Merge pull request #86 from FrancescoCasalegno/master

Merge "readi" miniapp for reaction-diffusion ssa in steps

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 2.8.10)
+cmake_minimum_required (VERSION 3.1)
 project (neuromapp)
 
 
@@ -38,6 +38,10 @@ if (BLUEGENE)
 endif()
 set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${C_DIALECT_OPT_C99EXT}")
 
+# Check if c++11 is available: if not, we don't compile what requires it
+include(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+
 
 include(BlueGenePortability)
 

README.md

@@ -22,8 +22,9 @@ of coreneuron, 3 miniapps are available: kernel and solver
 * cstep: It combines the kernel and the solver to mimic a step time of neuron simulator
 
 * queue: This miniapp simulates the queueing system of CoreNeuron.
+
 
-##hello
+## neuromapp/hello
 
 This directory provides an example of how could be design a miniapp (C++)
 
@@ -55,6 +56,20 @@ For more information, run the mini-app with the --help argument.
 You can disable the compilation of this mini-app by using the following variable in cmake
 command: '-DNEUROMAPP_DISABLE_KEYVALUE=TRUE'
 
+## neuromapp/readi
+
+This directory contains a miniapp implementing a reaction-diffusion simulator
+based on operator splitting, as in TetOpSplit solver of STEPS software package.
+To run the simulation on a simple model with 10 species and 8 reactions, go to
+the `build` directory and execute the mini-app with the following arguments:
+
+`./neuromapp/app/app readi --filename_mesh ../neuromapp/readi/dataset/data_mesh --filename_model ../neuromapp/readi/dataset/data_model`
+
+For more information, run the mini-app with the `--help` argument.
+
+You can disable the compilation of this mini-app by setting
+`-DNEUROMAPP_DISABLE_READI=TRUE` when running cmake.
+
 ## neuromapp/replib
 
 This directory contains a miniapp that mimics the behavior of Neuron's ReportingLib. 

neuromapp/CMakeLists.txt

@@ -11,4 +11,7 @@ add_subdirectory (keyvalue)
 add_subdirectory (coreneuron_1.0)
 add_subdirectory (replib)
 add_subdirectory (iobench)
+if(COMPILER_SUPPORTS_CXX11)
+    add_subdirectory(readi)
+endif()
 add_subdirectory (app)

neuromapp/app/CMakeLists.txt

@@ -38,20 +38,20 @@ else()
 endif()
 
 # CoreNeuron mini-apps
-#if(NEUROMAPP_CORENEURON_MAPP)
+if(NEUROMAPP_CORENEURON_MAPP)
     target_link_libraries (app
                            coreneuron10_kernel
                            coreneuron10_solver
                            coreneuron10_cstep
                            coreneuron10_event
                            coreneuron10_queue
                            storage)
-#    add_definitions(-DNEUROMAPP_CORENEURON_MAPP=1)
-    message(STATUS "Adding CoreNeuron mini-apps")
-#else()
-#    add_definitions(-DNEUROMAPP_CORENEURON_MAPP=0)
-#    message(STATUS "Ignoring CoreNeuron mini-apps")
-#endif()
+    add_definitions(-DNEUROMAPP_CORENEURON_MAPP=1)
+   message(STATUS "Adding CoreNeuron mini-apps")
+else()
+    add_definitions(-DNEUROMAPP_CORENEURON_MAPP=0)
+    message(STATUS "Ignoring CoreNeuron mini-apps")
+endif()
 
 # Keyvalue mini-app
 if(NEUROMAPP_KEYVALUE_MAPP)
@@ -86,6 +86,17 @@ else()
     message(STATUS "Ignoring iobench mini-app")
 endif()
 
+# Readi mini-app
+if(NEUROMAPP_READI_MAPP)
+    target_link_libraries (app
+                           readi)
+    add_definitions(-DNEUROMAPP_READI_MAPP=1)
+    message(STATUS "Adding readi mini-app")
+else()
+    add_definitions(-DNEUROMAPP_READI_MAPP=0)
+    message(STATUS "Ignoring readi mini-app")
+endif()
+
 # compression mini-app
 if(NEUROMAPP_COMPRESSION_MAPP)
     target_link_libraries (app

neuromapp/app/miniapp.h

@@ -42,13 +42,13 @@
 #include "hdf5/drivers/h5read.h"
 #endif
 
-//#if NEUROMAPP_CORENEURON_MAPP
+#if NEUROMAPP_CORENEURON_MAPP
 #include "coreneuron_1.0/event_passing/drivers/drivers.h"
 #include "coreneuron_1.0/kernel/kernel.h"
 #include "coreneuron_1.0/solver/solver.h"
 #include "coreneuron_1.0/cstep/cstep.h"
 #include "coreneuron_1.0/queue/queue.h"
-//#endif
+#endif
 
 #if NEUROMAPP_KEYVALUE_MAPP
 #include "keyvalue/keyvalue.h"
@@ -62,7 +62,10 @@
 #include "iobench/iobench.h"
 #endif
 
-//should I include all of the headers?
+#if NEUROMAPP_READI_MAPP
+#include "readi/readi.h"
+#endif
+
 #if NEUROMAPP_COMPRESSION_MAPP
 #include "compression/compression.h"
 #endif
@@ -84,13 +87,13 @@ void register_miniapps(mapp::driver &d) {
 #if NEUROMAPP_HDF5_MAPP
     d.insert("h5read", hdf5::h5read::execute);
 #endif
-//#if NEUROMAPP_CORENEURON_MAPP
+#if NEUROMAPP_CORENEURON_MAPP
     d.insert("event",event_execute);
     d.insert("kernel",coreneuron10_kernel_execute);
     d.insert("solver",coreneuron10_solver_execute);
     d.insert("cstep",coreneuron10_cstep_execute);
     d.insert("queue",coreneuron10_queue_execute);
-//#endif
+#endif
 #if NEUROMAPP_KEYVALUE_MAPP
     d.insert("keyvalue",keyvalue_execute);
 #endif
@@ -100,6 +103,9 @@ void register_miniapps(mapp::driver &d) {
 #if NEUROMAPP_IOBENCH_MAPP
     d.insert("iobench",iobench_execute);
 #endif
+#if NEUROMAPP_READI_MAPP
+    d.insert("readi",readi_execute);
+#endif
 //note should change suffix to execute when time comes
 #if NEUROMAPP_COMPRESSION_MAPP
     d.insert("compression",comp_execute);

neuromapp/readi/CMakeLists.txt

@@ -0,0 +1,10 @@
+# Use -DNEUROMAPP_DISABLE_READI=TRUE to disable compilation/installation of this mini-app
+if(NOT NEUROMAPP_DISABLE_READI)
+    add_library (readi main.cpp)
+    install (TARGETS readi DESTINATION lib)
+    install (FILES readi.h DESTINATION include)
+
+    set(NEUROMAPP_READI_MAPP ON CACHE BOOL "True if readi mini-app will be installed")
+else()
+    set(NEUROMAPP_READI_MAPP OFF CACHE BOOL "True if readi mini-app will be installed")
+endif()