scnc
/
phono3py
mirror of https://github.com/phonopy/phono3py.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

enh: major refactoring of setup.py 

Instead of manually adding compilers and flags it is
now left to the user to create the appropriate site.cfg
for configuration purposes.

This is much cleaner and provides users to fully customize the build.

This also enables pip installs, for instance I can build:

   pip3 install . -vvv

Which works.
In order for pip to fully function with the numpy versions it
is important that pip uses the oldest possible numpy version
that may be pip installed. This is what oldest-supported-numpy
is for.

The PHPYOPENMP flag is not needed. The OPENMP specification states
that any C-compiler which implements preprocessor statements should
include _OPENMP when compiling with OPENMP. Therefore we simply check
for this now. I don't know of any compilers that do not define this
flag while compiling for openmp.

When retrieving MKL from numpy there is an additional macro defined:
  SCIPY_MKL_H
so now the code checks for either this macro, or the old one (MKL_LAPACKE).

I have removed support for distutils. It is far deprecated and no installations
should use this one. So better to not rely on it.
In fact it was never used since pyproject.toml had setuptools as a requirement for
building the package. So it couldn't be used in these environments in
any case.

If this is to be adopted, then the installation documentation should be updated.
This commit is contained in:
Nick Papior 2021-12-07 10:18:55 +01:00
parent 0e6d455bd7
commit 3635eca7be
22 changed files with 148 additions and 337 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
c/_phono3py.c
View File

@ -1729,7 +1729,7 @@ static PyObject *py_get_default_colmat_solver(PyObject *self, PyObject *args) {
return NULL;
}
#ifdef MKL_LAPACKE
#if defined(MKL_LAPACKE) || defined(SCIPY_MKL_H)
return PyLong_FromLong((long)1);
#else
return PyLong_FromLong((long)4);
@ -1749,7 +1749,7 @@ static void pinv_from_eigensolution(double *data, const double *eigvals,
tmp_data = (double *)malloc(sizeof(double) * size * size);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < size * size; i++) {
@ -1770,7 +1770,7 @@ static void pinv_from_eigensolution(double *data, const double *eigvals,
}
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(ib, j, k, i_s, j_s, sum)
#endif
for (i = 0; i < size / 2; i++) {

4
c/collision_matrix.c
View File

@ -117,7 +117,7 @@ static void get_collision_matrix(
gp2tp_map = create_gp2tp_map(triplets_map, num_gp);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, l, m, n, ti, r_gp, collision, inv_sinh)
#endif
for (i = 0; i < num_ir_gp; i++) {
@ -186,7 +186,7 @@ static void get_reducible_collision_matrix(
gp2tp_map = create_gp2tp_map(triplets_map, num_gp);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, l, ti, collision, inv_sinh)
#endif
for (i = 0; i < num_gp; i++) {

2
c/dynmat.c
View File

@ -75,7 +75,7 @@ long dym_get_dynamical_matrix_at_q(double *dynamical_matrix,
long i, j, ij;
if (with_openmp) {
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (ij = 0; ij < num_patom * num_patom; ij++) {

2
c/fc3.c
View File

@ -124,7 +124,7 @@ void fc3_set_permutation_symmetry_fc3(double *fc3, const long num_atom) {
double fc3_elem[27];
long i, j, k;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, fc3_elem)
#endif
for (i = 0; i < num_atom; i++) {

6
c/imag_self_energy_with_g.c
View File

@ -99,7 +99,7 @@ void ise_get_imag_self_energy_at_bands_with_g(
g_index_shift = frequency_point_index * num_band * num_band;
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(num_g_pos, j, g_pos)
#endif
for (i = 0; i < num_triplets; i++) {
@ -167,7 +167,7 @@ void ise_get_detailed_imag_self_energy_at_bands_with_g(
/* detailed_imag_self_energy has the same shape as fc3_normal_squared. */
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < num_triplets; i++) {
@ -187,7 +187,7 @@ void ise_get_detailed_imag_self_energy_at_bands_with_g(
for (i = 0; i < num_band0; i++) {
N = 0;
U = 0;
/* #ifdef PHPYOPENMP */
/* #ifdef _OPENMP */
/* #pragma omp parallel for private(ise_tmp) reduction(+:N,U) */
/* #endif */
for (j = 0; j < num_triplets; j++) {

