From c4143bfe021ec3f9823f6f500bb4808f2fc172e0 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Thu, 20 Sep 2018 15:31:30 +0200
Subject: [PATCH] introduce parameter for fftw_plan_rigor
---
bfps/DNS.py | 1 +
bfps/PP.py | 1 +
bfps/TEST.py | 1 +
bfps/cpp/fftw_interface.hpp | 2 ++
bfps/cpp/fftw_tools.cpp | 7 +++++
bfps/cpp/fftw_tools.hpp | 2 ++
bfps/cpp/full_code/NSVE.cpp | 6 ++--
bfps/cpp/full_code/NSVE.hpp | 1 +
bfps/cpp/full_code/NSVE_field_stats.cpp | 4 ++-
bfps/cpp/full_code/NSVE_field_stats.hpp | 2 ++
bfps/cpp/full_code/field_output_test.cpp | 2 +-
bfps/cpp/full_code/field_test.cpp | 4 +--
bfps/cpp/full_code/filter_test.cpp | 2 +-
bfps/cpp/full_code/joint_acc_vel_stats.cpp | 2 +-
bfps/cpp/full_code/native_binary_to_hdf5.cpp | 2 +-
bfps/cpp/full_code/symmetrize_test.cpp | 6 ++--
bfps/cpp/full_code/symmetrize_test.hpp | 1 +
bfps/cpp/full_code/test_interpolation.cpp | 6 ++--
bfps/cpp/hdf5_tools.cpp | 31 +++++++++++++-------
setup.py | 2 +-
20 files changed, 59 insertions(+), 26 deletions(-)
diff --git a/bfps/DNS.py b/bfps/DNS.py
index e6ace758..b22a309a 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -120,6 +120,7 @@ class DNS(_code):
return None
def generate_default_parameters(self):
# these parameters are relevant for all DNS classes
+ self.parameters['fftw_planner_type'] = 'FFTW_ESTIMATE'
self.parameters['dealias_type'] = int(1)
self.parameters['dkx'] = float(1.0)
self.parameters['dky'] = float(1.0)
diff --git a/bfps/PP.py b/bfps/PP.py
index 27a35928..867864e0 100644
--- a/bfps/PP.py
+++ b/bfps/PP.py
@@ -118,6 +118,7 @@ class PP(_code):
return None
def generate_default_parameters(self):
# these parameters are relevant for all PP classes
+ self.parameters['fftw_planner_type'] = 'FFTW_ESTIMATE'
self.parameters['dealias_type'] = int(1)
self.parameters['dkx'] = float(1.0)
self.parameters['dky'] = float(1.0)
diff --git a/bfps/TEST.py b/bfps/TEST.py
index cd4d3e4a..2a8b37ba 100644
--- a/bfps/TEST.py
+++ b/bfps/TEST.py
@@ -119,6 +119,7 @@ class TEST(_code):
return None
def generate_default_parameters(self):
# these parameters are relevant for all TEST classes
+ self.parameters['fftw_planner_type'] = 'FFTW_ESTIMATE'
self.parameters['dealias_type'] = int(1)
self.parameters['dkx'] = float(1.0)
self.parameters['dky'] = float(1.0)
diff --git a/bfps/cpp/fftw_interface.hpp b/bfps/cpp/fftw_interface.hpp
index 7f5e0144..0a840dd5 100644
--- a/bfps/cpp/fftw_interface.hpp
+++ b/bfps/cpp/fftw_interface.hpp
@@ -26,6 +26,8 @@
#define FFTW_INTERFACE_HPP
#include <fftw3-mpi.h>
+#include <map>
+#include <string>
#ifdef USE_FFTWESTIMATE
#define DEFAULT_FFTW_FLAG FFTW_ESTIMATE
diff --git a/bfps/cpp/fftw_tools.cpp b/bfps/cpp/fftw_tools.cpp
index 61e03d29..9f6e9bfd 100644
--- a/bfps/cpp/fftw_tools.cpp
+++ b/bfps/cpp/fftw_tools.cpp
@@ -31,6 +31,13 @@
#define NDEBUG
+std::map<std::string, unsigned> fftw_planner_string_to_flag = {
+ {"FFTW_ESTIMATE", FFTW_ESTIMATE},
+ {"FFTW_MEASURE", FFTW_MEASURE},
+ {"FFTW_PATIENT", FFTW_PATIENT},
+ {"parameter does not exist", DEFAULT_FFTW_FLAG},
+};
+
template <class rnumber>
int clip_zero_padding(
field_descriptor<rnumber> *f,
diff --git a/bfps/cpp/fftw_tools.hpp b/bfps/cpp/fftw_tools.hpp
index d0f3dbf3..f4480714 100644
--- a/bfps/cpp/fftw_tools.hpp
+++ b/bfps/cpp/fftw_tools.hpp
@@ -34,6 +34,8 @@
extern int myrank, nprocs;
+extern std::map<std::string, unsigned> fftw_planner_string_to_flag;
+
/* given two arrays of the same dimension, we do a simple resize in
* Fourier space: either chop off high modes, or pad with zeros.
