Add heat diffusion example application.

heat_diffusion/Makefile

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+##------------------------------------------------------------------------------
+##
+## Makefile        Makefile for a simple SpiNNaker application
+##
+## Copyright (C)   The University of Manchester - 2013
+##
+## Author          Steve Temple, APT Group, School of Computer Science
+##
+## Email           [email protected]
+##
+##------------------------------------------------------------------------------
+
+# Makefile for a simple SpiNNaker application. This will compile
+# a single C source file into an APLX file which can be loaded onto
+# SpiNNaker. It will link with either a 'bare' SARK library or a
+# combined SARK/API library.
+
+# The options below can be overridden from the command line or via
+# environment variables. For example, to compile and link "my_example.c"
+# with the ARM tools and generate ARM (as opposed to Thumb) code
+#
+# make APP=my_example GNU=0 THUMB=0
+
+# Name of app (derived from C source - eg sark.c)
+
+APP := sark
+
+# Configuration options
+
+# Set to 1 for GNU tools, 0 for ARM
+
+GNU := 1
+
+# Set to 1 if using SARK/API (0 for SARK)
+
+API := 1
+
+# Set to 1 to make Thumb code (0 for ARM)
+
+THUMB := 1
+
+# Prefix for GNU tool binaries
+
+GP  := arm-none-eabi
+
+# Set to 1 if making a library (advanced!)
+
+LIB := 0
+
+# If SPINN_DIRS is defined, use that to find include and lib directories
+# otherwise look two levels up
+
+ifdef SPINN_DIRS
+  LIB_DIR := $(SPINN_DIRS)/lib
+  INC_DIR := $(SPINN_DIRS)/include
+else
+  LIB_DIR := ../../lib
+  INC_DIR := ../../include
+endif
+
+#-------------------------------------------------------------------------------
+
+# Set up the various compile/link options for GNU and ARM tools
+
+# GNU tool setup
+
+ifeq ($(GNU),1)
+  AS := $(GP)-as --defsym GNU=1 -mthumb-interwork -march=armv5te
+
+  CA := $(GP)-gcc -c -Os -mthumb-interwork -march=armv5te -std=gnu99 \
+	-I $(INC_DIR)
+
+  CT := $(CA) -mthumb -DTHUMB
+
+ifeq ($(LIB),1)
+  CFLAGS += -fdata-sections -ffunction-sections
+endif
+
+ifeq ($(API),1)
+#  LIBRARY := -L$(LIB_DIR) -lspin1_api
+  LIBRARY := $(LIB_DIR)/libspin1_api.a
+else
+#  LIBRARY := -L$(LIB_DIR) -lsark
+  LIBRARY := $(LIB_DIR)/libsark.a
+endif
+
+  SCRIPT := $(LIB_DIR)/sark.lnk
+
+  LD := $(GP)-gcc -T$(SCRIPT) -Wl,-e,cpu_reset -Wl,--gc-sections -Wl,--use-blx 
+
+  AR := $(GP)-ar -rcs
+  OC := $(GP)-objcopy
+  OD := $(GP)-objdump -dxt > $(APP).txt
+
+# ARM tool setup
+
+else
+  AS := armasm --keep --cpu=5te --apcs /interwork
+
+  CA := armcc -c --c99 --cpu=5te --apcs /interwork --min_array_alignment=4 \
+	-I $(INC_DIR)
+
+  CT := $(CA) --thumb -DTHUMB
+
+ifeq ($(LIB),1)
+  CFLAGS += --split_sections
+endif
+
+ifeq ($(API),1)
+  LIBRARY := $(LIB_DIR)/spin1_api.a
+else
+  LIBRARY := $(LIB_DIR)/sark.a
+endif
+
+  SCRIPT := $(LIB_DIR)/sark.sct
+
+  LD := armlink --scatter=$(SCRIPT) --remove --entry cpu_reset
+
+  AR := armar -rcs
+  OC := fromelf
+  OD := fromelf -cds --output $(APP).txt
+
+endif
+
+ifeq ($(THUMB),1)
+  CC := $(CT)
+else
+  CC := $(CA)
+endif
+
+CAT := \cat
+RM  := \rm -f
+LS  := \ls -l
+
+#-------------------------------------------------------------------------------
+
+# Build the application
+
+# List of objects making up the application. If there are other files
+# in the application, add their object file names to this variable.
+
+OBJECTS := $(APP).o
+
+
+# Primary target is an APLX file - built from the ELF
+
+#  1) Create a binary file which is the concatenation of RO and RW sections
+#  2) Make an APLX header from the ELF file with "mkaplx" and concatenate
+#     that with the binary to make the APLX file
+#  3) Remove temporary files and "ls" the APLX file
+
+$(APP).aplx: $(APP).elf
+ifeq ($(GNU),1)
+	$(OC) -O binary -j RO_DATA -j .ARM.exidx $(APP).elf RO_DATA.bin
+	$(OC) -O binary -j RW_DATA $(APP).elf RW_DATA.bin
+	mkbin RO_DATA.bin RW_DATA.bin > $(APP).bin
+else
+	$(OC) --bin --output $(APP).bin $(APP).elf
+endif
+	mkaplx $(APP).elf | $(CAT) - $(APP).bin > $(APP).aplx
+	$(RM) $(APP).bin RO_DATA.bin RW_DATA.bin
+	$(LS) $(APP).aplx
+
+
+# Build the ELF file
+
+#  1) Make a "sark_build.c" file containing app. name and build time
+#     with "mkbuild" and compile it
+#  2) Link application object(s), build file and library to make the ELF
+#  3) Tidy up temporaries and create a list file
+
+$(APP).elf: $(OBJECTS) $(SCRIPT) $(LIBRARY) 
+	mkbuild $(APP) > sark_build.c
+	$(CC) sark_build.c
+	$(LD) $(LFLAGS) $(OBJECTS) sark_build.o $(LIBRARY) -o $(APP).elf
+	$(RM) sark_build.c sark_build.o
+	$(OD) $(APP).elf
+
+
+# Build the main object file. If there are other files in the
+# application, place their build dependencies below this one.
+
+$(APP).o: $(APP).c $(INC_DIR)/spinnaker.h $(INC_DIR)/sark.h \
+	  $(INC_DIR)/spin1_api.h
+	$(CC) $(CFLAGS) $(APP).c
+
+
+# Tidy and cleaning dependencies
+
+tidy:
+	$(RM) $(OBJECTS) $(APP).elf $(APP).txt
+clean:
+	$(RM) $(OBJECTS) $(APP).elf $(APP).txt $(APP).aplx
+
+#-------------------------------------------------------------------------------