2
c/interaction.c
View File

@ -99,7 +99,7 @@ void itr_get_interaction(Darray *fc3_normal_squared, const char *g_zero,
openmp_per_triplets = 0;
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for schedule(guided) private( \
num_g_pos, g_pos) if (openmp_per_triplets)
#endif

6
c/isotope.c
View File

@ -73,7 +73,7 @@ void iso_get_isotope_scattering_strength(
continue;
}
sum_g = 0;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(k, l, m, f, e1_r, e1_i, a, b, dist, sum_g_k) reduction(+ \
: sum_g)
#endif
@ -151,14 +151,14 @@ void iso_get_thm_isotope_scattering_strength(
}
gamma_ij = (double *)malloc(sizeof(double) * num_grid_points * num_band0);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < num_grid_points * num_band0; i++) {
gamma_ij[i] = 0;
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, l, m, f, gp, e1_r, e1_i, a, b, dist, \
sum_g_k)
#endif

4
c/lapack_wrapper.c
View File

@ -36,7 +36,7 @@
#define min(a, b) ((a) > (b) ? (b) : (a))
#ifdef MKL_LAPACKE
#if defined(MKL_LAPACKE) || defined(SCIPY_MKL_H)
MKL_Complex16 lapack_make_complex_double(double re, double im) {
MKL_Complex16 z;
z.real = re;
@ -108,7 +108,7 @@ void phonopy_pinv_mt(double *data_out, int *info_out, const double *data_in,
const double cutoff) {
int i;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < num_thread; i++) {

2
c/lapack_wrapper.h
View File

@ -35,7 +35,7 @@
#ifndef __lapack_wrapper_H__
#define __lapack_wrapper_H__
#ifdef MKL_LAPACKE
#if defined(MKL_LAPACKE) || defined(SCIPY_MKL_H)
#include <mkl.h>
#define lapack_complex_double MKL_Complex16
#define lapack_complex_double_real(z) ((z).real)

10
c/phono3py.c
View File

@ -531,7 +531,7 @@ void ph3py_symmetrize_collision_matrix(double *collision_matrix,
adrs_shift = (i * num_column * num_column * num_temp +
j * num_column * num_column);
/* show_colmat_info(py_collision_matrix, i, j, adrs_shift); */
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for schedule(guided) private(l, val)
#endif
for (k = 0; k < num_column; k++) {
@ -567,7 +567,7 @@ void ph3py_expand_collision_matrix(double *collision_matrix,
num_column = num_grid_points * num_band;
num_bgb = num_band * num_grid_points * num_band;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for schedule(guided) private(j, ir_gp)
#endif
for (i = 0; i < num_ir_gp; i++) {
@ -584,7 +584,7 @@ void ph3py_expand_collision_matrix(double *collision_matrix,
for (j = 0; j < num_temp; j++) {
adrs_shift = (i * num_column * num_column * num_temp +
j * num_column * num_column);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(ir_gp, adrs_shift_plus, colmat_copy, l, gp_r, \
m, n, p)
#endif
@ -650,7 +650,7 @@ long ph3py_get_neighboring_gird_points(
bzgrid->D_diag[i] = D_diag[i];
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < num_grid_points; i++) {
@ -695,7 +695,7 @@ long ph3py_get_thm_integration_weights_at_grid_points(
bzgrid->D_diag[i] = D_diag[i];
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, bi, vertices, freq_vertices)
#endif
for (i = 0; i < num_gp; i++) {

2
c/phono3py.h
View File

@ -35,7 +35,7 @@
#ifndef __phono3py_H__
#define __phono3py_H__
#ifdef MKL_LAPACKE
#if defined(MKL_LAPACKE) || defined(SCIPY_MKL_H)
#include <mkl.h>
#else
#include <lapacke.h>

