Omp

CMakeLists.txt

@@ -31,12 +31,25 @@ if(WITH_TRACE)
     add_definitions("-DWITH_TRACE")
 endif()
 
-# TBB support
-set(WITH_TBB OFF CACHE BOOL "use TBB for on-node threading" )
-if(WITH_TBB)
+#threading model selection
+set(THREADING_MODEL "serial" CACHE STRING "set the threading model, one of serial/tbb/omp")
+if(THREADING_MODEL MATCHES "tbb")
+    # TBB support
     find_package(TBB REQUIRED)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TBB_DEFINITIONS}")
     add_definitions(-DWITH_TBB)
+
+elseif(THREADING_MODEL MATCHES "omp")
+    # OpenMP support
+    find_package(OpenMP REQUIRED)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    add_definitions(-DWITH_OMP)
+
+elseif(THREADING_MODEL MATCHES "serial")
+    #setup previously done
+
+else()
+    message( FATAL_ERROR "-- Threading model '${THREADING_MODEL}' not supported, use one of serial/tbb/omp")
 endif()
 
 # MPI support
@@ -50,12 +63,15 @@ if(WITH_MPI)
     set_property(DIRECTORY APPEND_STRING PROPERTY COMPILE_OPTIONS "${MPI_C_COMPILE_FLAGS}")
 endif()
 
-# Profiler support
+
+# Internal profiler support
 set(WITH_PROFILING OFF CACHE BOOL "use built-in profiling of miniapp" )
 if(WITH_PROFILING)
     add_definitions(-DWITH_PROFILING)
 endif()
 
+
+
 # Cray systems
 set(SYSTEM_CRAY OFF CACHE BOOL "add flags for compilation on Cray systems")
 if(SYSTEM_CRAY)
@@ -88,16 +104,34 @@ else()
     set(use_external_modcc ON BOOL)
 endif()
 
-# whether to attempt to use nrniv to build validation data
+# Validation data generation
+
+# destination directory for generated data
+set(VALIDATION_DATA_DIR "${CMAKE_SOURCE_DIR}/validation/data" CACHE PATH "location of generated validation data")
+
+# Whether to build validation data at all
+set(BUILD_VALIDATION_DATA ON CACHE BOOL "generate validation data")
+
+# Whether to attempt to use julia to build validation data
+find_program(JULIA_BIN julia)
+if(JULIA_BIN STREQUAL "JULIA_BIN-NOTFOUND")
+    message(STATUS "julia not found; will not automatically build validation data sets from julia scripts")
+    set(BUILD_JULIA_VALIDATION_DATA FALSE)
+else()
+    set(BUILD_JULIA_VALIDATION_DATA TRUE)
+endif()
+
+# Whether to attempt to use nrniv to build validation data
 # (if we find nrniv, do)
 find_program(NRNIV_BIN nrniv)
 if(NRNIV_BIN STREQUAL "NRNIV_BIN-NOTFOUND")
-    message(STATUS "nrniv not found; will not automatically build validation data sets")
-    set(BUILD_VALIDATION_DATA FALSE)
+    message(STATUS "nrniv not found; will not automatically build NEURON validation data sets")
+    set(BUILD_NRN_VALIDATION_DATA FALSE)
 else()
-    set(BUILD_VALIDATION_DATA TRUE)
+    set(BUILD_NRN_VALIDATION_DATA TRUE)
 endif()
 
+
 include_directories(${CMAKE_SOURCE_DIR}/tclap/include)
 include_directories(${CMAKE_SOURCE_DIR}/vector)
 include_directories(${CMAKE_SOURCE_DIR}/include)
@@ -109,12 +143,17 @@ if( "${WITH_TBB}" STREQUAL "ON" )
     include_directories(${TBB_INCLUDE_DIRS})
 endif()
 
+# only include validation data if flag is set
+if(BUILD_VALIDATION_DATA)
+    add_subdirectory(validation)
+endif()
+
 # only compile modcc if it is not provided externally
 if(use_external_modcc)
     add_subdirectory(modcc)
 endif()
+
 add_subdirectory(mechanisms)
-add_subdirectory(nrn)
 add_subdirectory(src)
 add_subdirectory(tests)
 add_subdirectory(miniapp)

cmake/FindTBB.cmake

@@ -158,6 +158,7 @@ if(NOT TBB_FOUND)
     elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^i.86$")
       set(TBB_LIB_PATH_SUFFIX "lib/ia32/gcc4.4")
     endif()
+    list(APPEND TBB_LIB_PATH_SUFFIX "lib")
   endif()
 
