Make the splitted setup work
Former-commit-id: 9c8a7e4d1131c40ceb27a4b1a9c54d80c319394b
This commit is contained in:
Marek Nečada
parent
371a8a5f7c
commit
0504f98bc0
10
cyquat.pxd
10
cyquat.pxd
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@ -1,10 +0,0 @@
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from qpms_cdefs cimport *
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cdef class CQuat:
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cdef readonly qpms_quat_t q
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cdef class IRot3:
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cdef readonly qpms_irot3_t qd
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cdef void cset(self, qpms_irot3_t qd)
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@ -10,7 +10,8 @@ add_definitions(-DQPMS_VECTORS_NICE_TRANSFORMATIONS)
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set (DIRS ${GSL_INCLUDE_DIRS} ${GSLCBLAS_INCLUDE_DIRS})
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include_directories(${DIRS})
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add_library (qpms translations.c tmatrices.c vecprint.c vswf.c wigner.c
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add_library (qpms translations.c tmatrices.c vecprint.c vswf.c wigner.c ewald.c
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ewaldsf.c pointgroups.c latticegens.c
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lattices2d.c gaunt.c error.c legendre.c symmetries.c vecprint.c
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bessel.c own_zgemm.c parsing.c scatsystem.c materials.c drudeparam_data.c)
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use_c99()
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@ -1,8 +1,10 @@
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from pkg_resources import get_distribution
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__version__ = get_distribution('qpms').version
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from qpms_c import *
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from .qpms_c import *
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from .qpms_p import *
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from .cyquaternions import CQuat, IRot3
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from .cybspec import VSWFNorm, BaseSpec
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from .lattices2d import *
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from .hexpoints import *
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from .tmatrices import *
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@ -169,7 +169,8 @@ def generate_trianglepoints_hexcomplement(maxlayer, v3d = True, circular = True,
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}
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from qpms_c import get_mn_y, trans_calculator
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from .cycommon import get_mn_y
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from .qpms_c import trans_calculator
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from .qpms_p import cart2sph
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def hexlattice_precalc_AB_save(file, lMax, k_hexside, maxlayer, circular=True, savepointinfo = False, J_scat=3):
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@ -11,9 +11,9 @@ import numpy as np
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import cmath
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#from qpms_cdefs cimport *
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from cyquaternions cimport *
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from cyquaternions import *
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#from cyquaternions import *
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from cybspec cimport *
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from cybspec import *
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#from cybspec import *
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from cycommon import *
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cimport cython
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from cython.parallel cimport parallel, prange
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@ -9,7 +9,8 @@ except ImportError:
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import re
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from scipy import interpolate
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from scipy.constants import hbar, e as eV, pi, c
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from qpms_c import get_mn_y, get_nelem, CQuat
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from .cycommon import get_mn_y, get_nelem
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from .cyquaternions import CQuat
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ň = np.newaxis
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from .types import NormalizationT, TMatrixSpec
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@ -1834,123 +1834,4 @@ int qpms_trans_calculator_get_AB_arrays_ext(const qpms_trans_calculator *c,
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return qpms_trans_calculator_get_AB_arrays(c,Adest,Bdest,deststride,srcstride,
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kdlj, r_ge_d, J);
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}
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#ifdef QPMS_COMPILE_PYTHON_EXTENSIONS
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#include <string.h>
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#ifdef QPMS_USE_OMP
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#include <omp.h>
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#endif
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int qpms_cython_trans_calculator_get_AB_arrays_loop(
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const qpms_trans_calculator *c, const qpms_bessel_t J, const int resnd,
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const int daxis, const int saxis,
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char *A_data, const npy_intp *A_shape, const npy_intp *A_strides,
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char *B_data, const npy_intp *B_shape, const npy_intp *B_strides,
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const char *r_data, const npy_intp *r_shape, const npy_intp *r_strides,
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const char *theta_data, const npy_intp *theta_shape, const npy_intp *theta_strides,
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const char *phi_data, const npy_intp *phi_shape, const npy_intp *phi_strides,
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const char *r_ge_d_data, const npy_intp *r_ge_d_shape, const npy_intp *r_ge_d_strides){
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assert(daxis != saxis);
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assert(resnd >= 2);
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int longest_axis = 0;
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int longestshape = 1;
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const npy_intp *resultshape = A_shape, *resultstrides = A_strides;
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// TODO put some restrict's everywhere?