8
c/phonon.c
View File

@ -195,7 +195,7 @@ static void get_undone_phonons(
num_band = num_patom * 3;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, q, gp, is_nac)
#endif
for (i = 0; i < num_undone_grid_points; i++) {
@ -214,7 +214,7 @@ static void get_undone_phonons(
}
/* To avoid multithreaded BLAS in OpenMP loop */
#ifdef PHPYOPENMP
#ifdef _OPENMP
#ifndef MULTITHREADED_BLAS
#pragma omp parallel for private(j, gp, freqs_tmp, info)
#endif
@ -255,7 +255,7 @@ static void get_gonze_undone_phonons(
num_band = num_patom * 3;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, q, gp, is_nac)
#endif
for (i = 0; i < num_undone_grid_points; i++) {
@ -274,7 +274,7 @@ static void get_gonze_undone_phonons(
}
/* To avoid multithreaded BLAS in OpenMP loop */
#ifdef PHPYOPENMP
#ifdef _OPENMP
#ifndef MULTITHREADED_BLAS
#pragma omp parallel for private(j, gp, freqs_tmp, info)
#endif

4
c/pp_collision.c
View File

@ -106,7 +106,7 @@ void ppc_get_pp_collision(
tpl_set_relative_grid_address(tp_relative_grid_address,
relative_grid_address, 2);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for schedule(guided) private( \
g, g_zero) if (openmp_per_triplets)
#endif
@ -186,7 +186,7 @@ void ppc_get_pp_collision_with_sigma(
cutoff = sigma * sigma_cutoff;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for schedule(guided) private( \
g, g_zero) if (openmp_per_triplets)
#endif

2
c/real_self_energy.c
View File

@ -118,7 +118,7 @@ static double get_real_self_energy_at_band(
num_band = fc3_normal_squared->dims[2];
shift = 0;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(gp1, gp2) reduction(+ : shift)
#endif
for (i = 0; i < num_triplets; i++) {

2
c/real_to_reciprocal.c
View File

@ -138,7 +138,7 @@ static void real_to_reciprocal_openmp(
for (i = 0; i < num_patom; i++) {
pre_phase_factor = get_pre_phase_factor(i, q_vecs, svecs, multi_dims,
multiplicity, p2s_map);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, k, l, m, n, fc3_rec_elem)
#endif
for (jk = 0; jk < num_patom * num_patom; jk++) {

2
c/reciprocal_to_normal.c
View File

@ -114,7 +114,7 @@ void reciprocal_to_normal_squared(
loopStartCPUTime = clock();
#endif
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for if (openmp_at_bands)
#endif
for (i = 0; i < num_g_pos; i++) {

4
c/triplet.c
View File

@ -72,7 +72,7 @@ void tpl_get_integration_weight(
relative_grid_address, tp_type);
num_band_prod = num_band0 * num_band1 * num_band2;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for if (openmp_per_triplets)
#endif
for (i = 0; i < num_triplets; i++) {
@ -98,7 +98,7 @@ void tpl_get_integration_weight_with_sigma(
num_band_prod = num_band0 * num_band * num_band;
const_adrs_shift = num_triplets * num_band0 * num_band * num_band;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (i = 0; i < num_triplets; i++) {

8
c/triplet_grid.c
View File

@ -158,7 +158,7 @@ static long get_ir_triplets_at_q_perm_q1q2(long *map_triplets,
num_grid = D_diag[0] * D_diag[1] * D_diag[2];
grg_get_grid_address_from_index(adrs0, grid_point, D_diag);
// #ifdef PHPYOPENMP
// #ifdef _OPENMP
// #pragma omp parallel for private(j, gp2, adrs1, adrs2)
// #endif
for (gp1 = 0; gp1 < num_grid; gp1++) {
@ -181,7 +181,7 @@ static long get_ir_triplets_at_q_perm_q1q2(long *map_triplets,
}
/* Fill unfilled elements of map_triplets. */
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (gp1 = 0; gp1 < num_grid; gp1++) {
@ -275,7 +275,7 @@ static void get_BZ_triplets_at_q_type1(long (*triplets)[3],
num_gp = bzgrid->D_diag[0] * bzgrid->D_diag[1] * bzgrid->D_diag[2];
num_bzgp = num_gp * 8;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, gp2, bzgp, G, bz_adrs1, bz_adrs2, d2, \
min_d2, bz0, bz1, bz2)
#endif
@ -360,7 +360,7 @@ static void get_BZ_triplets_at_q_type2(long (*triplets)[3],
}
gp0 = grg_get_grid_index(bz_adrs0, bzgrid->D_diag);
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, gp2, bzgp, G, bz_adrs1, bz_adrs2, d2, \
min_d2)
#endif

