Fix compilation errros

clinssen · Jan 29, 2024 · 5cd6533 · 5cd6533
1 parent a6717ab
commit 5cd6533
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Showing 3 changed files with 32 additions and 3 deletions.
diff --git a/pynestml/codegeneration/nest_gpu_code_generator.py b/pynestml/codegeneration/nest_gpu_code_generator.py
@@ -59,6 +59,7 @@ def replace_text_between_tags(filepath, replace_str, begin_tag="// <<BEGIN_NESTM
     file_str = file_str[:start_pos] + replace_str + file_str[end_pos:]
     with open(filepath, "w") as f:
         f.write(file_str)
+    f.close()
 
 
 class NESTGPUCodeGenerator(NESTCodeGenerator):
@@ -133,6 +134,9 @@ def generate_module_code(self, neurons: Sequence[ASTNeuron], synapses: Sequence[
             self.add_model_name_to_neuron_header(neuron)
             self.add_model_to_neuron_class(neuron)
             self.add_files_to_makefile(neuron)
+            if neuron.get_name() in self.numeric_solver.keys() \
+                and self.numeric_solver[neuron.get_name()] is not None:
+                self.add_model_header_to_rk5_interface(neuron)
 
     def copy_models_from_target_path(self, neuron: ASTNeuron):
         """Copies all the files related to the neuron model to the NEST GPU src directory"""
@@ -190,3 +194,22 @@ def add_files_to_makefile(self, neuron: ASTNeuron):
         replace_text_between_tags(cmakelists_path, code_block,
                                   begin_tag="# <<BEGIN_NESTML_GENERATED>>",
                                   end_tag="# <<END_NESTML_GENERATED>>")
+
+    def add_model_header_to_rk5_interface(self, neuron: ASTNeuron):
+        """
+        Modifies the rk5_interface.h header file to add the model rk5 header file. This is only for 
+        neuron models with a numeric solver.
+        """
+        rk5_interface_path = str(os.path.join(self.nest_gpu_path, "src", "rk5_interface.h"))
+        shutil.copy(rk5_interface_path, rk5_interface_path + ".bak")
+
+        code_block = f"#include \"{neuron.get_name()}_rk5.h\""
+
+        replace_text_between_tags(rk5_interface_path, code_block)
+
+        # with open(rk5_interface_path, "a+") as f:
+        #     lines  = f.readlines()
+        #     lines.append(f"#include \"{neuron.get_name()}_rk5.h\"")
+        #     f.writelines(lines)
+
+        # f.close()
diff --git a/pynestml/codegeneration/resources_nest_gpu/point_neuron/@[email protected] b/pynestml/codegeneration/resources_nest_gpu/point_neuron/@[email protected]
@@ -46,7 +46,9 @@ __global__ void {{ neuronName }}_Calibrate(int n_node, float *param_arr,
 {%- for internals_block in neuron.get_internals_blocks() %}
 {%-     for decl in internals_block.get_declarations() %}
 {%-         for variable in decl.get_variables() %}
+{%-           if variable.get_name() != "__h" %}
 {%-             include "directives/MemberInitialization.jinja2" %}
+{%-           endif %}
 {%-         endfor %}
 {%-     endfor %}
 {%- endfor %}
@@ -124,7 +126,7 @@ void NodeCalibrate(int n_var, int n_param, double x, float *y,
 {%- for internals_block in neuron.get_internals_blocks() %}
 {%-     for decl in internals_block.get_declarations() %}
 {%-         for variable in decl.get_variables() %}
-{%-           if variable.get_name() != "h" %}
+{%-           if variable.get_name() != "__h" %}
 {%-             include "directives/MemberInitialization.jinja2" %}
 {%-           endif %}
 {%-         endfor %}
@@ -151,6 +153,8 @@ void NodeCalibrate(int n_var, int n_param, double x, float *y,
 }
 {%- endif %}
 
+using namespace {{ neuronName }}_ns;
+
 int {{ neuronName }}::Init(int i_node_0, int n_node, int /*n_port*/,
 			 int i_group, unsigned long long *seed)
 {
@@ -166,8 +170,10 @@ int {{ neuronName }}::Init(int i_node_0, int n_node, int /*n_port*/,
   group_param_ = new float[N_GROUP_PARAM];
 {%- endif %}
 
+{%- if not uses_numeric_solver %}
   AllocParamArr();
   AllocVarArr();
+{%- endif %}
 
   scal_var_name_ = {{ neuronName }}_scal_var_name;
   scal_param_name_ = {{ neuronName }}_scal_param_name;

diff --git a/pynestml/codegeneration/resources_nest_gpu/point_neuron/@NEURON_NAME@_kernel.h.jinja2 b/pynestml/codegeneration/resources_nest_gpu/point_neuron/@NEURON_NAME@_kernel.h.jinja2
@@ -40,7 +40,7 @@ __device__
     void Derivatives(double x, float *y, float *dydx, float *param,
 		     {{ neuronName }}_rk5 data_struct)
 {
-  float I_syn_tot = 0.0;
+  {# float I_syn_tot = 0.0;
   I_syn_tot += I_syn_ex - I_syn_in;
 
   float V = ( refractory_step > 0 ) ? V_reset :  MIN(V_m, V_peak);
@@ -52,7 +52,7 @@ __device__
   // Adaptation current w.
   dwdt = (a*(V - E_L) - w) / tau_w;
   dI_syn_exdt = -I_syn_ex / tau_syn_ex;
-  dI_syn_indt = -I_syn_in / tau_syn_in;
+  dI_syn_indt = -I_syn_in / tau_syn_in; #}
 }
 
  template<int NVAR, int NPARAM> //, class DataStruct>