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for (int ax = 0; ax < resnd; ++ax){
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assert(A_shape[ax] == B_shape[ax]);
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assert(A_strides[ax] == B_strides[ax]);
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if (daxis == ax || saxis == ax) continue;
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if (A_shape[ax] > longestshape) {
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longest_axis = ax;
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longestshape = 1;
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}
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}
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const npy_intp longlen = resultshape[longest_axis];
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npy_intp innerloop_shape[resnd];
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for (int ax = 0; ax < resnd; ++ax) {
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innerloop_shape[ax] = resultshape[ax];
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}
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/* longest axis will be iterated in the outer (parallelized) loop.
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* Therefore, longest axis, together with saxis and daxis,
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* will not be iterated in the inner loop:
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*/
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innerloop_shape[longest_axis] = 1;
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innerloop_shape[daxis] = 1;
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innerloop_shape[saxis] = 1;
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// these are the 'strides' passed to the qpms_trans_calculator_get_AB_arrays_ext
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// function, which expects 'const double *' strides, not 'char *' ones.
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const npy_intp dstride = resultstrides[daxis] / sizeof(complex double);
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const npy_intp sstride = resultstrides[saxis] / sizeof(complex double);
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int errval = 0;
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// TODO here start parallelisation
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//#pragma omp parallel
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{
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npy_intp local_indices[resnd];
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memset(local_indices, 0, sizeof(local_indices));
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int errval_local = 0;
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size_t longi;
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//#pragma omp for
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for(longi = 0; longi < longlen; ++longi) {
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// this might be done also in the inverse order, but this is more
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// 'c-contiguous' way of incrementing the indices
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int ax = resnd - 1;
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while(ax >= 0) {
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/* calculate the correct index/pointer for each array used.
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* This can be further optimized from O(resnd * total size of
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* the result array) to O(total size of the result array), but
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* fick that now
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*/
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const char *r_p = r_data + r_strides[longest_axis] * longi;
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const char *theta_p = theta_data + theta_strides[longest_axis] * longi;
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const char *phi_p = phi_data + phi_strides[longest_axis] * longi;
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const char *r_ge_d_p = r_ge_d_data + r_ge_d_strides[longest_axis] * longi;
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char *A_p = A_data + A_strides[longest_axis] * longi;
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char *B_p = B_data + B_strides[longest_axis] * longi;
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for(int i = 0; i < resnd; ++i) {
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// following two lines are probably not needed, as innerloop_shape is there 1 anyway
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// so if i == daxis, saxis, or longest_axis, local_indices[i] is zero.