4
c/triplet_iw.c
View File

@ -96,7 +96,7 @@ void tpi_get_integration_weight(
max_i = 1;
}
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, b1, b2, adrs_shift, g, \
freq_vertices) if (openmp_per_bands)
#endif
@ -136,7 +136,7 @@ void tpi_get_integration_weight_with_sigma(
long j, b12, b1, b2, adrs_shift;
double f0, f1, f2, g0, g1, g2;
#ifdef PHPYOPENMP
#ifdef _OPENMP
#pragma omp parallel for private(j, b1, b2, f0, f1, f2, g0, g1, g2, \
adrs_shift) if (openmp_per_bands)
#endif

13
doc/install.md
View File

@ -56,6 +56,19 @@ Ubuntu linux, it is installed by:
% sudo apt-get install libgomp1
```
Users mays customize flags and additional libraries by adding a `site.cfg`
that conforms to numpy stile distutils (`numpy.distutils.site.cfg` file).
A basic example to add include directories and openmp flags would be:
```
[phono3py]
include_dirs = /opt/lapack/include
extra_compile_args = -fopenmp
extra_link_args = -fopenmp
```
(install_lapacke)=
### Installation of LAPACKE

5
pyproject.toml
View File

@ -1,5 +1,8 @@
[build-system]
requires = ["setuptools", "wheel", "numpy"]
requires = ["setuptools", "wheel", "numpy", "oldest-supported-numpy"]
[project]
requires-python = ">=3.6"
[tool.flake8]
max-line-length = 88

387
setup.py
View File

@ -4,257 +4,88 @@ import platform
import sys
import sysconfig
# Never use distutils, it is deprecated
import setuptools
import numpy
try:
from setuptools import Extension, setup
git_num = None
use_setuptools = True
print("setuptools is used.")
except ImportError:
from distutils.core import Extension, setup
# Retrieve the default flags from the numpy installation
# This also means one can override this with a site.cfg
# configuration file
from numpy.distutils.system_info import system_info, get_info, lapack_info, dict_append
use_setuptools = False
print("distutils is used.")
# use flags defined in numpy
all_info_d = get_info('ALL')
lapack_info_d = get_info('lapack_opt')
try:
from setuptools_scm import get_version
except ImportError:
git_num = None
class phono3py_info(system_info):
# This enables one
section = "phono3py"
if "setuptools_scm" in sys.modules.keys():
try:
git_ver = get_version()
git_num = int(git_ver.split(".")[3].split("+")[0].replace("dev", ""))
except Exception:
git_num = None
def calc_info(self):
""" Read in *all* options in the [phono3py] section of site.cfg """
info = self.calc_libraries_info()
dict_append(info, **self.calc_extra_info())
dict_append(info, include_dirs=self.get_include_dirs())
self.set_info(**info)
include_dirs_numpy = [numpy.get_include()]
extra_link_args = []
# Workaround Python issue 21121
config_var = sysconfig.get_config_var("CFLAGS")
if (
config_var is not None and "-Werror=declaration-after-statement" in config_var
): # noqa E129
os.environ["CFLAGS"] = config_var.replace("-Werror=declaration-after-statement", "")
# Define compilation flags
extra_compile_args = ""
extra_link_args = extra_compile_args
macros = []
extra_compile_args = [
"-fopenmp",
]
include_dirs = [
"c",
] + include_dirs_numpy
define_macros = []
if use_setuptools:
extra_compile_args += [
"-DPHPYOPENMP",
]
else:
define_macros += [
("PHPYOPENMP", None),
]
# in numpy>=1.16.0, silence build warnings about deprecated API usage
macros.append(("NPY_NO_DEPRECATED_API", "0"))
use_mkl = False
include_dirs_lapacke = []
extra_link_args_lapacke = []