heat_diffusion/README.rst

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+Heat Diffusion Model
+====================
+
+This application uses SpiNNaker to model heat diffusion in a 2D surface and
+demonstrates how data can be extracted from SpiNNaker and plotted
+interactively.
+
+Each SpiNNaker core models a single square fragment of the 2D surface. Every
+1ms, cores multicast their current temperature to their immediate neighbours in
+2D space and update their own temperatures according to the reported
+temperatures of the cores around them. Every 64 ms, every chip reports the
+current temperature of all cores on its chip back to the host in an SDP packet.
+The application also listens for SDP packets which allow the host to set the
+temperature of the periphery of the simulation.
+
+The host application is responsible for loading the SpiNNaker application,
+generating appropriate multicast routes, plotting the temperatures received
+from the machine and allowing the user to set the temperature of the boarders
+of the machine.
+
+`Source code on GitHub
+<https://github.com/project-rig/rig_examples/tree/master/heat_diffusion>`_
+
+Usage
+-----
+
+You'll need to install some Python dependencies before you start::
+
+    $ pip install rig numpy matplotlib
+
+Then make sure your board has been booted, e.g.::
+
+    $ rig-boot spinnaker-board-hostname --spin5
+
+You can then start the example using::
+
+    $ python run.py spinnaker-board-hostname
+
+Or if you want to specify your own constant of diffusivity::
+
+    $ python run.py spinnaker-board-hostname 0.5
+
+Once the application has been loaded, a GUI should launch in which looks like
+the screenshot below (taken using a single SpiNN-5 board). Click on the sliders
+to adjust the temperature around the periphery of the model. Closing the window
+will stop the application runnning.
+
+.. image:: heat_diffusion_gui.png
+    :alt: A screenshot of the heat diffusion GUI.
+
+
+SpiNNaker Binary Compilation
+----------------------------
+
+Precompiled binaries are included in the repository so you don't need to
+compile the binaries in order to play with the program as it stands. If you
+want to compile the SpiNNaker binaries, after sourcing the setup script in the
+official spinnaker low-level software release simply compile ``heat.c`` as
+usual::
+
+    make APP=heat
+