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if (i == longest_axis) continue;
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if (daxis == i || saxis == i) continue;
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r_p += r_strides[i] * local_indices[i];
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theta_p += theta_strides[i] * local_indices[i];
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phi_p += phi_strides[i] * local_indices[i];
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A_p += A_strides[i] * local_indices[i];
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B_p += B_strides[i] * local_indices[i];
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}
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// perform the actual task here
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errval_local |= qpms_trans_calculator_get_AB_arrays_ext(c, (complex double *)A_p,
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(complex double *)B_p,
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dstride, sstride,
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// FIXME change all the _ext function types to npy_... so that
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// these casts are not needed
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*((double *) r_p), *((double *) theta_p), *((double *)phi_p),
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(int)(*((npy_bool *) r_ge_d_p)), J);
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if (errval_local) abort();
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// increment the last index 'digit' (ax is now resnd-1; we don't have do-while loop in python)
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++local_indices[ax];
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while(local_indices[ax] == innerloop_shape[ax] && ax >= 0) {
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// overflow to the next digit but stop when reached below the last one
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local_indices[ax] = 0;
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//local_indices[--ax]++; // dekrementace indexu pod nulu a následná inkrementace poruší paměť FIXME
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ax--;
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if (ax >= 0) local_indices[ax]++;
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}
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if (ax >= 0) // did not overflow, get back to the lowest index
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ax = resnd - 1;
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}
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}
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errval |= errval_local;
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}
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// FIXME when parallelizing
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// TODO Here end parallelisation
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return errval;
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}
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#endif // QPMS_COMPILE_PYTHON_EXTENSIONS
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@ -0,0 +1,137 @@
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#include <math.h>
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#include "qpms_types.h"
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#include "qpms_specfunc.h"
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#include "gaunt.h"
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#include "translations.h"
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#include "indexing.h" // TODO replace size_t and int with own index types here
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#include <stdbool.h>
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#include <gsl/gsl_sf_legendre.h>
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#include <gsl/gsl_sf_bessel.h>
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#include "tiny_inlines.h"
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#include "assert_cython_workaround.h"
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#include "kahansum.h"
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#include <stdlib.h> //abort()
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#include <gsl/gsl_sf_coupling.h>
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#include "qpms_error.h"
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#include "normalisation.h"
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//#ifdef QPMS_COMPILE_PYTHON_EXTENSIONS
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#include <string.h>
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#ifdef QPMS_USE_OMP
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#include <omp.h>
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#endif
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int qpms_cython_trans_calculator_get_AB_arrays_loop(
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const qpms_trans_calculator *c, const qpms_bessel_t J, const int resnd,
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const int daxis, const int saxis,
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char *A_data, const npy_intp *A_shape, const npy_intp *A_strides,
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char *B_data, const npy_intp *B_shape, const npy_intp *B_strides,
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const char *r_data, const npy_intp *r_shape, const npy_intp *r_strides,
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const char *theta_data, const npy_intp *theta_shape, const npy_intp *theta_strides,
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const char *phi_data, const npy_intp *phi_shape, const npy_intp *phi_strides,
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const char *r_ge_d_data, const npy_intp *r_ge_d_shape, const npy_intp *r_ge_d_strides){
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assert(daxis != saxis);
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assert(resnd >= 2);
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int longest_axis = 0;
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int longestshape = 1;
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const npy_intp *resultshape = A_shape, *resultstrides = A_strides;
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// TODO put some restrict's everywhere?
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for (int ax = 0; ax < resnd; ++ax){
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assert(A_shape[ax] == B_shape[ax]);
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assert(A_strides[ax] == B_strides[ax]);
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if (daxis == ax || saxis == ax) continue;
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if (A_shape[ax] > longestshape) {
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longest_axis = ax;
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longestshape = 1;
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}
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}
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const npy_intp longlen = resultshape[longest_axis];
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npy_intp innerloop_shape[resnd];
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for (int ax = 0; ax < resnd; ++ax) {
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innerloop_shape[ax] = resultshape[ax];
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}
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/* longest axis will be iterated in the outer (parallelized) loop.
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* Therefore, longest axis, together with saxis and daxis,
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* will not be iterated in the inner loop:
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*/
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innerloop_shape[longest_axis] = 1;
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innerloop_shape[daxis] = 1;
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innerloop_shape[saxis] = 1;
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// these are the 'strides' passed to the qpms_trans_calculator_get_AB_arrays_ext
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// function, which expects 'const double *' strides, not 'char *' ones.
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const npy_intp dstride = resultstrides[daxis] / sizeof(complex double);
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const npy_intp sstride = resultstrides[saxis] / sizeof(complex double);
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int errval = 0;
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// TODO here start parallelisation
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//#pragma omp parallel
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{
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npy_intp local_indices[resnd];
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memset(local_indices, 0, sizeof(local_indices));
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int errval_local = 0;
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size_t longi;
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//#pragma omp for
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for(longi = 0; longi < longlen; ++longi) {
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// this might be done also in the inverse order, but this is more
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// 'c-contiguous' way of incrementing the indices
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int ax = resnd - 1;
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while(ax >= 0) {
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/* calculate the correct index/pointer for each array used.