# C macro definitions:
# - MULTITHREADED_BLAS
# This deactivates OpenMP multithread harmonic phonon calculation,
# since inside each phonon calculation, zheev is called.
# When using multithread BLAS, this macro has to be set and
# by this all phonons on q-points should be calculated in series.
# - MKL_LAPACKE:
# This sets definitions and functions needed when using MKL lapacke.
# Phono3py complex values are handled based on those provided by Netlib
# lapacke. However MKL lapacke doesn't provide some macros and functions
# that provided Netlib. This macro defines those used in phono3py among them.
if os.path.isfile("setup_mkl.py"):
# This supposes that MKL multithread BLAS is used.
# This is invoked when setup_mkl.py exists on the current directory.
with_threaded_blas = False
if "--with-threaded-blas" in sys.argv:
del sys.argv["--with-threaded-blas"]
with_threaded_blas = True
print("MKL LAPACKE is to be used.")
print("Use of icc is assumed (CC='icc').")
with_mkl = False
if "--with-mkl" in sys.argv:
del sys.argv["--with-mkl"]
with_mkl = True
# MKL generally uses multi-threaded blas
with_threaded_blas = True
from setup_mkl import mkl_extra_link_args_lapacke, mkl_include_dirs_lapacke
# Examples of setup_mkl.py
# For 2015
# intel_root = "/opt/intel/composer_xe_2015.7.235"
# mkl_root = "%s/mkl" % intel_root
# compiler_root = "%s/compiler" % intel_root
#
# For 2016
# intel_root = "/opt/intel/parallel_studio_xe_2016"
# mkl_root = "%s/mkl" % intel_root
# compiler_root = "%s" % intel_root
#
# For both
# mkl_extra_link_args_lapacke = ['-L%s/lib/intel64' % mkl_root,
# '-lmkl_rt']
# mkl_extra_link_args_lapacke += ['-L%s/lib/intel64' % compiler_root,
# '-lsvml',
# '-liomp5',
# '-limf',
# '-lpthread']
# mkl_include_dirs_lapacke = ["%s/include" % mkl_root]
# define options
# these are the basic definitions for all extensions
opts = lapack_info_d.copy()
if "mkl" in opts.get("libraries", ""):
with_mkl = True
use_mkl = True
extra_link_args_lapacke = mkl_extra_link_args_lapacke
include_dirs_lapacke = mkl_include_dirs_lapacke
if with_mkl:
with_threaded_blas = True
# generally this should not be needed since the numpy distutils
# finding of MKL creates the SCIPY_MKL_H flag
macros.append(("MKL_LAPACKE", None))
if use_setuptools:
extra_compile_args += ["-DMKL_LAPACKE", "-DMULTITHREADED_BLAS"]
else:
define_macros += [("MKL_LAPACKE", None), ("MULTITHREADED_BLAS", None)]
elif os.path.isfile("libopenblas.py"):
# This supposes that multithread openBLAS is used.
# This is invoked when libopenblas.py exists on the current directory.
if with_threaded_blas:
macros.append(("MULTITHREADED_BLAS", None))
# Example of libopenblas.py
# extra_link_args_lapacke += ['-lopenblas']
from libopenblas import extra_link_args_lapacke as obl_extra_link_args_lapacke
from libopenblas import include_dirs_lapacke as obl_include_dirs_lapacke
# Create the dictionary for compiling the codes
dict_append(opts, **all_info_d)
dict_append(opts, include_dirs=['c'])
dict_append(opts, define_macros=macros)
# Add numpy's headers
include_dirs = numpy.get_include()
if include_dirs is not None:
dict_append(opts, include_dirs=[include_dirs])
extra_link_args_lapacke = obl_extra_link_args_lapacke
include_dirs_lapacke = obl_include_dirs_lapacke
# Add any phono3py manual flags from here
add_opts = phono3py_info().get_info()
dict_append(opts, **add_opts)
if use_setuptools:
extra_compile_args += ["-DMULTITHREADED_BLAS"]
else:
define_macros += [("MULTITHREADED_BLAS", None)]
