Encapsulating global data into containers and data structures (#203)

This merge brings a number of code modernizations and improvements:

* Improvements for raw pointers in coreneuron:
  - Replace NULL and nil with C++ nullptr, which allows us to better detect
  type confusion
  - do proper pointer initialization
  - Use references in some places wehre pointers aren't needed
  - Use a vector for the helper array rather than having to explicitly
    alloc/dealloc.
* Added scopmath as a dependency to coreneuron as it is needed for the
  custom command to succeed (it links with scopmath down the line).
* Created Coreneuron class that has for now a global instance
  - moved most other global data structures into this class.
* Updated headers and build system accordingly
* Replaced a few for loops by algorithms and range-based loops
  Many more to consider, but it's a start.
* Added a simple CUDA managed allocation handling for C++ classes. Aligned memory 
  allocation on CPU still missing.
* Switched to class member initialization rather then setting the
  members of `NrnThread` in `nrn_threads_create`. We now create instances of the class 
  through construction (and used CUDA managed allocation if built with CUDA).
* Remove option to set version for libcorenrnmech library
  - we are integrating coreneuron into neuron
  - nrnivmodl will invoke nrnivmodl-core
  - neuron has auto-detection logic to find out libcorenrnmech so it
  doesn't make sense set version explicitly
* Update submodules to latest master; do not track branches


* Many code improvements thanks to @pramodk, @tristan0x and others!


Note: For now the accesses to any of the Coreneuron class members is through a reference
getter, which is really not how it should be done, but in the next step
many of the involved functions will become methods that access the
private data. In other cases the data will be rearranged and accessed
through it's own container class.

Author: Omar Awile

.gitmodules

@@ -1,7 +1,6 @@
 [submodule "external/mod2c"]
-	path = external/mod2c
+  path = external/mod2c
   url = https://github.com/BlueBrain/mod2c
-  branch = master
 [submodule "external/nmodl"]
-	path = external/nmodl
-	url = https://github.com/BlueBrain/nmodl
+  path = external/nmodl
+  url = https://github.com/BlueBrain/nmodl

CMakeLists.txt

@@ -13,7 +13,7 @@ project(coreneuron)
 set(VERSION_MAJOR "0")
 set(VERSION_MINOR "16")
 set(VERSION_PATCH "0")
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(VERSION_STRING "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")

