diff --git a/bfps/NSVorticityEquation.py b/bfps/NSVorticityEquation.py
index e3a3c2c376a9b706e19e4ddb54baa182234e3dd2..50e62275111d55d0237cf902a6d38f2a56189573 100644
--- a/bfps/NSVorticityEquation.py
+++ b/bfps/NSVorticityEquation.py
@@ -217,6 +217,42 @@ class NSVorticityEquation(_fluid_particle_base):
field_H5T = 'H5T_NATIVE_FLOAT'
elif self.dtype == np.float64:
field_H5T = 'H5T_NATIVE_DOUBLE'
+ self.variables += 'int checkpoint;\n'
+ self.read_checkpoint = """
+ //begincpp
+ if (myrank == 0)
+ {
+ hid_t dset = H5Dopen(stat_file, "checkpoint", H5P_DEFAULT);
+ H5Dread(
+ dset,
+ H5T_NATIVE_INT,
+ H5S_ALL,
+ H5S_ALL,
+ H5P_DEFAULT,
+ &checkpoint);
+ H5Dclose(dset);
+ }
+ MPI_Bcast(&checkpoint, 1, MPI_INT, 0, MPI_COMM_WORLD);
+ fs->checkpoint = checkpoint;
+ //endcpp
+ """
+ self.store_checkpoint = """
+ //begincpp
+ checkpoint = fs->checkpoint;
+ if (myrank == 0)
+ {
+ hid_t dset = H5Dopen(stat_file, "checkpoint", H5P_DEFAULT);
+ H5Dwrite(
+ dset,
+ H5T_NATIVE_INT,
+ H5S_ALL,
+ H5S_ALL,
+ H5P_DEFAULT,
+ &checkpoint);
+ H5Dclose(dset);
+ }
+ //endcpp
+ """
self.fluid_start += """
//begincpp
char fname[512];
@@ -233,6 +269,7 @@ class NSVorticityEquation(_fluid_particle_base):
nx, ny, nz,
MPI_COMM_WORLD,
{1});
+ fs->checkpoints_per_file = checkpoints_per_file;
fs->nu = nu;
fs->fmode = fmode;
fs->famplitude = famplitude;
@@ -240,16 +277,25 @@ class NSVorticityEquation(_fluid_particle_base):
fs->fk1 = fk1;
strncpy(fs->forcing_type, forcing_type, 128);
fs->iteration = iteration;
+ {2}
fs->cvorticity->real_space_representation = false;
fs->io_checkpoint();
//endcpp
- """.format(self.C_dtype, self.fftw_plan_rigor, field_H5T)
+ """.format(
+ self.C_dtype,
+ self.fftw_plan_rigor,
+ self.read_checkpoint)
self.fluid_start += self.store_kspace
self.fluid_loop = 'fs->step(dt);\n'
self.fluid_loop += ('if (fs->iteration % niter_out == 0)\n{\n' +
- self.fluid_output + '\n}\n')
+ self.fluid_output +
+ self.store_checkpoint +
+ '\n}\n')
self.fluid_end = ('if (fs->iteration % niter_out != 0)\n{\n' +
- self.fluid_output + '\n}\n' +
+ self.fluid_output +
+ self.store_checkpoint +
+ 'DEBUG_MSG("checkpoint value is %d\\n", checkpoint);\n' +
+ '\n}\n' +
'delete fs;\n' +
'delete tmp_vec_field;\n' +
'delete tmp_scal_field;\n')
@@ -470,6 +516,7 @@ class NSVorticityEquation(_fluid_particle_base):
self.parameters['histogram_bins'],
4),
dtype = np.int64)
+ ofile['checkpoint'] = int(0)
return None
def specific_parser_arguments(
self,
@@ -580,7 +627,6 @@ class NSVorticityEquation(_fluid_particle_base):
spectra_slope = 2.0,
amplitude = 0.05)
f['vorticity/complex/{0}'.format(0)] = data
- f['fields_stored'] = int(1)
f.close()
self.run(
nb_processes = opt.nb_processes,
diff --git a/bfps/_code.py b/bfps/_code.py
index 2f21c16abf9aaff1e6a83e59bf9070a83b61ec0e..3ff3de341b20c578262c1111835ba799359db1f6 100644
--- a/bfps/_code.py
+++ b/bfps/_code.py
@@ -118,8 +118,15 @@ class _code(_base):
sprintf(fname, "%s.h5", simname);
parameter_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
Cdset = H5Dopen(parameter_file, "iteration", H5P_DEFAULT);
- H5Dread(Cdset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &iteration);
- DEBUG_MSG("simname is %s and iteration is %d\\n", simname, iteration);
+ H5Dread(
+ Cdset,
+ H5T_NATIVE_INT,
+ H5S_ALL,
+ H5S_ALL,
+ H5P_DEFAULT,
+ &iteration);
+ DEBUG_MSG("simname is %s and iteration is %d\\n",
+ simname, iteration);
H5Dclose(Cdset);
H5Fclose(parameter_file);
read_parameters();
diff --git a/bfps/cpp/vorticity_equation.cpp b/bfps/cpp/vorticity_equation.cpp
index f40c105c2eedf76be5495357418ac74600a04399..87bcf331ff4d6b6bf215fdc34f713bc9372e87b3 100644
