From 7f6fc147bb2c1a0e2bb5b4d4574c0174caf3ad42 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 17:13:19 +0200
Subject: [PATCH 1/6] mark intel-only pragma as such
---
cpp/kspace.cpp | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/cpp/kspace.cpp b/cpp/kspace.cpp
index b1f40ae4..3628893d 100644
--- a/cpp/kspace.cpp
+++ b/cpp/kspace.cpp
@@ -172,7 +172,9 @@ kspace<be, dt>::kspace(
// I chose the last option because there's no reason to optimize this
// loop. Furthermore, it seems like the solution that's most readable,
// and with the least amount of side effects.
- # pragma novector
+ #if defined(__INTEL_COMPILER)
+ #pragma novector
+ #endif
for (int n=0; n<this->nshells; n++){
if (this->nshell[n] > 0)
this->kshell[n] /= this->nshell[n];
--
GitLab
From 1c46242f7742d3378f182aee3f3363fad6c7e815 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 18:27:16 +0200
Subject: [PATCH 2/6] gets rid of GCC warnings
---
cpp/field.cpp | 8 ++++++++
cpp/full_code/NSVE.cpp | 5 ++---
cpp/full_code/NSVE.hpp | 7 ++++---
cpp/full_code/postprocess.cpp | 5 ++---
cpp/full_code/postprocess.hpp | 9 +++++----
cpp/vorticity_equation.cpp | 28 ++++++++++++++--------------
cpp/vorticity_equation.hpp | 6 ++++--
7 files changed, 39 insertions(+), 29 deletions(-)
diff --git a/cpp/field.cpp b/cpp/field.cpp
index 16091a6b..2f7a7a90 100644
--- a/cpp/field.cpp
+++ b/cpp/field.cpp
@@ -1017,6 +1017,13 @@ void field<rnumber, be, fc>::compute_rspace_stats(
// dset_name.c_str());
assert(ndims == int(ndim(fc))-1);
assert(dims[1] == nmoments);
+ // gcc complains about the following code, when ndim(fc)-1 is too small
+ // since I already assert what the value of ndims is, I know the code
+ // is safe, so I just tell GCC to ignore the apparent problem with this
+ // pragma. See link below for more info:
+ // https://gcc.gnu.org/onlinedocs/gcc/Diagnostic-Pragmas.html
+#pragma GCC diagnostic ignored "-Warray-bounds"
+#pragma GCC diagnostic push
switch(ndims)
{
case 2:
@@ -1029,6 +1036,7 @@ void field<rnumber, be, fc>::compute_rspace_stats(
nvals = dims[2]*dims[3];
break;
}
+#pragma GCC diagnostic pop
H5Sclose(wspace);
H5Dclose(dset);
dset = H5Dopen(group, ("histograms/" + dset_name).c_str(), H5P_DEFAULT);
diff --git a/cpp/full_code/NSVE.cpp b/cpp/full_code/NSVE.cpp
index 5c0d360c..20591057 100644
--- a/cpp/full_code/NSVE.cpp
+++ b/cpp/full_code/NSVE.cpp
@@ -84,7 +84,7 @@ int NSVE<rnumber>::initialize(void)
this->fs->fk0 = fk0;
this->fs->fk1 = fk1;
this->fs->dt = dt;
- strncpy(this->fs->forcing_type, forcing_type, 128);
+ this->fs->forcing_type = forcing_type;
this->fs->iteration = this->iteration;
this->fs->checkpoint = this->checkpoint;
@@ -193,8 +193,7 @@ int NSVE<rnumber>::read_parameters(void)
this->histogram_bins = hdf5_tools::read_value<int>(parameter_file, "parameters/histogram_bins");
this->max_velocity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_velocity_estimate");
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->forcing_type = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
this->fftw_plan_rigor = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_rigor");
H5Fclose(parameter_file);
// the following ensures the file is free after exiting this method
diff --git a/cpp/full_code/NSVE.hpp b/cpp/full_code/NSVE.hpp
index 15a388dc..60809a88 100644
--- a/cpp/full_code/NSVE.hpp
+++ b/cpp/full_code/NSVE.hpp
@@ -28,12 +28,13 @@
#define NSVE_HPP
-
-#include <cstdlib>
#include "base.hpp"
#include "vorticity_equation.hpp"
#include "full_code/direct_numerical_simulation.hpp"
+#include <cstdlib>
+#include <string>
+
/** \brief Navier-Stokes solver.