   ##################################
@@ -179,12 +180,12 @@ if(NOT TBB_FOUND)
     find_library(TBB_${_comp}_LIBRARY_RELEASE ${_comp}
         HINTS ${TBB_LIBRARY} ${TBB_SEARCH_DIR}
         PATHS ${TBB_DEFAULT_SEARCH_DIR} ENV LIBRARY_PATH
-        PATH_SUFFIXES "${TBB_LIB_PATH_SUFFIX}")
+        PATH_SUFFIXES ${TBB_LIB_PATH_SUFFIX})
 
     find_library(TBB_${_comp}_LIBRARY_DEBUG ${_comp}_debug
         HINTS ${TBB_LIBRARY} ${TBB_SEARCH_DIR}
         PATHS ${TBB_DEFAULT_SEARCH_DIR} ENV LIBRARY_PATH
-        PATH_SUFFIXES "${TBB_LIB_PATH_SUFFIX}")
+        PATH_SUFFIXES ${TBB_LIB_PATH_SUFFIX})
 
 
     # Set the library to be used for the component

data/test.mod

@@ -10,7 +10,7 @@ NEURON  {
 }
 
 STATE {
-    h
+    h (nA)
     m r
 }
 

docs/passive_cable/cable_computation.tex

@@ -54,16 +54,16 @@ \section{The Rallpack 1 model}
 \begin{table}[ht]
     \centering
     \begin{tabular}{lSl}
-	\toprule
-	Term & {Value} & Property\\
-	\midrule
-	$d$    & \SI{1.0}{\um}                 & cable diameter \\
-	$L$    & \SI{1.0}{\mm}                 & cable length \\
-	$R_A$  & \SI{1.0}{\ohm\m}              & bulk axial resistivity \\
-	$R_M$  & \SI{4.0}{\ohm\m\squared}      & areal membrane resistivity \\
-	$C_M$  & \SI{0.01}{\F\per\m\squared}   & areal membrane capacitance \\
-	$E_M$  & \SI{-65.0}{\mV}               & membrane reversal potential \\
-	\bottomrule
+        \toprule
+        Term & {Value} & Property\\
+        \midrule
+        $d$    & \SI{1.0}{\um}                 & cable diameter \\
+        $L$    & \SI{1.0}{\mm}                 & cable length \\
+        $R_A$  & \SI{1.0}{\ohm\m}              & bulk axial resistivity \\
+        $R_M$  & \SI{4.0}{\ohm\m\squared}      & areal membrane resistivity \\
+        $C_M$  & \SI{0.01}{\F\per\m\squared}   & areal membrane capacitance \\
+        $E_M$  & \SI{-65.0}{\mV}               & membrane reversal potential \\
+        \bottomrule
     \end{tabular}
     \caption{Cable properties for the Rallpack 1 model.}
     \label{tbl:rallpack1}
@@ -87,9 +87,9 @@ \section{The Rallpack 1 model}
 With the model boundary conditions,
 \begin{subequations}
     \begin{align}
-	v(x, 0) &= E, \\
-	\left.\frac{\partial v}{\partial x}\right\vert_{x=0} & = -Ir, \\
-	 \left.\frac{\partial v}{\partial x}\right\vert_{x=L} & = 0,
+        v(x, 0) &= E, \\
+        \left.\frac{\partial v}{\partial x}\right\vert_{x=0} & = -Ir, \\
+         \left.\frac{\partial v}{\partial x}\right\vert_{x=L} & = 0,
     \end{align}
 \end{subequations}
 where $I$ is the injected current and $L$ is the cable length.
@@ -98,18 +98,18 @@ \section{The Rallpack 1 model}
 to a normalized version of the cable equation,
 \begin{subequations}
     \begin{align}
-	\label{eq:normcable}
-	\frac{\partial^2 g}{\partial x^2} & =
-	\frac{\partial g}{\partial t} + g,
+        \label{eq:normcable}
+        \frac{\partial^2 g}{\partial x^2} & =
+        \frac{\partial g}{\partial t} + g,
         \\
-	\label{eq:normcableinitial}
-	g(x, 0) &= 0,
-	\\
-	\label{eq:normcableleft}
-	\left.\frac{\partial g}{\partial x}\right\vert_{x=0} & = 1,
-	\\
-	\label{eq:normcableright}
-	\left.\frac{\partial g}{\partial x}\right\vert_{x=L} & = 0
+        \label{eq:normcableinitial}
+        g(x, 0) &= 0,
+        \\
+        \label{eq:normcableleft}
+        \left.\frac{\partial g}{\partial x}\right\vert_{x=0} & = 1,
+        \\
+        \label{eq:normcableright}
+        \left.\frac{\partial g}{\partial x}\right\vert_{x=L} & = 0
     \end{align}
 \end{subequations}
 by
@@ -158,7 +158,7 @@ \section{Solution to the normalized cable equation}
 Consequently,
 \begin{equation}
     \begin{aligned}
-	G(x, s) &= \frac{1}{ms}\cdot\frac{e^{mx}+e^{2mL-mx}}{1-e^{2mL}}\\
+        G(x, s) &= \frac{1}{ms}\cdot\frac{e^{mx}+e^{2mL-mx}}{1-e^{2mL}}\\
                 &= - \frac{1}{ms}\cdot\frac{\cosh m(L-x)}{\sinh mL}.
     \end{aligned}
 \end{equation}
@@ -199,10 +199,10 @@ \subsection*{Inversion}
 For $|s+1|>\epsilon$,
 \begin{equation}
     \begin{aligned}
-	|s^{3/2}G(x,s)|^2
-	    & \leq (1+\epsilon)^{-1} \left| \frac{\cosh m(L-x)}{\sinh mL} \right|^2
-	\\
-	    & \leq (1+\epsilon)^{-1} (1+|\coth mL|)^2
+        |s^{3/2}G(x,s)|^2
+            & \leq (1+\epsilon)^{-1} \left| \frac{\cosh m(L-x)}{\sinh mL} \right|^2
+        \\
+            & \leq (1+\epsilon)^{-1} (1+|\coth mL|)^2
     \label{eq:gbounds}
     \end{aligned}
 \end{equation}
@@ -218,8 +218,8 @@ \subsection*{Inversion}
 a neighbourhood of $s=0$, and so the pole is simple and
 \begin{equation}
     \begin{aligned}
-	\Res(G; 0) & = - \frac{1}{m}\cdot\left.\frac{\cosh m(L-x)}{\sinh mL}\right|_{s=0}\\
-		   & = - \frac{\cosh (L-x)}{\sinh L}.
+        \Res(G; 0) & = - \frac{1}{m}\cdot\left.\frac{\cosh m(L-x)}{\sinh mL}\right|_{s=0}\\
+                   & = - \frac{\cosh (L-x)}{\sinh L}.
     \end{aligned}
 \end{equation}
 
