BROKEN - code compiles and segfaults

bfps/TEST.py

@@ -124,6 +124,16 @@ class TEST(_code):
         self.parameters['dkz'] = float(1.0)
         self.parameters['filter_length'] = float(1.0)
         return None
+    def generate_extra_parameters(
+            self,
+            dns_type = None):
+        pars = {}
+        if dns_type == 'test_interpolation':
+            pars['nparticles'] = 10
+            pars['tracers0_integration_steps'] = int(4)
+            pars['tracers0_neighbours'] = int(1)
+            pars['tracers0_smoothness'] = int(1)
+        return pars
     def get_kspace(self):
         kspace = {}
         if self.parameters['dealias_type'] == 1:
@@ -254,21 +264,25 @@ class TEST(_code):
         parser_filter_test = subparsers.add_parser(
                 'filter_test',
                 help = 'plain filter test')
-        self.simulation_parser_arguments(parser_filter_test)
-        self.job_parser_arguments(parser_filter_test)
-        self.parameters_to_parser_arguments(parser_filter_test)
         parser_field_test = subparsers.add_parser(
                 'field_test',
                 help = 'plain field test')
-        self.simulation_parser_arguments(parser_field_test)
-        self.job_parser_arguments(parser_field_test)
-        self.parameters_to_parser_arguments(parser_field_test)
         parser_field_output_test = subparsers.add_parser(
                 'field_output_test',
                 help = 'plain field output test')
-        self.simulation_parser_arguments(parser_field_output_test)
-        self.job_parser_arguments(parser_field_output_test)
-        self.parameters_to_parser_arguments(parser_field_output_test)
+        parser_test_interpolation = subparsers.add_parser(
+                'test_interpolation',
+                help = 'test velocity gradient interpolation')
+        for parser in ['parser_filter_test',
+                       'parser_field_test',
+                       'parser_field_output_test',
+                       'parser_test_interpolation']:
+            eval('self.simulation_parser_arguments(' + parser + ')')
+            eval('self.job_parser_arguments(' + parser + ')')
+            eval('self.parameters_to_parser_arguments(' + parser + ')')
+            eval('self.parameters_to_parser_arguments(' + parser + ',' +
+                    'parameters = self.generate_extra_parameters(dns_type = \'' + parser + '\'))')
+        print(self.parameters.keys())
         return None
     def prepare_launch(
             self,
@@ -285,6 +299,8 @@ class TEST(_code):
             args = [],
             **kwargs):
         opt = self.prepare_launch(args = args)
+        self.parameters.update(
+                self.generate_extra_parameters(dns_type = self.dns_type))
         self.launch_jobs(opt = opt, **kwargs)
         return None
     def launch_jobs(
@@ -293,7 +309,36 @@ class TEST(_code):
             particle_initial_condition = None):
         if not os.path.exists(os.path.join(self.work_dir, self.simname + '.h5')):
             self.write_par(
-                    particle_ic = None)
+                    particle_ic = particle_initial_condition)
+            if self.dns_type == 'test_interpolation':
+                if type(particle_initial_condition) == type(None):
+                    pbase_shape = (self.parameters['nparticles'],)
+                    number_of_particles = self.parameters['nparticles']
+                else:
+                    pbase_shape = particle_initial_condition.shape[:-1]
+                    assert(particle_initial_condition.shape[-1] == 3)
+                    number_of_particles = 1
+                    for val in pbase_shape[1:]:
+                        number_of_particles *= val
+                ncomponents = 3
+                with h5py.File(os.path.join(self.work_dir, self.simname + '_input.h5'), 'a') as ofile:
+                    s = 0
+                    ofile.create_group('tracers{0}'.format(s))
+                    ofile.create_group('tracers{0}/rhs'.format(s))
+                    ofile.create_group('tracers{0}/state'.format(s))
+                    ofile['tracers{0}/rhs'.format(s)].create_dataset(
+                            '0',
+                            shape = (
+                                (self.parameters['tracers{0}_integration_steps'.format(s)],) +
+                                pbase_shape +
+                                (ncomponents,)),
+                            dtype = np.float)
+                    ofile['tracers{0}/state'.format(s)].create_dataset(
+                            '0',
+                            shape = (
+                                pbase_shape +
+                                (ncomponents,)),
+                            dtype = np.float)
         self.run(
                 nb_processes = opt.nb_processes,
                 nb_threads_per_process = opt.nb_threads_per_process,

bfps/cpp/full_code/test_interpolation.cpp

@@ -5,12 +5,10 @@ template <typename rnumber>
 int test_interpolation<rnumber>::read_parameters(void)
 {
     this->test::read_parameters();
-    hid_t parameter_file;
-    hid_t dset, memtype, space;
-    char fname[256];
-    hsize_t dims[1];
-    char *string_data;
-    sprintf(fname, "%s.h5", this->simname.c_str());
+    hid_t parameter_file = H5Fopen(
+            (this->simname + std::string(".h5")).c_str(),
+            H5F_ACC_RDONLY,
+            H5P_DEFAULT);
     this->nparticles = hdf5_tools::read_value<int>(
             parameter_file, "/parameters/nparticles");
     this->tracers0_integration_steps = hdf5_tools::read_value<int>(
@@ -26,8 +24,6 @@ int test_interpolation<rnumber>::read_parameters(void)
 template <typename rnumber>
 int test_interpolation<rnumber>::initialize(void)
 {
-    this->test::initialize();
-
     this->vorticity = new field<rnumber, FFTW, THREE>(
             this->nx, this->ny, this->nz,
             this->comm,
@@ -92,7 +88,6 @@ int test_interpolation<rnumber>::finalize(void)
     delete this->velocity;
     delete this->vorticity;
     this->ps.release();
-    this->test::finalize();
     delete this->kk;
     return EXIT_SUCCESS;
 }