*
* Solves the vorticity equation for a Navier-Stokes fluid.
@@ -58,7 +59,7 @@ class NSVE: public direct_numerical_simulation
double energy;
double injection_rate;
int fmode;
- char forcing_type[512];
+ std::string forcing_type;
int histogram_bins;
double max_velocity_estimate;
double max_vorticity_estimate;
diff --git a/cpp/full_code/postprocess.cpp b/cpp/full_code/postprocess.cpp
index 2fe20c34..2c136a7b 100644
--- a/cpp/full_code/postprocess.cpp
+++ b/cpp/full_code/postprocess.cpp
@@ -73,8 +73,7 @@ int postprocess::read_parameters()
this->variation_time_scale = hdf5_tools::read_value<double>(parameter_file, "parameters/variation_time_scale");
this->energy = hdf5_tools::read_value<double>(parameter_file, "parameters/energy");
this->injection_rate = hdf5_tools::read_value<double>(parameter_file, "parameters/injection_rate");
- std::string tmp = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
- snprintf(this->forcing_type, 511, "%s", tmp.c_str());
+ this->forcing_type = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
H5Fclose(parameter_file);
MPI_Barrier(this->comm);
return EXIT_SUCCESS;
@@ -96,7 +95,7 @@ int postprocess::copy_parameters_into(
dst->friction_coefficient = this->friction_coefficient;
dst->variation_strength = this->variation_strength;
dst->variation_time_scale = this->variation_time_scale;
- strncpy(dst->forcing_type, this->forcing_type, 128);
+ dst->forcing_type = this->forcing_type;
return EXIT_SUCCESS;
}
diff --git a/cpp/full_code/postprocess.hpp b/cpp/full_code/postprocess.hpp
index 4a8fab39..52826cf7 100644
--- a/cpp/full_code/postprocess.hpp
+++ b/cpp/full_code/postprocess.hpp
@@ -27,13 +27,14 @@
#ifndef POSTPROCESS_HPP
#define POSTPROCESS_HPP
+#include "full_code/code_base.hpp"
+#include "vorticity_equation.hpp"
+#include "base.hpp"
+
#include <cstdlib>
#include <sys/types.h>
#include <sys/stat.h>
#include <vector>
-#include "base.hpp"
-#include "vorticity_equation.hpp"
-#include "full_code/code_base.hpp"
class postprocess: public code_base
{
@@ -56,7 +57,7 @@ class postprocess: public code_base
double variation_strength;
double variation_time_scale;
int fmode;
- char forcing_type[512];
+ std::string forcing_type;
double nu;
postprocess(
diff --git a/cpp/vorticity_equation.cpp b/cpp/vorticity_equation.cpp
index c32c0331..7ce50a76 100644
--- a/cpp/vorticity_equation.cpp
+++ b/cpp/vorticity_equation.cpp
@@ -289,12 +289,12 @@ void vorticity_equation<rnumber, be>::add_forcing(
double t)
{
TIMEZONE("vorticity_equation::add_forcing");
- if (strcmp(this->forcing_type, "Kolmogorov") == 0)
+ if (this->forcing_type == std::string("Kolmogorov"))
{
this->add_Kolmogorov_forcing(dst, this->fmode, this->famplitude);
return;
}
- if (strcmp(this->forcing_type, "2Kolmogorov") == 0)
+ if (this->forcing_type == std::string("2Kolmogorov"))
{
// 2 Kolmogorov forces
// first one wavenumber fk0, amplitude 1 - A
@@ -307,7 +307,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->add_Kolmogorov_forcing(dst, fmode, amplitude);
return;
}
- if (strcmp(this->forcing_type, "Kolmogorov_and_drag") == 0)
+ if (this->forcing_type == std::string("Kolmogorov_and_drag"))
{
this->add_Kolmogorov_forcing(dst, this->fmode, this->famplitude);
this->add_field_band(
@@ -316,7 +316,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "Kolmogorov_and_compensated_drag") == 0)