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* This can be further optimized from O(resnd * total size of
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* the result array) to O(total size of the result array), but
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* fick that now
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*/
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const char *r_p = r_data + r_strides[longest_axis] * longi;
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const char *theta_p = theta_data + theta_strides[longest_axis] * longi;
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const char *phi_p = phi_data + phi_strides[longest_axis] * longi;
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const char *r_ge_d_p = r_ge_d_data + r_ge_d_strides[longest_axis] * longi;
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char *A_p = A_data + A_strides[longest_axis] * longi;
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char *B_p = B_data + B_strides[longest_axis] * longi;
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for(int i = 0; i < resnd; ++i) {
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// following two lines are probably not needed, as innerloop_shape is there 1 anyway
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// so if i == daxis, saxis, or longest_axis, local_indices[i] is zero.
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if (i == longest_axis) continue;
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if (daxis == i || saxis == i) continue;
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r_p += r_strides[i] * local_indices[i];
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theta_p += theta_strides[i] * local_indices[i];
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phi_p += phi_strides[i] * local_indices[i];
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A_p += A_strides[i] * local_indices[i];
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B_p += B_strides[i] * local_indices[i];
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}
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// perform the actual task here
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errval_local |= qpms_trans_calculator_get_AB_arrays_ext(c, (complex double *)A_p,
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(complex double *)B_p,
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dstride, sstride,
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// FIXME change all the _ext function types to npy_... so that
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// these casts are not needed
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*((double *) r_p), *((double *) theta_p), *((double *)phi_p),
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(int)(*((npy_bool *) r_ge_d_p)), J);
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if (errval_local) abort();
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// increment the last index 'digit' (ax is now resnd-1; we don't have do-while loop in python)
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++local_indices[ax];
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while(local_indices[ax] == innerloop_shape[ax] && ax >= 0) {
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// overflow to the next digit but stop when reached below the last one
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local_indices[ax] = 0;
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//local_indices[--ax]++; // dekrementace indexu pod nulu a následná inkrementace poruší paměť FIXME
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ax--;
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if (ax >= 0) local_indices[ax]++;
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}
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if (ax >= 0) // did not overflow, get back to the lowest index
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ax = resnd - 1;
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}
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}
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errval |= errval_local;
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}
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// FIXME when parallelizing
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// TODO Here end parallelisation
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return errval;
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}
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//#endif // QPMS_COMPILE_PYTHON_EXTENSIONS
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62
setup.py
62
setup.py
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@ -9,15 +9,18 @@ from distutils.extension import Extension
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# m.Extension.__dict__ = m._Extension.__dict__
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# TODO CHECK THIS OUT http://stackoverflow.com/questions/4056657/what-is-the-easiest-way-to-make-an-optional-c-extension-for-a-python-package
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# AND THIS https://groups.google.com/forum/#!topic/cython-users/GAAPYb2X304
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# also this: https://docs.python.org/2/extending/building.html
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import os
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print("You might want to add additional library path to LD_LIBRARY_PATH (especially if you are not using"