@@ -235,9 +235,9 @@ \subsection*{Inversion}
 Noting that $dm/ds = \frac{1}{2}m^{-1}$,
 \begin{equation}
     \begin{aligned}
-	h'(s) &= \frac{1}{2}m^{-1}\sinh mL + \frac{1}{2}L\cosh mL \\
-	      &= \frac{1}{2}L + \frac{1}{2}L + O(m^2) \quad(m\to 0) \\
-	      &= L + O(s+1) \quad(s\to -1).
+        h'(s) &= \frac{1}{2}m^{-1}\sinh mL + \frac{1}{2}L\cosh mL \\
+              &= \frac{1}{2}L + \frac{1}{2}L + O(m^2) \quad(m\to 0) \\
+              &= L + O(s+1) \quad(s\to -1).
     \label{eq:hprime}
     \end{aligned}
 \end{equation}
@@ -255,11 +255,11 @@ \subsection*{Inversion}
 Consequently the pole is simple and
 \begin{equation}
     \begin{aligned}
-	\Res(G; s_k)
-	    & = f(x, s_k)/h'(s_k)\\
-	    & =  -\frac{2}{s_k L}\frac{\cosh m_k(L-x)}{\cosh m_kL} \\
-	    & =  -\frac{2}{s_k L}\frac{\cosh m_kL\cosh m_kx-\sinh m_kL\sinh m_kL}{\cosh m_kL} \\
-	    & =  -\frac{2}{s_k L}\cosh m_k x,
+        \Res(G; s_k)
+            & = f(x, s_k)/h'(s_k)\\
+            & =  -\frac{2}{s_k L}\frac{\cosh m_k(L-x)}{\cosh m_kL} \\
+            & =  -\frac{2}{s_k L}\frac{\cosh m_kL\cosh m_kx-\sinh m_kL\sinh m_kL}{\cosh m_kL} \\
+            & =  -\frac{2}{s_k L}\cosh m_k x,
     \end{aligned}
 \end{equation}
 as $\sinh m_k=0$.
@@ -272,7 +272,7 @@ \subsection*{Inversion}
 The series exapnsion for $g(x, t)$ therefore is
 \begin{equation}
     g(x, t) = -\frac{\cosh(L-x)}{\sinh L} + \frac{1}{L}e^{-t}\left\{
-	1+2\sum_{k=1}^\infty \frac{e^{-ta_k^2}}{1+a_k^2}\cos a_k x\right\}.
+        1+2\sum_{k=1}^\infty \frac{e^{-ta_k^2}}{1+a_k^2}\cos a_k x\right\}.
     \label{eq:theg}
 \end{equation}
 