* the arrays are assumed to use 3D mpi fftw layout.
diff --git a/bfps/cpp/full_code/NSVE.cpp b/bfps/cpp/full_code/NSVE.cpp
index d9cb72a2..74593b37 100644
--- a/bfps/cpp/full_code/NSVE.cpp
+++ b/bfps/cpp/full_code/NSVE.cpp
@@ -2,6 +2,7 @@
#include <cmath>
#include "NSVE.hpp"
#include "scope_timer.hpp"
+#include "fftw_tools.hpp"
template <typename rnumber>
@@ -37,11 +38,11 @@ int NSVE<rnumber>::initialize(void)
simname.c_str(),
nx, ny, nz,
dkx, dky, dkz,
- DEFAULT_FFTW_FLAG);
+ fftw_planner_string_to_flag[this->fftw_plan_type]);
this->tmp_vec_field = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ fftw_planner_string_to_flag[this->fftw_plan_type]);
this->fs->checkpoints_per_file = checkpoints_per_file;
@@ -161,6 +162,7 @@ int NSVE<rnumber>::read_parameters(void)
this->max_vorticity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_vorticity_estimate");
std::string tmp = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
snprintf(this->forcing_type, 511, "%s", tmp.c_str());
+ this->fftw_plan_type = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_type");
H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/NSVE.hpp b/bfps/cpp/full_code/NSVE.hpp
index 062627fd..c3ad7a0a 100644
--- a/bfps/cpp/full_code/NSVE.hpp
+++ b/bfps/cpp/full_code/NSVE.hpp
@@ -53,6 +53,7 @@ class NSVE: public direct_numerical_simulation
double max_velocity_estimate;
double max_vorticity_estimate;
double nu;
+ std::string fftw_plan_type;
/* other stuff */
vorticity_equation<rnumber, FFTW> *fs;
diff --git a/bfps/cpp/full_code/NSVE_field_stats.cpp b/bfps/cpp/full_code/NSVE_field_stats.cpp
index 15980a20..142c51e7 100644
--- a/bfps/cpp/full_code/NSVE_field_stats.cpp
+++ b/bfps/cpp/full_code/NSVE_field_stats.cpp
@@ -1,6 +1,7 @@
#include <string>
#include <cmath>
#include "NSVE_field_stats.hpp"
+#include "fftw_tools.hpp"
#include "scope_timer.hpp"
@@ -12,7 +13,7 @@ int NSVE_field_stats<rnumber>::initialize(void)
this->vorticity = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ fftw_planner_string_to_flag[this->fftw_plan_type]);
this->vorticity->real_space_representation = false;
hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
@@ -43,6 +44,7 @@ int NSVE_field_stats<rnumber>::initialize(void)
this->vorticity->clayout->starts,
this->vorticity->clayout->comm);
}
+ this->fftw_plan_type = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_type");
H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/NSVE_field_stats.hpp b/bfps/cpp/full_code/NSVE_field_stats.hpp
index d544c0c7..ae519fc7 100644
--- a/bfps/cpp/full_code/NSVE_field_stats.hpp
+++ b/bfps/cpp/full_code/NSVE_field_stats.hpp
@@ -42,6 +42,8 @@ class NSVE_field_stats: public postprocess
private:
field_binary_IO<rnumber, COMPLEX, THREE> *bin_IO;
public:
+ std::string fftw_plan_type;
+
field<rnumber, FFTW, THREE> *vorticity;
NSVE_field_stats(
diff --git a/bfps/cpp/full_code/field_output_test.cpp b/bfps/cpp/full_code/field_output_test.cpp
index 30df4e75..72406099 100644
--- a/bfps/cpp/full_code/field_output_test.cpp
+++ b/bfps/cpp/full_code/field_output_test.cpp
@@ -36,7 +36,7 @@ int field_output_test<rnumber>::do_work(void)
field<rnumber, FFTW, ONE> *scal_field = new field<rnumber, FFTW, ONE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
