( const IntVect& a_iv);
+
+/// gets proto box from chombo box
+  extern Proto::Box  getProtoBox( const Box& a_box);
+
+///get intvect from point
+  extern IntVect getIntVect(const  Point  & a_pt);
+
+///get chombo box from proto box
+  extern Box getBox(const Proto::Box & a_bx);
+
+///
+  template <typename T, int ncomp>
+   void  aliasBoxData(BoxData<T, ncomp> & a_boxdata, const BaseFab<T>& a_bfr, const int a_startcomp = 0)
+    {
+      CH_assert( a_bfr.nComp() == (ncomp + a_startcomp));
+      Proto::Box region = getProtoBox(a_bfr.box());
+      a_boxdata.define(a_bfr.dataPtr(a_startcomp), region, ncomp);
+    }
+
+
+} 
+
+#endif
+
+#endif

lib/src/BoxTools/ProtoInterface.cpp

@@ -0,0 +1,64 @@
+#ifdef CH_LANG_CC
+/*
+ *      _______              __
+ *     / ___/ /  ___  __ _  / /  ___
+ *    / /__/ _ \/ _ \/  V \/ _ \/ _ \
+ *    \___/_//_/\___/_/_/_/_.__/\___/
+ *    Please refer to Copyright.txt, in Chombo's root directory.
+ */
+#endif
+
+#include "ProtoInterface.H"
+#include "SPACE.H"
+#include "UsingNamespace.H"
+
+#ifdef USE_PROTO
+
+///get point from intvect
+Point
+ProtoCh::getPoint( const IntVect& a_iv)
+{
+  Point retval;
+  for(int idir = 0; idir < SpaceDim; idir++)
+  {
+    retval[idir] = a_iv[idir];
+  }
+  return retval;
+
+}
+
+/// gets proto box from chombo box
+Proto::Box  
+ProtoCh::getProtoBox( const Box& a_box)
+{
+  Point ptlo = getPoint(a_box.smallEnd());
+  Point pthi = getPoint(a_box.bigEnd());
+  return Proto::Box(ptlo, pthi);
+}
+
+///get intvect from point
+IntVect 
+ProtoCh::getIntVect(const  Point  & a_pt)
+{
+  IntVect retval;
+  for(int idir = 0; idir < SpaceDim; idir++)
+  {
+    retval[idir] = a_pt[idir];
+  }
+  return retval;
+}
+
+///get chombo box from proto box
+Box 
+ProtoCh::getBox(const Proto::Box & a_bx)
+{
+  IntVect ivlo = getIntVect(a_bx.low());
+  IntVect ivhi = getIntVect(a_bx.high());
+  return Box(ivlo, ivhi);
+}
+
+
+
+#endif
+
+

releasedExamples/Proto/Poisson/doc/proto_poisson.tex

@@ -0,0 +1,96 @@
+\documentclass[12pt,a4paper]{article}
+\title{Chombo/Proto Poisson example }
+\date{}
+\begin{document}
+\maketitle
+
+\begin{abstract}
+
+Given a charge distribution $\rho$, and a field $\phi$
+the spatial Helmoltz equation is given by
+\begin{equation}
+(\alpha I + \beta \nabla) \phi = \rho.
+\end{equation}
+where $\alpha$ and $\beta$ are constants.
+The Chombo Proto example solves the spatial Helmholtz equation in two
+or three dimensions using geometric multigrid with standard V-cycles.
+
+We present the performance for a single level calculation on a single
+node of a Cori Haswell node.    The boundary conditions are periodic
+and the charge distribution has compact support of $r = 0.2$.  
+Further parameters are as follows.
+\begin{itemize}
+\item Identity coefficient, $\alpha = 1$.
+\item Laplacian coefficient, $\beta  = -0.1$.
+\item Number of smoothings per relaxation, $n_{s} = 4$.
+\item Grid dimensions = $512^3$.
+\item Domain size $L_x=L_y=L_z =1$.
+\end{itemize}
+
+All calculations are done with a varying number of threads, keeping
+the number of computational units constant.   If $N_t$ is the number
+of OpenMP threads and $N_m$ is the number of MPI processes, for all
+calculations, $N_t N_m = 32$.  Floating point rates are calculated as
+a post-processing step.
+
+\end{abstract}
+
+
+\begin{table}[h]
+\begin{center}
+\begin{tabular}{|c|c||c|c|} \hline
+$N_t$ & $N_m$ & $T_{vcycle}$  & $F_{resid}$  \\
+\hline 
+1  &  32 &    1.223  & 78.1 GFlop \\ 
+2  &  16 &    2.450  & 39.0 GFlop \\ 
+4  &  8  &    2.480  & 30.6 GFlop \\ 
+8  &  4  &    2.334  & 18.4 GFlop \\ 
+16 &  2  &    2.695  & 10.5 GFlop \\
+32 &  1  &    2.361  &  6.5 MFlop \\
+\hline 
+\end{tabular}
+\end{center}
+\caption{AMRPoisson performance.  } 
+\label{fig::solut2dl0}
+\end{table}
+
+
+\begin{table}[h]
+\begin{center}
+\begin{tabular}{|c|c||c|c|} \hline
+$N_t$ & $N_m$ & $T_{vcycle}$ & $F_{resid}$ \\
+\hline 
+1  &  32 &    3.89   & 20.1 GFlop\\ 
+2  &  16 &    6.53   & 12.7 GFlop\\ 
+4  &  8  &    6.47   & 12.6 GFlop\\ 
+8  &  4  &    6.27   & 12.6 GFlop\\ 
+16 &  2  &    6.00   & 12.6 GFlop\\
+32 &  1  &    5.85   & 12.7 GFlop\\
+\hline 
+\end{tabular}
+\end{center}
+\caption{7 point stencil proto performance.  Same stencil as AMRPoisson} 
+\label{fig::solut2dl0}
+\end{table}
+
+
+\begin{table}[h]
+\begin{center}
+\begin{tabular}{|c|c||c|c|} \hline
+$N_t$ & $N_m$ & $T_{vcycle}$  & $F_{resid}$\\
+\hline 
+1  &  32 &    12.4 &  22.9 GFlop\\ 
+2  &  16 &    20.7 &  14.7 GFlop\\ 
+4  &  8  &    20.7 &  14.4 GFlop\\ 
+8  &  4  &    19.7 &  14.7 GFlop\\ 
+16 &  2  &    18.8 &  14.9 GFlop\\
+32 &  1  &    18.6 &  14.9 GFlop\\
+\hline 
+\end{tabular}
+\end{center}
+\caption{27 point stencil proto performance.  } 
+\label{fig::solut2dl0}
+\end{table}
+
+
+\end{document}

releasedExamples/Proto/Poisson/exec/GNUmakefile

@@ -0,0 +1,22 @@
+
+ebase = Multigrid
+
+# the location of the Chombo "lib" directory
+CHOMBO_HOME = ../../../../lib
+
+# names of Chombo libraries needed by this program, in order of search.
+LibNames = BoxTools
+
+# the locations of the source code directories
+base_dir = .
+src_dirs = ../src
+
+
+# input file for 'run' target
+INPUT = regression.inputs
+# shared code for building example programs
+include $(CHOMBO_HOME)/mk/Make.example
+
+# application-specific variables
+
+# application-specific targets