+ if (this->forcing_type == std::string("Kolmogorov_and_compensated_drag"))
{
double amplitude = this->famplitude * (
1 + this->friction_coefficient / sqrt(this->fmode * this->famplitude));
@@ -327,7 +327,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "linear") == 0)
+ if (this->forcing_type == std::string("linear"))
{
this->add_field_band(
dst, vort_field,
@@ -335,9 +335,9 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->famplitude);
return;
}
- if ((strcmp(this->forcing_type, "fixed_energy_injection_rate") == 0) ||
- (strcmp(this->forcing_type, "fixed_energy_injection_rate_and_drag") == 0) ||
- (strcmp(this->forcing_type, "sinusoidal_energy_injection_rate") == 0))
+ if (this->forcing_type == std::string("fixed_energy_injection_rate") ||
+ this->forcing_type == std::string("fixed_energy_injection_rate_and_drag") ||
+ this->forcing_type == std::string("sinusoidal_energy_injection_rate"))
{
// first, compute energy in shell
shared_array<double> local_energy_in_shell(1);
@@ -377,7 +377,7 @@ void vorticity_equation<rnumber, be>::add_forcing(
if (energy_in_shell < 10*std::numeric_limits<rnumber>::epsilon())
energy_in_shell = 1;
double temp_famplitude = 0;
- if (strcmp(this->forcing_type, "sinusoidal_energy_injection_rate") == 0){
+ if (this->forcing_type == std::string("sinusoidal_energy_injection_rate")){
temp_famplitude = (this->injection_rate + this->variation_strength
*sin(t/this->variation_time_scale))
/ energy_in_shell;
@@ -389,18 +389,18 @@ void vorticity_equation<rnumber, be>::add_forcing(
this->fk0, this->fk1,
temp_famplitude);
// and add drag if desired
- if (strcmp(this->forcing_type, "fixed_energy_injection_rate_and_drag") == 0)
+ if (this->forcing_type == std::string("fixed_energy_injection_rate_and_drag"))
this->add_field_band(
dst, vort_field,
this->fmode, this->fmode + (this->fk1 - this->fk0),
-this->friction_coefficient);
return;
}
- if (strcmp(this->forcing_type, "fixed_energy") == 0)
+ if (this->forcing_type == std::string("fixed_energy"))
return;
else
{
- DEBUG_MSG("unknown forcing type printed on next line\n%s", this->forcing_type);
+ DEBUG_MSG("unknown forcing type printed on next line\n%s", this->forcing_type.c_str());
throw std::invalid_argument("unknown forcing type");
}
}
@@ -412,7 +412,7 @@ void vorticity_equation<rnumber, be>::impose_forcing(
field<rnumber, be, THREE> *oold)
{
TIMEZONE("vorticity_equation::impose_forcing");
- if (strcmp(this->forcing_type, "fixed_energy") == 0)
+ if (this->forcing_type == std::string("fixed_energy"))
{
// first, compute energy in shell
shared_array<double> local_energy_in_shell(1);
@@ -802,7 +802,7 @@ void vorticity_equation<rnumber, be>::compute_Eulerian_acceleration(
for (int i=0; i<2; i++)
acceleration->get_cdata()[tindex+cc][i] = \
- this->nu*k2*this->cvelocity->get_cdata()[tindex+cc][i];
- if (strcmp(this->forcing_type, "linear") == 0)
+ if (this->forcing_type == std::string("linear"))
{
double knorm = sqrt(k2);
if ((this->fk0 <= knorm) &&
diff --git a/cpp/vorticity_equation.hpp b/cpp/vorticity_equation.hpp
index 90803b4b..e48196f3 100644
--- a/cpp/vorticity_equation.hpp
+++ b/cpp/vorticity_equation.hpp
@@ -27,12 +27,14 @@
#ifndef VORTICITY_EQUATION
#define VORTICITY_EQUATION
+#include "field.hpp"
+
#include <sys/stat.h>
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