coreneuron/coreneuron.h

@@ -0,0 +1,254 @@
+/*
+Copyright (c) 2016, Blue Brain Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.
+*/
+#pragma once
+
+/***
+ * Includes all headers required to communicate and run all methods
+ * described in CoreNEURON, neurox, and mod2c C-generated mechanisms
+ * functions.
+ **/
+
+
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
+#include <string.h>
+#include <vector>
+#include <array>
+
+#include "coreneuron/utils/randoms/nrnran123.h"      //Random Number Generator
+#include "coreneuron/scopmath_core/newton_struct.h"  //Newton Struct
+#include "coreneuron/nrnoc/membdef.h"                //static definitions
+#include "coreneuron/nrnoc/nrnoc_ml.h"               //Memb_list and mechs info
+
+#include "coreneuron/nrniv/memory.h"  //Memory alignments and padding
+#include "coreneuron/nrnconf.h"
+#include "coreneuron/nrnoc/multicore.h"
+#include "coreneuron/nrnoc/nrnoc_decl.h"
+#include "coreneuron/nrnoc/mech_mapping.hpp"
+
+namespace coreneuron {
+
+// from nrnoc/capac.c
+extern void nrn_init_capacitance(NrnThread*, Memb_list*, int);
+extern void nrn_cur_capacitance(NrnThread* _nt, Memb_list* ml, int type);
+extern void nrn_alloc_capacitance(double* data, Datum* pdata, int type);
+
+// from nrnoc/eion.c
+extern void nrn_init_ion(NrnThread*, Memb_list*, int);
+extern void nrn_cur_ion(NrnThread* _nt, Memb_list* ml, int type);
+extern void nrn_alloc_ion(double* data, Datum* pdata, int type);
+extern void second_order_cur(NrnThread* _nt, int secondorder);
+
+using DependencyTable = std::vector<std::vector<int>>;
+
+/**
+ * A class representing the CoreNEURON state, holding pointers to the various data structures
+ *
+ * The pointers to "global" data such as the NrnThread, Memb_list and Memb_func data structures
+ * are managed here. they logically share their lifetime and runtime scope with instances of
+ * this class.
+ */
+class CoreNeuron {
+
+
+    /// Local to coreneuron, used to keep track of point process IDs
+    int pointtype = 1; /* starts at 1 since 0 means not point in pnt_map*/
+
+    /**
+     * map if mech is a point process
+     * In the future only a field of Mechanism class
+     */
+    std::vector<char> pnt_map; /* so prop_free can know its a point mech*/
+
+    /** Vector mapping the types (IDs) of different mechanisms of mod files between NEURON and
+     * CoreNEURON
+     */
+    std::vector<int> different_mechanism_type;
+
+    /**
+     * dependency helper filled by calls to hoc_register_dparam_semantics
+     * used when nrn_mech_depend is called
+     * vector-of-vector DS. First idx is the mech, second idx is the dependent mech.
+     */
+    DependencyTable ion_write_dependency;
+
+    std::vector<Memb_func> memb_funcs;
+
+    /**
+     * Net send / Net receive
+     * only used in CoreNEURON for book keeping synapse mechs, should go into CoreNEURON class
+     */
+    std::vector<std::pair<NetBufReceive_t, int>> net_buf_receive;
+    std::vector<int> net_buf_send_type;
+
+    /**
+     * before-after-blocks from nmodl are registered here as function pointers
+     */
+    std::array<BAMech*, BEFORE_AFTER_SIZE> bamech;
+
+    /**
+     * Internal lookup tables. Number of float and int variables in each mechanism and memory layout
+     * future --> mech class
+     */
+    std::vector<int> nrn_prop_param_size;
+    std::vector<int> nrn_prop_dparam_size;
+    std::vector<int> nrn_mech_data_layout; /* 1 AoS (default), 0 SoA */
+    /* array is parallel to memb_func. All are 0 except 1 for ARTIFICIAL_CELL */
+    std::vector<short> nrn_artcell_qindex;
+    std::vector<bool> nrn_is_artificial;
+
+    /**
+     * Net Receive function pointer lookup tables
+     */
+    std::vector<pnt_receive_t> pnt_receive; /* for synaptic events. */
+    std::vector<pnt_receive_t> pnt_receive_init;
+    std::vector<short> pnt_receive_size;
+
+    /**
+     * Holds function pointers for WATCH callback
+     */
+    std::vector<nrn_watch_check_t> nrn_watch_check;
+
+    /**
+     * values are type numbers of mechanisms which do net_send call
+     * related to NMODL net_event()
+     *
+     */
+    std::vector<int> nrn_has_net_event;
+
+    /**
+     * inverse of nrn_has_net_event_ maps the values of nrn_has_net_event_ to the index of
+     * ptntype2presyn
+     */
+    std::vector<int> pnttype2presyn;
+
+
+    std::vector<bbcore_read_t> nrn_bbcore_read;
+    std::vector<bbcore_write_t> nrn_bbcore_write;
+
+  public:
+
+    auto& get_memb_funcs() {
+        return memb_funcs;
+    }
+
+    auto& get_memb_func(size_t idx) {
+        return memb_funcs[idx];
+    }
+
+    auto& get_different_mechanism_type() {
+        return different_mechanism_type;
+    }
+
+    auto& get_pnt_map() {
+        return pnt_map;
+    }
+
+    auto& get_ion_write_dependency() {
+        return ion_write_dependency;
+    }
+
+    auto& get_net_buf_receive() {
+        return net_buf_receive;
+    }
+
+    auto& get_net_buf_send_type() {
+        return net_buf_send_type;
+    }
+
+    auto& get_bamech() {
+        return bamech;
+    }
+
+    auto& get_prop_param_size() {
+        return nrn_prop_param_size;
+    }
+
+    auto& get_prop_dparam_size() {
+        return nrn_prop_dparam_size;
+    }
+
+    auto& get_mech_data_layout() {
+        return nrn_mech_data_layout;
+    }
+
+    auto& get_is_artificial() {
+        return nrn_is_artificial;
+    }
+
+    auto& get_artcell_qindex() {
+        return nrn_artcell_qindex;
+    }
+
+    auto& get_pnt_receive() {
+        return pnt_receive;
+    }
+
+    auto& get_pnt_receive_init() {
+        return pnt_receive_init;
+    }
+
+    auto& get_pnt_receive_size() {
+        return pnt_receive_size;
+    }
+
+    auto& get_watch_check() {
+        return nrn_watch_check;
+    }
+
+    auto& get_has_net_event() {
+        return nrn_has_net_event;
+    }
+
+    auto& get_pnttype2presyn() {
+        return pnttype2presyn;
+    }
+
+    auto& get_bbcore_read() {
+        return nrn_bbcore_read;
+    }
+
+    auto& get_bbcore_write() {
+        return nrn_bbcore_write;
+    }
+
+
+    /**
+     * Generate point process IDs for pnt_map starting at 1 (since 0 means no point process)
+     * \return the next available point process ID
+     */
+    int get_next_pointtype() {
+        return pointtype++;
+    }
+
+};
+
+extern CoreNeuron corenrn;
+
+}  // namespace coreneuron

coreneuron/coreneuron.hpp

@@ -39,15 +39,10 @@ namespace coreneuron {
 
 #define NRNBBCORE 1
 
-#define nil NULL
-#define Sprintf sprintf
-
 typedef int Datum;
-//#define Datum int
 typedef int (*Pfri)();
 typedef char Symbol;
 
-#define CACHEVEC 2
 #define VEC_A(i) (_nt->_actual_a[(i)])
 #define VEC_B(i) (_nt->_actual_b[(i)])
 #define VEC_D(i) (_nt->_actual_d[(i)])