DNS code is written, compiles, but doesn't link

I need to figure out how to define the read_parameters method properly

bfps/_base.py

@@ -74,11 +74,16 @@ class _base(object):
             self,
             parameters = None,
             function_suffix = '',
+            template_class = '',
+            template_prefix = '',
             file_group = 'parameters'):
         if type(parameters) == type(None):
             parameters = self.parameters
         key = sorted(list(parameters.keys()))
-        src_txt = ('int read_parameters' + function_suffix + '()\n{\n' +
+        src_txt = (template_prefix +
+                   'int ' +
+                   template_class +
+                   'read_parameters' + function_suffix + '()\n{\n' +
                    'hid_t parameter_file;\n' +
                    'hid_t dset, memtype, space;\n' +
                    'char fname[256];\n' +

bfps/cpp/full_code/NSVE.cpp

@@ -2,6 +2,36 @@
 #include <cmath>
 #include "NSVE.hpp"
 
+int grow_single_dataset(hid_t dset, int tincrement)
+{
+    int ndims;
+    hsize_t space;
+    space = H5Dget_space(dset);
+    ndims = H5Sget_simple_extent_ndims(space);
+    hsize_t *dims = new hsize_t[ndims];
+    H5Sget_simple_extent_dims(space, dims, NULL);
+    dims[0] += tincrement;
+    H5Dset_extent(dset, dims);
+    H5Sclose(space);
+    delete[] dims;
+    return EXIT_SUCCESS;
+}
+
+herr_t grow_dataset_visitor(
+    hid_t o_id,
+    const char *name,
+    const H5O_info_t *info,
+    void *op_data)
+{
+    if (info->type == H5O_TYPE_DATASET)
+    {
+        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
+        grow_single_dataset(dset, *((int*)(op_data)));
+        H5Dclose(dset);
+    }
+    return EXIT_SUCCESS;
+}
+
 template <typename rnumber>
 int NSVE<rnumber>::read_iteration(void)
 {

bfps/cpp/full_code/NSVE.hpp

@@ -34,35 +34,13 @@
 #include "vorticity_equation.hpp"
 #include "full_code/direct_numerical_simulation.hpp"
 
-int grow_single_dataset(hid_t dset, int tincrement)
-{
-    int ndims;
-    hsize_t space;
-    space = H5Dget_space(dset);
-    ndims = H5Sget_simple_extent_ndims(space);
-    hsize_t *dims = new hsize_t[ndims];
-    H5Sget_simple_extent_dims(space, dims, NULL);
-    dims[0] += tincrement;
-    H5Dset_extent(dset, dims);
-    H5Sclose(space);
-    delete[] dims;
-    return EXIT_SUCCESS;
-}
+int grow_single_dataset(hid_t dset, int tincrement);
 
 herr_t grow_dataset_visitor(
     hid_t o_id,
     const char *name,
     const H5O_info_t *info,
-    void *op_data)
-{
-    if (info->type == H5O_TYPE_DATASET)
-    {
-        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
-        grow_single_dataset(dset, *((int*)(op_data)));
-        H5Dclose(dset);
-    }
-    return EXIT_SUCCESS;
-}
+    void *op_data);
 
 template <typename rnumber>
 class NSVE: public direct_numerical_simulation

bfps/cpp/full_code/main_code.hpp

@@ -28,26 +28,41 @@
 #define MAIN_CODE_HPP
 
 
+
+#include <cfenv>
+#include <string>
+#include <iostream>
 #include "base.hpp"
 #include "field.hpp"
 #include "scope_timer.hpp"
 
+int myrank, nprocs;
+
 template <class DNS>
-main_code(
-        const std::string &simname,
+int main_code(
+        int argc,
+        char *argv[],
         const bool floating_point_exceptions)
 {
     /* floating point exception switch */
-    if (this->floating_point_exceptions)
+    if (floating_point_exceptions)
         feenableexcept(FE_INVALID | FE_OVERFLOW);
     else
         // using std::cerr because DEBUG_MSG requires myrank to be defined
-        std::cerr << ("FPE have been turned OFF" << std::endl;
+        std::cerr << "FPE have been turned OFF" << std::endl;
 
+    if (argc != 2)
+    {
+        std::cerr <<
+            "Wrong number of command line arguments. Stopping." <<
+            std::endl;
+        MPI_Finalize();
+        return EXIT_SUCCESS;
+    }
+    std::string simname = std::string(argv[1]);
 
 
     /* initialize MPI environment */
-    int myrank, nprocs;
 #ifdef NO_FFTWOMP
     MPI_Init(&argc, &argv);
     MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
@@ -83,11 +98,8 @@ main_code(
 
     /* import fftw wisdom */
     if (myrank == 0)
-    {
-        char fname[256];
-        sprintf(fname, "%s_fftw_wisdom.txt", simname.c_str());
-        fftwf_import_wisdom_from_filename(fname);
-    }
+        fftwf_import_wisdom_from_filename(
+                (simname + std::string("_fftw_wisdom.txt")).c_str());
     fftwf_mpi_broadcast_wisdom(MPI_COMM_WORLD);
 
 
@@ -105,7 +117,7 @@ main_code(
      * recover from should not be important enough to not clean up fftw and MPI
      * things.
      */
-    DNS *dns(
+    DNS *dns = new DNS(
             MPI_COMM_WORLD,
             simname);
     int return_value;
@@ -124,17 +136,16 @@ main_code(
         DEBUG_MSG("problem calling dns->finalize(), return value is %d",
                   return_value);
 
+    delete dns;
+
 
 
     /* export fftw wisdom */
     fftwf_mpi_gather_wisdom(MPI_COMM_WORLD);
     MPI_Barrier(MPI_COMM_WORLD);
     if (myrank == 0)
-    {
-        char fname[256];
-        sprintf(fname, "%s_fftw_wisdom.txt", simname);
-        fftwf_export_wisdom_to_filename(fname);
-    }
+        fftwf_export_wisdom_to_filename(
+                (simname + std::string("_fftw_wisdom.txt")).c_str());
 
 
 
@@ -142,7 +153,7 @@ main_code(
     fftwf_mpi_cleanup();
     fftw_mpi_cleanup();
 #ifndef NO_FFTWOMP
-    if (nbThreads > 1){
+    if (nThreads > 1){
         fftw_cleanup_threads();
         fftwf_cleanup_threads();
     }

tests/test_DNS.py

+from bfps.DNS import DNS
+
+
+def main():
+    c = DNS()
+    c.write_src()
+    c.compile_code()
+    return None
+
+if __name__ == '__main__':
+    main()
+