std::default_random_engine rgen;
std::normal_distribution<rnumber> rdist;
rgen.seed(1);
diff --git a/bfps/cpp/full_code/field_test.cpp b/bfps/cpp/full_code/field_test.cpp
index 1627bc40..a9d531bc 100644
--- a/bfps/cpp/full_code/field_test.cpp
+++ b/bfps/cpp/full_code/field_test.cpp
@@ -44,11 +44,11 @@ int field_test<rnumber>::do_work(void)
field<rnumber, FFTW, ONE> *scal_field = new field<rnumber, FFTW, ONE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
field<rnumber, FFTW, ONE> *scal_field_alt = new field<rnumber, FFTW, ONE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
std::default_random_engine rgen;
std::normal_distribution<rnumber> rdist;
rgen.seed(2);
diff --git a/bfps/cpp/full_code/filter_test.cpp b/bfps/cpp/full_code/filter_test.cpp
index 4db13843..6dbd05a9 100644
--- a/bfps/cpp/full_code/filter_test.cpp
+++ b/bfps/cpp/full_code/filter_test.cpp
@@ -12,7 +12,7 @@ int filter_test<rnumber>::initialize(void)
this->scal_field = new field<rnumber, FFTW, ONE>(
nx, ny, nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
this->kk = new kspace<FFTW, SMOOTH>(
this->scal_field->clayout, this->dkx, this->dky, this->dkz);
diff --git a/bfps/cpp/full_code/joint_acc_vel_stats.cpp b/bfps/cpp/full_code/joint_acc_vel_stats.cpp
index 1c28527e..fff2e2f5 100644
--- a/bfps/cpp/full_code/joint_acc_vel_stats.cpp
+++ b/bfps/cpp/full_code/joint_acc_vel_stats.cpp
@@ -110,7 +110,7 @@ int joint_acc_vel_stats<rnumber>::work_on_current_iteration(void)
vel = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ this->vorticity->fftw_plan_rigor);
invert_curl(kk, this->ve->cvorticity, vel);
vel->ift();
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.cpp b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
index fb5a39c2..fe8e1c41 100644
--- a/bfps/cpp/full_code/native_binary_to_hdf5.cpp
+++ b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
@@ -12,7 +12,7 @@ int native_binary_to_hdf5<rnumber>::initialize(void)
this->vec_field = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
this->vec_field->real_space_representation = false;
this->bin_IO = new field_binary_IO<rnumber, COMPLEX, THREE>(
this->vec_field->clayout->sizes,
diff --git a/bfps/cpp/full_code/symmetrize_test.cpp b/bfps/cpp/full_code/symmetrize_test.cpp
index 821161da..45225fcb 100644
--- a/bfps/cpp/full_code/symmetrize_test.cpp
+++ b/bfps/cpp/full_code/symmetrize_test.cpp
@@ -2,6 +2,7 @@
#include <cmath>
#include <random>
#include "symmetrize_test.hpp"
+#include "fftw_tools.hpp"
#include "scope_timer.hpp"
@@ -31,6 +32,7 @@ int symmetrize_test<rnumber>::read_parameters()
H5P_DEFAULT);
this->random_seed = hdf5_tools::read_value<int>(
parameter_file, "/parameters/random_seed");
+ this->fftw_plan_type = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_type");
H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
@@ -44,13 +46,13 @@ int symmetrize_test<rnumber>::do_work(void)
field<rnumber, FFTW, THREE> *test_field0 = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ fftw_planner_string_to_flag[this->fftw_plan_type]);
DEBUG_MSG("finished allocating field0\n");
DEBUG_MSG("about to allocate field1\n");