elif platform.system() == "Darwin" and os.path.isfile("/opt/local/lib/libopenblas.a"):
# This supposes lapacke with single-thread openBLAS provided by MacPort is
# used.
# % sudo port install gcc6
# % sudo port select --set gcc mp-gcc
# % sudo port install OpenBLAS +gcc6
extra_link_args_lapacke = ["/opt/local/lib/libopenblas.a"]
include_dirs_lapacke = ["/opt/local/include"]
elif "CONDA_PREFIX" in os.environ and (
os.path.isfile(os.path.join(os.environ["CONDA_PREFIX"], "lib", "liblapacke.dylib"))
or os.path.isfile(os.path.join(os.environ["CONDA_PREFIX"], "lib", "liblapacke.so"))
):
# This is for the system prepared with conda openblas.
extra_link_args_lapacke = ["-llapacke"]
include_dirs_lapacke = [
os.path.join(os.environ["CONDA_PREFIX"], "include"),
]
if os.path.isfile(os.path.join(os.environ["CONDA_PREFIX"], "include", "mkl.h")):
use_mkl = True
if use_setuptools:
extra_compile_args += ["-DMKL_LAPACKE", "-DMULTITHREADED_BLAS"]
else:
define_macros += [("MKL_LAPACKE", None), ("MULTITHREADED_BLAS", None)]
else:
if use_setuptools:
extra_compile_args += ["-DMULTITHREADED_BLAS"]
else:
define_macros += [("MULTITHREADED_BLAS", None)]
elif (
"CONDA_PREFIX" in os.environ
and (
os.path.isfile(
os.path.join(os.environ["CONDA_PREFIX"], "lib", "libmkl_rt.dylib")
)
or os.path.isfile(
os.path.join(os.environ["CONDA_PREFIX"], "lib", "libmkl_rt.so")
)
)
and (
os.path.isfile(
os.path.join(os.environ["CONDA_PREFIX"], "include", "mkl_lapacke.h")
)
)
):
include_dirs_lapacke = [
os.path.join(os.environ["CONDA_PREFIX"], "include"),
]
extra_link_args_lapacke = ["-lmkl_rt"]
if use_setuptools:
extra_compile_args += ["-DMKL_LAPACKE", "-DMULTITHREADED_BLAS"]
else:
define_macros += [("MKL_LAPACKE", None), ("MULTITHREADED_BLAS", None)]
elif os.path.isfile("/usr/lib/liblapacke.so"):
# This supposes that lapacke with single-thread BLAS is installed on
# system.
extra_link_args_lapacke = ["-llapacke", "-llapack", "-lblas"]
include_dirs_lapacke = []
else:
# Here is the default lapacke linkage setting.
# Please modify according to your system environment.
# Without using multithreaded BLAS, DMULTITHREADED_BLAS is better to be
# removed to activate OpenMP multithreading harmonic phonon calculation,
# but this is not mandatory.
#
# The below supposes that lapacke with multithread openblas is used.
# Even if using single-thread BLAS and deactivating OpenMP
# multithreading for harmonic phonon calculation, the total performance
# decrease is considered marginal.
#
# For conda: Try installing with dynamic link library of openblas by
# % conda install numpy scipy h5py pyyaml matplotlib openblas libgfortran
extra_link_args_lapacke = ["-lopenblas", "-lgfortran"]
if "CONDA_PREFIX" in os.environ:
include_dirs_lapacke = [
os.path.join(os.environ["CONDA_PREFIX"], "include"),
]
if use_setuptools:
extra_compile_args += ["-DMULTITHREADED_BLAS"]
else:
define_macros += [("MULTITHREADED_BLAS", None)]
# Different extensions
extensions = []
cc = None
lib_omp = None
if "CC" in os.environ:
if "clang" in os.environ["CC"]:
cc = "clang"
if not use_mkl:
lib_omp = "-lomp"
# lib_omp = '-liomp5'
if "gcc" in os.environ["CC"] or "gnu-cc" in os.environ["CC"]:
cc = "gcc"
if cc == "gcc" or cc is None:
lib_omp = "-lgomp"
if "CC" in os.environ and "gcc-" in os.environ["CC"]:
# For macOS & homebrew gcc:
# Using conda's gcc is more recommended though. Suppose using
# homebrew gcc whereas conda is used as general environment.
# This is to avoid linking conda libgomp that is incompatible
# with homebrew gcc.
try:
v = int(os.environ["CC"].split("-")[1])
except ValueError:
pass
else:
ary = [
os.sep,
"usr",
"local",
"opt",
"gcc@%d" % v,
"lib",
"gcc",
"%d" % v,
"libgomp.a",
]
libgomp_a = os.path.join(*ary)
if os.path.isfile(libgomp_a):
lib_omp = libgomp_a
if lib_omp:
extra_link_args.append(lib_omp)
# Uncomment below to measure reciprocal_to_normal_squared_openmp performance
# define_macros += [('MEASURE_R2N', None)]
extra_link_args += extra_link_args_lapacke
include_dirs += include_dirs_lapacke
print("extra_link_args", extra_link_args)
# Define the modules
sources_phono3py = [
"c/_phono3py.c",
"c/bzgrid.c",
@ -278,14 +109,11 @@ sources_phono3py = [
"c/triplet_grid.c",
"c/triplet_iw.c",
]
extension_phono3py = Extension(
extensions.append(setuptools.Extension(
"phono3py._phono3py",
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
define_macros=define_macros,
sources=sources_phono3py,
)
**opts))
sources_phononmod = [
"c/_phononmod.c",
@ -294,22 +122,16 @@ sources_phononmod = [
"c/phonon.c",
"c/phononmod.c",
]
extension_phononmod = Extension(
extensions.append(setuptools.Extension(
"phono3py._phononmod",
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
sources=sources_phononmod,
)
**opts))
sources_lapackepy = ["c/_lapackepy.c", "c/lapack_wrapper.c"]
extension_lapackepy = Extension(
extensions.append(setuptools.Extension(
"phono3py._lapackepy",
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
include_dirs=include_dirs,
sources=sources_lapackepy,
)
**opts))
packages_phono3py = [
"phono3py",
@ -328,10 +150,6 @@ scripts_phono3py = [
"scripts/phono3py-coleigplot",
]
########################
# _lapackepy extension #
########################
if __name__ == "__main__":
version_nums = [None, None, None]
with open("phono3py/version.py") as w:
@ -364,48 +182,25 @@ if __name__ == "__main__":
if len(version_nums) > 3:
version += "-%d" % version_nums[3]
if use_setuptools:
setup(
name="phono3py",
version=version,
description="This is the phono3py module.",
author="Atsushi Togo",
author_email="atz.togo@gmail.com",
url="http://phonopy.github.io/phono3py/",
packages=packages_phono3py,
python_requires=">=3.6",
install_requires=[
"numpy>=1.11.0",
"scipy",
"PyYAML",
"matplotlib>=2.0.0",
"h5py",
"spglib",
"phonopy>=2.12,<2.13",
],
provides=["phono3py"],
scripts=scripts_phono3py,
ext_modules=[extension_phono3py, extension_lapackepy, extension_phononmod],
)
else:
setup(
name="phono3py",
version=version,
description="This is the phono3py module.",
author="Atsushi Togo",
author_email="atz.togo@gmail.com",
url="http://phonopy.github.io/phono3py/",
packages=packages_phono3py,
requires=[
"numpy",
"scipy",
"PyYAML",
"matplotlib",
"h5py",
"phonopy",
"spglib",
],
provides=["phono3py"],
scripts=scripts_phono3py,
ext_modules=[extension_phono3py, extension_lapackepy, extension_phononmod],
)
setuptools.setup(
name="phono3py",
version=version,
description="This is the phono3py module.",
author="Atsushi Togo",
author_email="atz.togo@gmail.com",
url="http://phonopy.github.io/phono3py/",
packages=packages_phono3py,
python_requires=">=3.6",
install_requires=[
"numpy>=1.11.0",
"scipy",
"PyYAML",
"matplotlib>=2.0.0",
"h5py",
"spglib",
"phonopy>=2.12,<2.13",
],
provides=["phono3py"],
scripts=scripts_phono3py,
ext_modules=extensions
)