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" GNU GSL in your system library path) and if import fails. ")
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if("LD_LIBRARY_PATH" in os.environ):
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print(os.environ['LD_LIBRARY_PATH'].split(':'))
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#print("You might want to add additional library path to LD_LIBRARY_PATH (especially if you are not using"
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# " GNU GSL in your system library path) and if import fails. ")
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#if("LD_LIBRARY_PATH" in os.environ):
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# print(os.environ['LD_LIBRARY_PATH'].split(':'))
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'''
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amos_sources = [
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'amos/d1mach.f',
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'amos/dgamln.f',
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@ -60,13 +63,7 @@ amos_sources = [
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'amos/zwrsk.f',
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]
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qpms_c = Extension('qpms_c',
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sources = [
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'qpms/cycommon.pyx',
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'qpms/cyquaternions.pyx',
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'qpms/cybspec.pyx',
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'qpms/qpms_c.pyx',
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libqpms_sources = [
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#'qpms/hexpoints_c.pyx',
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'qpms/gaunt.c',#'qpms/gaunt.h','qpms/vectors.h','qpms/translations.h',
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# FIXME http://stackoverflow.com/questions/4259170/python-setup-script-extensions-how-do-you-include-a-h-file
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@ -82,26 +79,44 @@ qpms_c = Extension('qpms_c',
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'qpms/bessel.c',
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'qpms/own_zgemm.c',
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'qpms/pointgroups.c',
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]
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'''
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cycommon = Extension('qpms.cycommon',
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sources = ['qpms/cycommon.pyx'],
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extra_link_args=['amos/libamos.a', 'qpms/libqpms.a'],
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libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
|
||||
)
|
||||
cybspec = Extension('qpms.cybspec',
|
||||
sources = ['qpms/cybspec.pyx'],
|
||||
extra_link_args=['amos/libamos.a', 'qpms/libqpms.a'],
|
||||
libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
|
||||
)
|
||||
cyquaternions = Extension('qpms.cyquaternions',
|
||||
sources = ['qpms/cyquaternions.pyx'],
|
||||
extra_link_args=['amos/libamos.a', 'qpms/libqpms.a'],
|
||||
libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread',]
|
||||
)
|
||||
|
||||
qpms_c = Extension('qpms.qpms_c',
|
||||
sources = [
|
||||
'qpms/qpms_c.pyx',
|
||||
'qpms/translations_python.c',
|
||||
],
|
||||
extra_compile_args=['-std=c99','-ggdb', '-O0',
|
||||
'-DQPMS_COMPILE_PYTHON_EXTENSIONS', # this is required
|
||||
#'-DQPMS_USE_OMP',
|
||||
'-DQPMS_SCATSYSTEM_USE_OWN_BLAS',
|
||||
'-DDISABLE_NDEBUG', # uncomment to enable assertions in the modules
|
||||
#'-fopenmp',
|
||||
extra_compile_args=['-std=c99',
|
||||
'-DQPMS_COMPILE_PYTHON_EXTENSIONS', # This is needed to enable it in translations.h
|
||||
],
|
||||
libraries=['gsl', 'lapacke', 'blas', 'gslcblas', 'pthread', #'omp'
|
||||
# TODO resolve the problem with openblas (missing gotoblas symbol) and preferable use other blas library
|
||||
#('amos', dict(sources=amos_sources) ),
|
||||
],
|
||||
include_dirs=['amos'],
|
||||
extra_link_args=['amos/libamos.a'],
|
||||
runtime_library_dirs=os.environ['LD_LIBRARY_PATH'].split(':') if 'LD_LIBRARY_PATH' in os.environ else [],
|
||||
include_dirs=['amos', 'qpms'],
|
||||
extra_link_args=[ 'qpms/libqpms.a','amos/libamos.a', ],
|
||||
#runtime_library_dirs=os.environ['LD_LIBRARY_PATH'].split(':') if 'LD_LIBRARY_PATH' in os.environ else [],
|
||||
#extra_objects = ['amos/libamos.a'], # FIXME apparently, I would like to eliminate the need to cmake/make first
|
||||
)
|
||||
|
||||
setup(name='qpms',
|
||||
version = "0.2.995",
|
||||
version = "0.2.996",
|
||||
packages=['qpms'],
|
||||
# libraries = [('amos', {'sources': amos_sources} )],
|
||||
setup_requires=['cython>=0.28',],
|
||||
|
|
@ -109,8 +124,9 @@ setup(name='qpms',
|
|||
#'quaternion','spherical_functions',
|
||||
'scipy>=0.18.0', 'sympy>=1.2'],
|
||||
#dependency_links=['https://github.com/moble/quaternion/archive/v2.0.tar.gz','https://github.com/moble/spherical_functions/archive/master.zip'],
|
||||
ext_modules=cythonize([qpms_c], include_path=['qpms', 'amos'], gdb_debug=True),
|
||||
ext_modules=cythonize([qpms_c, cycommon, cyquaternions, cybspec], include_path=['qpms', 'amos'], gdb_debug=True),
|
||||
cmdclass = {'build_ext': build_ext},
|
||||
zip_safe=False
|
||||
)
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue