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Commit 268acdb9 authored by Cristian Lalescu's avatar Cristian Lalescu
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make data_file a pointer

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bfps/NavierStokes.py
+ 28
− 22
View file @ 268acdb9
...@@ -50,7 +50,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -50,7 +50,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
hsize_t dims[4]; hsize_t dims[4];
hsize_t old_dims[4]; hsize_t old_dims[4];
// store kspace information // store kspace information
dset = data_file.openDataSet("/kspace/kshell"); dset = data_file->openDataSet("/kspace/kshell");
dspace = dset.getSpace(); dspace = dset.getSpace();
dspace.getSimpleExtentDims(dims); dspace.getSimpleExtentDims(dims);
if (fs->nshells != dims[0]) if (fs->nshells != dims[0])
...@@ -59,34 +59,34 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -59,34 +59,34 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
file_problems++; file_problems++;
} }
dset.write(fs->kshell, double_dtype); dset.write(fs->kshell, double_dtype);
dset = data_file.openDataSet("/kspace/nshell"); dset = data_file->openDataSet("/kspace/nshell");
dset.write(fs->nshell, ptrdiff_t_dtype); dset.write(fs->nshell, ptrdiff_t_dtype);
dset = data_file.openDataSet("/kspace/kM"); dset = data_file->openDataSet("/kspace/kM");
dset.write(&fs->kM, double_dtype); dset.write(&fs->kM, double_dtype);
dset = data_file.openDataSet("/kspace/dk"); dset = data_file->openDataSet("/kspace/dk");
dset.write(&fs->dk, double_dtype); dset.write(&fs->dk, double_dtype);
// moments // moments
dset = data_file.openDataSet("/statistics/moments/velocity"); dset = data_file->openDataSet("/statistics/moments/velocity");
dspace = dset.getSpace(); dspace = dset.getSpace();
dspace.getSimpleExtentDims(old_dims); dspace.getSimpleExtentDims(old_dims);
dims[0] = niter_todo + old_dims[0]; dims[0] = niter_todo + old_dims[0];
dims[1] = old_dims[1]; dims[1] = old_dims[1];
dims[2] = old_dims[2]; dims[2] = old_dims[2];
dset.extend(dims); dset.extend(dims);
dset = data_file.openDataSet("/statistics/moments/vorticity"); dset = data_file->openDataSet("/statistics/moments/vorticity");
dset.extend(dims); dset.extend(dims);
// histograms // histograms
dset = data_file.openDataSet("/statistics/histograms/velocity"); dset = data_file->openDataSet("/statistics/histograms/velocity");
dspace = dset.getSpace(); dspace = dset.getSpace();
dspace.getSimpleExtentDims(old_dims); dspace.getSimpleExtentDims(old_dims);
dims[0] = niter_todo + old_dims[0]; dims[0] = niter_todo + old_dims[0];
dims[1] = old_dims[1]; dims[1] = old_dims[1];
dims[2] = old_dims[2]; dims[2] = old_dims[2];
dset.extend(dims); dset.extend(dims);
dset = data_file.openDataSet("/statistics/histograms/vorticity"); dset = data_file->openDataSet("/statistics/histograms/vorticity");
dset.extend(dims); dset.extend(dims);
// spectra // spectra
dset = data_file.openDataSet("/statistics/spectra/velocity_velocity"); dset = data_file->openDataSet("/statistics/spectra/velocity_velocity");
dspace = dset.getSpace(); dspace = dset.getSpace();
dspace.getSimpleExtentDims(old_dims); dspace.getSimpleExtentDims(old_dims);
dims[0] = niter_todo + old_dims[0]; dims[0] = niter_todo + old_dims[0];
...@@ -94,8 +94,9 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -94,8 +94,9 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
dims[2] = old_dims[2]; dims[2] = old_dims[2];
dims[3] = old_dims[3]; dims[3] = old_dims[3];
dset.extend(dims); dset.extend(dims);
dset = data_file.openDataSet("/statistics/spectra/vorticity_vorticity"); dset = data_file->openDataSet("/statistics/spectra/vorticity_vorticity");
dset.extend(dims); dset.extend(dims);
dset.close();
//endcpp //endcpp
""" """
self.style = {} self.style = {}
...@@ -133,7 +134,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -133,7 +134,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
H5::DataSpace memspace, writespace; H5::DataSpace memspace, writespace;
hsize_t count[4], offset[4], old_dims[4]; hsize_t count[4], offset[4], old_dims[4];
//moments //moments
dset = data_file.openDataSet("statistics/moments/velocity"); dset = data_file->openDataSet("statistics/moments/velocity");
writespace = dset.getSpace(); writespace = dset.getSpace();
writespace.getSimpleExtentDims(old_dims); writespace.getSimpleExtentDims(old_dims);
count[0] = 1; count[0] = 1;
...@@ -145,10 +146,10 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -145,10 +146,10 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
offset[2] = 0; offset[2] = 0;
writespace.selectHyperslab(H5S_SELECT_SET, count, offset); writespace.selectHyperslab(H5S_SELECT_SET, count, offset);
dset.write(velocity_moments, H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(velocity_moments, H5::PredType::NATIVE_DOUBLE, memspace, writespace);
dset = data_file.openDataSet("statistics/moments/vorticity"); dset = data_file->openDataSet("statistics/moments/vorticity");
dset.write(vorticity_moments, H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(vorticity_moments, H5::PredType::NATIVE_DOUBLE, memspace, writespace);
//histograms //histograms
dset = data_file.openDataSet("statistics/histograms/velocity"); dset = data_file->openDataSet("statistics/histograms/velocity");
writespace = dset.getSpace(); writespace = dset.getSpace();
count[0] = 1; count[0] = 1;
count[1] = histogram_bins; count[1] = histogram_bins;