+#include <string>
-#include "field.hpp"
extern int myrank, nprocs;
@@ -79,7 +81,7 @@ class vorticity_equation
double friction_coefficient; // for Kolmogorov_and_drag
double variation_strength; // for time-varying forcing
double variation_time_scale; // for time-varying forcing
- char forcing_type[128];
+ std::string forcing_type;
/* constructor, destructor */
vorticity_equation(
--
GitLab
From 3edd6a0dd5835c28830b58202441bd3e29e17567 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 20:50:07 +0200
Subject: [PATCH 3/6] gets rid of intel warnings
---
cpp/hdf5_tools.cpp | 9 +++------
cpp/particles/abstract_particle_rhs.hpp | 2 +-
cpp/particles/rhs/deformation_tensor_rhs.hpp | 2 +-
cpp/particles/rhs/tracer_rhs.hpp | 2 +-
cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp | 2 +-
5 files changed, 7 insertions(+), 10 deletions(-)
diff --git a/cpp/hdf5_tools.cpp b/cpp/hdf5_tools.cpp
index 9a92c459..2db76f3a 100644
--- a/cpp/hdf5_tools.cpp
+++ b/cpp/hdf5_tools.cpp
@@ -1,7 +1,9 @@
#include "hdf5_tools.hpp"
#include "scope_timer.hpp"
+
#include <cfloat>
#include <climits>
+#include <limits>
template <> hid_t hdf5_tools::hdf5_type_id<char>()
{
@@ -258,12 +260,7 @@ number hdf5_tools::read_value(
{
DEBUG_MSG("attempted to read dataset %s which does not exist.\n",
dset_name.c_str());
- if (typeid(number) == typeid(int))
- result = INT_MAX;
- else if (typeid(number) == typeid(long long int))
- result = -1;
- else if (typeid(number) == typeid(double))
- result = number(DBL_MAX);
+ result = std::numeric_limits<number>::max();
}
H5Tclose(mem_dtype);
return result;
diff --git a/cpp/particles/abstract_particle_rhs.hpp b/cpp/particles/abstract_particle_rhs.hpp
index 947e1524..a0c68816 100644
--- a/cpp/particles/abstract_particle_rhs.hpp
+++ b/cpp/particles/abstract_particle_rhs.hpp
@@ -49,7 +49,7 @@ class abstract_particle_rhs
/** Probe the dimension of the ODE
*/
- virtual const int getStateSize() const = 0;
+ virtual int getStateSize() const = 0;
/** Compute right-hand-side of the ODE
diff --git a/cpp/particles/rhs/deformation_tensor_rhs.hpp b/cpp/particles/rhs/deformation_tensor_rhs.hpp
index 0835f986..43b75cb9 100644
--- a/cpp/particles/rhs/deformation_tensor_rhs.hpp
+++ b/cpp/particles/rhs/deformation_tensor_rhs.hpp
@@ -48,7 +48,7 @@ class deformation_tensor_rhs: public abstract_particle_rhs
deformation_tensor_rhs(){}
~deformation_tensor_rhs() noexcept(false){}
- const int getStateSize() const
+ int getStateSize() const
{
// 3 numbers for position
// 9 numbers for components of deformation tensor
diff --git a/cpp/particles/rhs/tracer_rhs.hpp b/cpp/particles/rhs/tracer_rhs.hpp
index 680b46fd..eca90024 100644
--- a/cpp/particles/rhs/tracer_rhs.hpp
+++ b/cpp/particles/rhs/tracer_rhs.hpp
@@ -43,7 +43,7 @@ class tracer_rhs: public abstract_particle_rhs
tracer_rhs(){}
~tracer_rhs() noexcept(false){}
- const int getStateSize() const
+ int getStateSize() const
{
return 3;
}
diff --git a/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp b/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
index 5aa15213..4fdc0686 100644
--- a/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
+++ b/cpp/particles/rhs/tracer_with_collision_counter_rhs.hpp
@@ -44,7 +44,7 @@ class tracer_with_collision_counter_rhs: public tracer_rhs<rnumber, be, tt>