field<rnumber, FFTW, THREE> *test_field1 = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ fftw_planner_string_to_flag[this->fftw_plan_type]);
DEBUG_MSG("finished allocating field1\n");
std::default_random_engine rgen;
std::normal_distribution<rnumber> rdist;
diff --git a/bfps/cpp/full_code/symmetrize_test.hpp b/bfps/cpp/full_code/symmetrize_test.hpp
index d3fbbaeb..f674d365 100644
--- a/bfps/cpp/full_code/symmetrize_test.hpp
+++ b/bfps/cpp/full_code/symmetrize_test.hpp
@@ -42,6 +42,7 @@ template <typename rnumber>
class symmetrize_test: public test
{
public:
+ std::string fftw_plan_type;
int random_seed;
symmetrize_test(
diff --git a/bfps/cpp/full_code/test_interpolation.cpp b/bfps/cpp/full_code/test_interpolation.cpp
index 5ef11de4..2acd3c27 100644
--- a/bfps/cpp/full_code/test_interpolation.cpp
+++ b/bfps/cpp/full_code/test_interpolation.cpp
@@ -30,18 +30,18 @@ int test_interpolation<rnumber>::initialize(void)
this->vorticity = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
this->vorticity->real_space_representation = false;
this->velocity = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
this->nabla_u = new field<rnumber, FFTW, THREExTHREE>(
this->nx, this->ny, this->nz,
this->comm,
- DEFAULT_FFTW_FLAG);
+ FFTW_ESTIMATE);
this->kk = new kspace<FFTW, SMOOTH>(
this->vorticity->clayout, this->dkx, this->dky, this->dkz);
diff --git a/bfps/cpp/hdf5_tools.cpp b/bfps/cpp/hdf5_tools.cpp
index c2ef6aae..25acaf21 100644
--- a/bfps/cpp/hdf5_tools.cpp
+++ b/bfps/cpp/hdf5_tools.cpp
@@ -208,17 +208,26 @@ std::string hdf5_tools::read_string(
const hid_t group,
const std::string dset_name)
{
- hid_t dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
- hid_t space = H5Dget_space(dset);
- hid_t memtype = H5Dget_type(dset);
- char *string_data = (char*)malloc(256);
- H5Dread(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &string_data);
- std::string std_string_data = std::string(string_data);
- free(string_data);
- H5Sclose(space);
- H5Tclose(memtype);
- H5Dclose(dset);
- return std_string_data;
+ if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
+ {
+ hid_t dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
+ hid_t space = H5Dget_space(dset);
+ hid_t memtype = H5Dget_type(dset);
+ char *string_data = (char*)malloc(256);
+ H5Dread(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &string_data);
+ std::string std_string_data = std::string(string_data);
+ free(string_data);
+ H5Sclose(space);
+ H5Tclose(memtype);
+ H5Dclose(dset);
+ return std_string_data;
+ }
+ else
+ {
+ DEBUG_MSG("attempted to read dataset %s which does not exist.\n",
+ dset_name.c_str());
+ return std::string("parameter does not exist");
+ }
}
template
diff --git a/setup.py b/setup.py
index 110f18d5..afb25f70 100644
--- a/setup.py
+++ b/setup.py
@@ -273,7 +273,7 @@ class CompileLibCommand(distutils.cmd.Command):
def get_file_dependency_list(src_file):
p = subprocess.Popen(
- ['g++', '-Ibfps/cpp', '-MM', 'bfps/cpp/' + src_file + '.cpp'],
+ ['g++', '-std=c++11', '-Ibfps/cpp', '-MM', 'bfps/cpp/' + src_file + '.cpp'],
stdout = subprocess.PIPE)
out, err = p.communicate()
p.terminate()
--
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