@@ -285,16 +285,16 @@ \section{Computation of series}
 Let $g_n$ be the partial sum
 \begin{equation}
     g_n(x, t) = -\frac{\cosh(L-x)}{\sinh L} + \frac{1}{L}e^{-t}\left\{
-	1+2\sum_{k=1}^n \frac{e^{-ta_k^2}}{1+a_k^2}\cos a_k x\right\}.
+        1+2\sum_{k=1}^n \frac{e^{-ta_k^2}}{1+a_k^2}\cos a_k x\right\}.
 \end{equation}
 so that $g(x, t) =\lim_{n\to\infty} g_n(x,t)$. Let $\bar{g}_n = |g-g_n|$ be the
 residual. The $a_k$ form an increasing sequence, so
 \begin{equation}
     \begin{aligned}
-	\bar{g}_n(x,t)
-	    & \leq \frac{2}{L}e^{-t}\sum_{n+1}^\infty\frac{e^{-ta_k^2}}{1+a_k^2}\\
-	    & \leq \frac{2}{L}e^{-t}\int_{a_n}^\infty \frac{e^{-tu^2}}{1+u^2}\,du\\
-	    & < \frac{2}{L}e^{-t}\int_{a_n}^\infty \frac{e^{-tu^2}}{u^2}\,du.
+        \bar{g}_n(x,t)
+            & \leq \frac{2}{L}e^{-t}\sum_{n+1}^\infty\frac{e^{-ta_k^2}}{1+a_k^2}\\
+            & \leq \frac{2}{L}e^{-t}\int_{a_n}^\infty \frac{e^{-tu^2}}{1+u^2}\,du\\
+            & < \frac{2}{L}e^{-t}\int_{a_n}^\infty \frac{e^{-tu^2}}{u^2}\,du.
     \end{aligned}
     \label{eq:gbar}
 \end{equation}
@@ -313,9 +313,9 @@ \section{Computation of series}
 Substituting into \eqref{eq:gbar} gives
 \begin{equation}
     \begin{aligned}
-	\bar{g}_n(x,t)
-	    & < \frac{1}{L}e^{-t}\sqrt{t}\,\Gamma(-\frac{1}{2},a_n^2 t) \\
-	    & \leq \frac{1}{L}e^{-t}\sqrt{t}\,(a_n^2 t)^{-\frac{3}{2}}e^{-a_n^2t} \\
+        \bar{g}_n(x,t)
+            & < \frac{1}{L}e^{-t}\sqrt{t}\,\Gamma(-\frac{1}{2},a_n^2 t) \\
+            & \leq \frac{1}{L}e^{-t}\sqrt{t}\,(a_n^2 t)^{-\frac{3}{2}}e^{-a_n^2t} \\
             & = \frac{e^{-t(1+a_n^2)}}{L t a_n^3}.
     \end{aligned}
 \end{equation}

modcc/blocks.hpp

@@ -26,6 +26,28 @@ enum class moduleKind {
     density
 };
 
+typedef std::vector<Token> unit_tokens;
+struct Id {
+    Token token;
+    std::string value; // store the value as a string, not a number : empty
+                       // string == no value
+    unit_tokens units;
+
+    Id(Token const& t, std::string const& v, unit_tokens const& u)
+        : token(t), value(v), units(u)
+    {}
+
+    Id() {}
+
+    bool has_value() const {
+        return value.size()>0;
+    }
+
+    std::string const& name() const {
+        return token.spelling;
+    }
+};
+
 // information stored in a NEURON {} block in mod file.
 struct NeuronBlock {
     bool threadsafe = false;
@@ -42,7 +64,7 @@ struct NeuronBlock {
 
 // information stored in a NEURON {} block in mod file
 struct StateBlock {
-    std::vector<std::string> state_variables;
+    std::vector<Id> state_variables;
     auto begin() -> decltype(state_variables.begin()) {
         return state_variables.begin();
     }
@@ -52,32 +74,11 @@ struct StateBlock {
 };
 
 // information stored in a NEURON {} block in mod file
-typedef std::vector<Token> unit_tokens;
 struct UnitsBlock {
     typedef std::pair<unit_tokens, unit_tokens> units_pair;
     std::vector<units_pair> unit_aliases;
 };
 
-struct Id {
-    Token token;
-    std::string value; // store the value as a string, not a number : empty string == no value
-    unit_tokens units;
-
-    Id(Token const& t, std::string const& v, unit_tokens const& u)
-        : token(t), value(v), units(u)
-    {}
-
-    Id() {}
-
-    bool has_value() const {
-        return value.size()>0;
-    }
-
-    std::string const& name() const {
-        return token.spelling;
-    }
-};
-
 // information stored in a NEURON {} block in mod file
 struct ParameterBlock {
     std::vector<Id> parameters;
@@ -164,4 +165,3 @@ inline std::ostream& operator<< (std::ostream& os, AssignedBlock const& A) {
 
     return os;
 }
-