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Merge pull request #81 from TREX-CoE/add-python-api

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Adapt python API
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Anthony Scemama 2022-08-23 08:38:57 +02:00 committed by GitHub
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6 changed files with 390 additions and 7 deletions
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2
Makefile.am
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@ -118,7 +118,7 @@ python-install: $(qmckl_h) $(lib_LTLIBRARIES) $(dist_python_DATA)
cp src/qmckl.py . ; \
export QMCKL_INCLUDEDIR="$(prefix)/include" ; \
export QMCKL_LIBDIR="$(prefix)/lib" ; \
pip install .
python3 -m pip install .
python-test: $(test_py)
cd $(abs_srcdir)/python/test/ && \

376
org/qmckl_blas.org
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@ -1084,6 +1084,225 @@ qmckl_exit_code test_qmckl_dgemm(qmckl_context context);
assert(QMCKL_SUCCESS == test_qmckl_dgemm(context));
#+end_src
** ~qmckl_dgemm_safe~
"Size-safe" proxy function with the same functionality as ~qmckl_dgemm~
but with 3 additional arguments. These arguments ~size_max_M~ (where ~M~ is a matix)
are required primarily for the Python API, where compatibility with
NumPy arrays implies that sizes of the input and output arrays are provided.
#+NAME: qmckl_dgemm_safe_args
| Variable | Type | In/Out | Description |
|--------------+-----------------+--------+---------------------------------------|
| ~context~ | ~qmckl_context~ | in | Global state |
| ~TransA~ | ~char~ | in | 'T' is transposed |
| ~TransB~ | ~char~ | in | 'T' is transposed |
| ~m~ | ~int64_t~ | in | Number of rows of the input matrix |
| ~n~ | ~int64_t~ | in | Number of columns of the input matrix |
| ~k~ | ~int64_t~ | in | Number of columns of the input matrix |
| ~alpha~ | ~double~ | in | \alpha |
| ~A~ | ~double[][lda]~ | in | Array containing the matrix $A$ |
| ~size_max_A~ | ~int64_t~ | in | Size of the matrix $A$ |
| ~lda~ | ~int64_t~ | in | Leading dimension of array ~A~ |
| ~B~ | ~double[][ldb]~ | in | Array containing the matrix $B$ |
| ~size_max_B~ | ~int64_t~ | in | Size of the matrix $B$ |
| ~ldb~ | ~int64_t~ | in | Leading dimension of array ~B~ |
| ~beta~ | ~double~ | in | \beta |
| ~C~ | ~double[][ldc]~ | out | Array containing the matrix $C$ |
| ~size_max_C~ | ~int64_t~ | in | Size of the matrix $C$ |
| ~ldc~ | ~int64_t~ | in | Leading dimension of array ~C~ |
Requirements:
- ~context~ is not ~QMCKL_NULL_CONTEXT~
- ~m > 0~
- ~n > 0~
- ~k > 0~
- ~lda >= m~
- ~ldb >= n~
- ~ldc >= n~
- ~A~ is allocated with at least $m \times k \times 8$ bytes
- ~B~ is allocated with at least $k \times n \times 8$ bytes
- ~C~ is allocated with at least $m \times n \times 8$ bytes
- ~size_max_A >= m * k~
- ~size_max_B >= k * n~
- ~size_max_C >= m * n~
#+CALL: generate_c_header(table=qmckl_dgemm_safe_args,rettyp="qmckl_exit_code",fname="qmckl_dgemm_safe")
#+RESULTS:
#+BEGIN_src c :tangle (eval h_func) :comments org
qmckl_exit_code qmckl_dgemm_safe (
const qmckl_context context,
const char TransA,
const char TransB,
const int64_t m,
const int64_t n,
const int64_t k,
const double alpha,
const double* A,
const int64_t size_max_A,
const int64_t lda,
const double* B,
const int64_t size_max_B,
const int64_t ldb,
const double beta,
double* const C,
const int64_t size_max_C,
const int64_t ldc );
#+END_src
#+begin_src f90 :tangle (eval f) :exports none
integer function qmckl_dgemm_safe_f(context, TransA, TransB, &
m, n, k, alpha, A, size_A, LDA, B, size_B, LDB, beta, C, size_C, LDC) &