...@@ -159,10 +160,10 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -159,10 +160,10 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
offset[2] = 0; offset[2] = 0;
writespace.selectHyperslab(H5S_SELECT_SET, count, offset); writespace.selectHyperslab(H5S_SELECT_SET, count, offset);
dset.write(hist_velocity, H5::PredType::NATIVE_INT64, memspace, writespace); dset.write(hist_velocity, H5::PredType::NATIVE_INT64, memspace, writespace);
dset = data_file.openDataSet("statistics/histograms/vorticity"); dset = data_file->openDataSet("statistics/histograms/vorticity");
dset.write(hist_vorticity, H5::PredType::NATIVE_INT64, memspace, writespace); dset.write(hist_vorticity, H5::PredType::NATIVE_INT64, memspace, writespace);
//spectra //spectra
dset = data_file.openDataSet("statistics/spectra/velocity_velocity"); dset = data_file->openDataSet("statistics/spectra/velocity_velocity");
writespace = dset.getSpace(); writespace = dset.getSpace();
count[1] = fs->nshells; count[1] = fs->nshells;
count[2] = 3; count[2] = 3;
...@@ -171,8 +172,11 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -171,8 +172,11 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
offset[3] = 0; offset[3] = 0;
writespace.selectHyperslab(H5S_SELECT_SET, count, offset); writespace.selectHyperslab(H5S_SELECT_SET, count, offset);
dset.write(spec_velocity, H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(spec_velocity, H5::PredType::NATIVE_DOUBLE, memspace, writespace);
dset = data_file.openDataSet("statistics/spectra/vorticity_vorticity"); dset = data_file->openDataSet("statistics/spectra/vorticity_vorticity");
dset.write(spec_vorticity, H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(spec_vorticity, H5::PredType::NATIVE_DOUBLE, memspace, writespace);
dset = data_file->openDataSet("iteration");
dset.write(&fs->iteration, H5::PredType::NATIVE_INT);
dset.close();
} }
fftw_free(spec_velocity); fftw_free(spec_velocity);
fftw_free(spec_vorticity); fftw_free(spec_vorticity);
...@@ -236,7 +240,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -236,7 +240,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
temp_string = (std::string("/particles/") + temp_string = (std::string("/particles/") +
std::string(ps{0}->name) + std::string(ps{0}->name) +
std::string("/{1}")); std::string("/{1}"));
dset = data_file.openDataSet(temp_string); dset = data_file->openDataSet(temp_string);
dspace = dset.getSpace(); dspace = dset.getSpace();
dspace.getSimpleExtentDims(dims); dspace.getSimpleExtentDims(dims);
dims[0] = niter_todo/niter_part + dims[0]; dims[0] = niter_todo/niter_part + dims[0];
...@@ -274,7 +278,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -274,7 +278,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
std::string temp_string = (std::string("/particles/") + std::string temp_string = (std::string("/particles/") +
std::string(ps{0}->name) + std::string(ps{0}->name) +
std::string("/velocity")); std::string("/velocity"));
H5::DataSet dset = data_file.openDataSet(temp_string); H5::DataSet dset = data_file->openDataSet(temp_string);
H5::DataSpace memspace, writespace; H5::DataSpace memspace, writespace;
hsize_t count[3], offset[3]; hsize_t count[3], offset[3];
writespace = dset.getSpace(); writespace = dset.getSpace();
...@@ -286,13 +290,15 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -286,13 +290,15 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
memspace = H5::DataSpace(3, count); memspace = H5::DataSpace(3, count);
writespace.selectHyperslab(H5S_SELECT_SET, count, offset); writespace.selectHyperslab(H5S_SELECT_SET, count, offset);
dset.write(ps{0}->rhs[0], H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(ps{0}->rhs[0], H5::PredType::NATIVE_DOUBLE, memspace, writespace);
dset.close();
//VELOCITY end //VELOCITY end
//ACCELERATION begin //ACCELERATION begin
temp_string = (std::string("/particles/") + temp_string = (std::string("/particles/") +
std::string(ps{0}->name) + std::string(ps{0}->name) +
std::string("/acceleration")); std::string("/acceleration"));
dset = data_file.openDataSet(temp_string); dset = data_file->openDataSet(temp_string);
dset.write(acceleration, H5::PredType::NATIVE_DOUBLE, memspace, writespace); dset.write(acceleration, H5::PredType::NATIVE_DOUBLE, memspace, writespace);
dset.close();
//ACCELERATION end //ACCELERATION end
}} }}
fftw_free(acceleration); fftw_free(acceleration);
...@@ -308,13 +314,13 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -308,13 +314,13 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
'ps{1}->dt = dt;\n' + 'ps{1}->dt = dt;\n' +
'ps{1}->iteration = iteration;\n' + 'ps{1}->iteration = iteration;\n' +
update_field + update_field +
'ps{1}->read(&data_file);\n').format(self.C_dtype, self.particle_species) 'ps{1}->read(data_file);\n').format(self.C_dtype, self.particle_species)
self.particle_loop += ((update_field + self.particle_loop += ((update_field +
'ps{0}->step();\n' + 'ps{0}->step();\n' +
'if (ps{0}->iteration % niter_part == 0)\n' + 'if (ps{0}->iteration % niter_part == 0)\n' +
'ps{0}->write(&data_file, false);\n').format(self.particle_species) + 'ps{0}->write(data_file, false);\n').format(self.particle_species) +
output_vel_acc) output_vel_acc)
self.particle_end += ('ps{0}->write(&data_file);\n' + self.particle_end += ('ps{0}->write(data_file);\n' +
'delete ps{0};\n').format(self.particle_species) 'delete ps{0};\n').format(self.particle_species)
self.particle_species += 1 self.particle_species += 1
return None return None
... ...
......
bfps/base.py
+ 1
− 1
View file @ 268acdb9
...@@ -63,7 +63,7 @@ class base(object): ...@@ -63,7 +63,7 @@ class base(object):
+ 'H5::DataSpace strdspace(H5S_SCALAR);\n' + 'H5::DataSpace strdspace(H5S_SCALAR);\n'
+ 'std::string tempstr;') + 'std::string tempstr;')
for i in range(len(key)): for i in range(len(key)):
src_txt += 'dset = data_file.openDataSet("parameters/{0}");\n'.format(key[i]) src_txt += 'dset = data_file->openDataSet("parameters/{0}");\n'.format(key[i])
if type(self.parameters[key[i]]) == int: if type(self.parameters[key[i]]) == int:
src_txt += 'dset.read(&{0}, H5::PredType::NATIVE_INT);\n'.format(key[i]) src_txt += 'dset.read(&{0}, H5::PredType::NATIVE_INT);\n'.format(key[i])
elif type(self.parameters[key[i]]) == str: elif type(self.parameters[key[i]]) == str:
... ...
......
bfps/code.py
+ 7
− 8
View file @ 268acdb9
...@@ -52,7 +52,7 @@ class code(base): ...@@ -52,7 +52,7 @@ class code(base):
self.variables = 'int myrank, nprocs;\n' self.variables = 'int myrank, nprocs;\n'
self.variables += 'int iteration;\n' self.variables += 'int iteration;\n'
self.variables += 'char simname[256];\n' self.variables += 'char simname[256];\n'
self.variables += ('H5::H5File data_file;\n' + self.variables += ('H5::H5File *data_file;\n' +
'H5::DataSet H5dset;\n') 'H5::DataSet H5dset;\n')
self.definitions = '' self.definitions = ''
self.main_start = """ self.main_start = """
...@@ -71,17 +71,17 @@ class code(base): ...@@ -71,17 +71,17 @@ class code(base):
else else
{ {
strcpy(simname, argv[1]); strcpy(simname, argv[1]);
if (myrank == 0) if (myrank != 0)
data_file.openFile(std::string(simname) + std::string(".h5"), H5F_ACC_RDWR); data_file = new H5::H5File(std::string(simname) + std::string(".h5"), H5F_ACC_RDONLY);
else else
data_file.openFile(std::string(simname) + std::string(".h5"), H5F_ACC_RDONLY); data_file = new H5::H5File(std::string(simname) + std::string(".h5"), H5F_ACC_RDWR);
H5dset = data_file.openDataSet("iteration"); H5dset = data_file->openDataSet("iteration");
H5dset.read(&iteration, H5::PredType::NATIVE_INT); H5dset.read(&iteration, H5::PredType::NATIVE_INT);
DEBUG_MSG("simname is %s and iteration is %d\\n", simname, iteration); DEBUG_MSG("simname is %s and iteration is %d\\n", simname, iteration);
} }
read_parameters(); read_parameters();
if (myrank != 0) if (myrank != 0)
data_file.close(); delete data_file;
//endcpp //endcpp
""" """
for ostream in ['cout', 'cerr']: for ostream in ['cout', 'cerr']:
...@@ -91,9 +91,8 @@ class code(base): ...@@ -91,9 +91,8 @@ class code(base):
// clean up // clean up
if (myrank == 0) if (myrank == 0)
{ {
H5dset = data_file.openDataSet("iteration"); H5dset = data_file->openDataSet("iteration");
H5dset.write(&iteration, H5::PredType::NATIVE_INT); H5dset.write(&iteration, H5::PredType::NATIVE_INT);
data_file.close();
} }
fftwf_mpi_cleanup(); fftwf_mpi_cleanup();
fftw_mpi_cleanup(); fftw_mpi_cleanup();
... ...
......
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