--- a/bfps/cpp/vorticity_equation.cpp
+++ b/bfps/cpp/vorticity_equation.cpp
@@ -46,6 +46,58 @@ void vorticity_equation<rnumber, be>::impose_zero_modes()
this->v[2]->impose_zero_mode();
}
+template <class rnumber,
+ field_backend be>
+void vorticity_equation<rnumber, be>::update_checkpoint()
+{
+ std::string fname = this->get_current_fname();
+ bool file_exists = false;
+ {
+ struct stat file_buffer;
+ file_exists = (stat(fname.c_str(), &file_buffer) == 0);
+ }
+ if (file_exists)
+ {
+ // check how many fields there are in the checkpoint file
+ // increment checkpoint if needed
+ hsize_t fields_stored;
+ hid_t fid, group_id;
+ fid = H5Fopen(fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ group_id = H5Gopen(fid, "vorticity/complex", H5P_DEFAULT);
+ H5Gget_num_objs(
+ group_id,
+ &fields_stored);
+ H5Gclose(group_id);
+ H5Fclose(fid);
+ if (fields_stored >= this->checkpoints_per_file)
+ this->checkpoint++;
+ }
+ else if (this->cvelocity->myrank == 0)
+ {
+ // create file, create fields_stored dset
+ hid_t fid = H5Fcreate(
+ fname.c_str(),
+ H5F_ACC_EXCL,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+ hid_t gg = H5Gcreate(
+ fid,
+ "vorticity",
+ H5P_DEFAULT,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+ hid_t ggg = H5Gcreate(
+ gg,
+ "complex",
+ H5P_DEFAULT,
+ H5P_DEFAULT,
+ H5P_DEFAULT);
+ H5Gclose(ggg);
+ H5Gclose(gg);
+ H5Fclose(fid);
+ }
+}
+
template <class rnumber,
field_backend be>
vorticity_equation<rnumber, be>::vorticity_equation(
diff --git a/bfps/cpp/vorticity_equation.hpp b/bfps/cpp/vorticity_equation.hpp
index aba96d5e2b08149636486e880c7d901eea13bb26..6c2621c98c15179b61f4cf52f6a6a227847574a4 100644
--- a/bfps/cpp/vorticity_equation.hpp
+++ b/bfps/cpp/vorticity_equation.hpp
@@ -103,68 +103,10 @@ class vorticity_equation
std::to_string(this->checkpoint) +
std::string(".h5"));
}
- inline void update_checkpoint()
- {
- std::string fname = this->get_current_fname();
- bool file_exists = false;
- {
- struct stat file_buffer;
- file_exists = (stat(fname.c_str(), &file_buffer) == 0);
- }
- if (file_exists)
- {
- // check how many fields there are in the checkpoint file
- // increment checkpoint if needed
- int fields_stored;
- hid_t fid, dset_id;
- fid = H5Fopen(fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- dset_id = H5Dopen(fid, "fields_stored", H5P_DEFAULT);
- H5Dread(dset_id,
- H5T_NATIVE_INT,
- H5S_ALL, H5S_ALL,
- H5P_DEFAULT,
- &fields_stored);
- H5Dclose(dset_id);
- H5Fclose(fid);
- if (fields_stored >= this->checkpoints_per_file)
- this->checkpoint++;
- else
- {
- // update fields_stored dset
- fields_stored++;
- if (this->cvelocity->myrank == 0)
- {
- fid = H5Fopen(fname.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
- dset_id = H5Dopen(fid, "fields_stored", H5P_DEFAULT);
- H5Dwrite(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &fields_stored);
- H5Dclose(dset_id);
- H5Fclose(fid);
- }
- }
- }
- else if (this->cvelocity->myrank == 0)
- {
- // create file, create fields_stored dset
- hid_t fid = H5Fcreate(fname.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
- hsize_t one[] = {1};
- hid_t fspace = H5Screate_simple(
- 1,
- one,
- NULL);
- hid_t dset = H5Dcreate(
- fid,
- "fields_stored",
- H5T_NATIVE_INT,
- fspace,
- H5P_DEFAULT,
- H5P_DEFAULT,
- H5P_DEFAULT);
- H5Dclose(dset);
- H5Fclose(fid);
- }
- }
+ void update_checkpoint(void);
inline void io_checkpoint(bool read = true)
{
+ assert(!this->cvorticity->real_space_representation);
if (!read)
this->update_checkpoint();
std::string fname = this->get_current_fname();