tracer_with_collision_counter_rhs(){}
~tracer_with_collision_counter_rhs() noexcept(false){}
- virtual const int getStateSize() const
+ virtual int getStateSize() const
{
return 3;
}
--
GitLab
From 1ae9d5baba9c637a401c7742bbf69c61a701c618 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 20:50:42 +0200
Subject: [PATCH 4/6] removes unused headers
---
cpp/hdf5_tools.cpp | 2 --
1 file changed, 2 deletions(-)
diff --git a/cpp/hdf5_tools.cpp b/cpp/hdf5_tools.cpp
index 2db76f3a..aadd0c74 100644
--- a/cpp/hdf5_tools.cpp
+++ b/cpp/hdf5_tools.cpp
@@ -1,8 +1,6 @@
#include "hdf5_tools.hpp"
#include "scope_timer.hpp"
-#include <cfloat>
-#include <climits>
#include <limits>
template <> hid_t hdf5_tools::hdf5_type_id<char>()
--
GitLab
From 302b8e472cbf59f1f38f1a5663151ec1c74c0daf Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 20:57:02 +0200
Subject: [PATCH 5/6] use hdf5_tools::hdf5_type_id to simplify code
---
cpp/hdf5_tools.cpp | 27 +++++----------------------
1 file changed, 5 insertions(+), 22 deletions(-)
diff --git a/cpp/hdf5_tools.cpp b/cpp/hdf5_tools.cpp
index aadd0c74..e75070b4 100644
--- a/cpp/hdf5_tools.cpp
+++ b/cpp/hdf5_tools.cpp
@@ -208,13 +208,7 @@ std::vector<number> hdf5_tools::read_vector(
hsize_t vector_length;
// first, read size of array
hid_t dset, dspace;
- hid_t mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return result;
+ hid_t mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
dspace = H5Dget_space(dset);
assert(H5Sget_simple_extent_ndims(dspace) == 1);
@@ -235,15 +229,7 @@ number hdf5_tools::read_value(
TIMEZONE("hdf5_tools::read_value");
number result;
hid_t dset;
- hid_t mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(long long int))
- mem_dtype = H5Tcopy(H5T_NATIVE_LLONG);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return result;
+ hid_t mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
{
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
@@ -270,13 +256,10 @@ int hdf5_tools::write_value_with_single_rank(
const std::string dset_name,
const number value)
{
+ assert(typeid(number) == typeid(int) ||
+ typeid(number) == typeid(double));
hid_t dset, mem_dtype;
- if (typeid(number) == typeid(int))
- mem_dtype = H5Tcopy(H5T_NATIVE_INT);
- else if (typeid(number) == typeid(double))
- mem_dtype = H5Tcopy(H5T_NATIVE_DOUBLE);
- else
- return EXIT_FAILURE;
+ mem_dtype = H5Tcopy(hdf5_tools::hdf5_type_id<number>());
if (H5Lexists(group, dset_name.c_str(), H5P_DEFAULT))
{
dset = H5Dopen(group, dset_name.c_str(), H5P_DEFAULT);
--
GitLab
From 1381dbea08cfb35c98a1de89e872b91dbcf68dde Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@mpcdf.mpg.de>
Date: Sat, 30 Jul 2022 21:19:08 +0200
Subject: [PATCH 6/6] fixes leftover conflict
---
TurTLE/test/collisions/stokes_rhs.hpp | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/TurTLE/test/collisions/stokes_rhs.hpp b/TurTLE/test/collisions/stokes_rhs.hpp
index 582f7089..41268149 100644
--- a/TurTLE/test/collisions/stokes_rhs.hpp
+++ b/TurTLE/test/collisions/stokes_rhs.hpp
@@ -43,7 +43,7 @@ class stokes_rhs: public abstract_particle_rhs
public:
stokes_rhs(){}
~stokes_rhs(){}
- const int getStateSize() const
+ int getStateSize() const
{
// 3 numbers for position
// // 9 numbers for components of deformation tensor // 3 numbers to store logarithmic factors
--
GitLab