result(info)
use qmckl
implicit none
integer(qmckl_context), intent(in) :: context
character , intent(in) :: TransA, TransB
integer*8 , intent(in) :: m, n, k
double precision , intent(in) :: alpha, beta
integer*8 , intent(in) :: lda
integer*8 , intent(in) :: size_A
double precision , intent(in) :: A(lda,*)
integer*8 , intent(in) :: ldb
integer*8 , intent(in) :: size_B
double precision , intent(in) :: B(ldb,*)
integer*8 , intent(in) :: ldc
integer*8 , intent(in) :: size_C
double precision , intent(out) :: C(ldc,*)
info = QMCKL_SUCCESS
if (context == QMCKL_NULL_CONTEXT) then
info = QMCKL_INVALID_CONTEXT
return
endif
if (m <= 0_8) then
info = QMCKL_INVALID_ARG_4
return
endif
if (n <= 0_8) then
info = QMCKL_INVALID_ARG_5
return
endif
if (k <= 0_8) then
info = QMCKL_INVALID_ARG_6
return
endif
if (LDA <= 0) then
info = QMCKL_INVALID_ARG_10
return
endif
if (LDB <= 0) then
info = QMCKL_INVALID_ARG_13
return
endif
if (LDC <= 0) then
info = QMCKL_INVALID_ARG_17
return
endif
if (size_A <= 0) then
info = QMCKL_INVALID_ARG_9
return
endif
if (size_B <= 0) then
info = QMCKL_INVALID_ARG_12
return
endif
if (size_C <= 0) then
info = QMCKL_INVALID_ARG_16
return
endif
call dgemm(transA, transB, int(m,4), int(n,4), int(k,4), &
alpha, A, int(LDA,4), B, int(LDB,4), beta, C, int(LDC,4))
end function qmckl_dgemm_safe_f
#+end_src
*** C interface :noexport:
#+CALL: generate_c_interface(table=qmckl_dgemm_safe_args,rettyp="qmckl_exit_code",fname="qmckl_dgemm_safe")
#+RESULTS:
#+begin_src f90 :tangle (eval f) :comments org :exports none
integer(c_int32_t) function qmckl_dgemm_safe &
(context, TransA, TransB, m, n, k, alpha, A, size_A, lda, B, size_B, ldb, beta, C, size_C, ldc) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
character , intent(in) , value :: TransA
character , intent(in) , value :: TransB
integer (c_int64_t) , intent(in) , value :: m
integer (c_int64_t) , intent(in) , value :: n
integer (c_int64_t) , intent(in) , value :: k
real (c_double ) , intent(in) , value :: alpha
real (c_double ) , intent(in) :: A(lda,*)
integer (c_int64_t) , intent(in) , value :: size_A
integer (c_int64_t) , intent(in) , value :: lda
real (c_double ) , intent(in) :: B(ldb,*)
integer (c_int64_t) , intent(in) , value :: size_B
integer (c_int64_t) , intent(in) , value :: ldb
real (c_double ) , intent(in) , value :: beta
real (c_double ) , intent(out) :: C(ldc,*)
integer (c_int64_t) , intent(in) , value :: size_C
integer (c_int64_t) , intent(in) , value :: ldc
integer(c_int32_t), external :: qmckl_dgemm_safe_f
info = qmckl_dgemm_safe_f &
(context, TransA, TransB, m, n, k, alpha, A, size_A, lda, B, size_B, ldb, beta, C, size_C, ldc)
end function qmckl_dgemm_safe
#+end_src
#+CALL: generate_f_interface(table=qmckl_dgemm_safe_args,rettyp="qmckl_exit_code",fname="qmckl_dgemm_safe")
#+RESULTS:
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
interface
integer(c_int32_t) function qmckl_dgemm_safe &
(context, TransA, TransB, m, n, k, alpha, A, size_A, lda, B, size_B, ldb, beta, C, size_C, ldc) &
bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
character , intent(in) , value :: TransA
character , intent(in) , value :: TransB
integer (c_int64_t) , intent(in) , value :: m
integer (c_int64_t) , intent(in) , value :: n
integer (c_int64_t) , intent(in) , value :: k
real (c_double ) , intent(in) , value :: alpha
real (c_double ) , intent(in) :: A(lda,*)
integer (c_int64_t) , intent(in) , value :: size_A
integer (c_int64_t) , intent(in) , value :: lda
real (c_double ) , intent(in) :: B(ldb,*)
integer (c_int64_t) , intent(in) , value :: size_B
integer (c_int64_t) , intent(in) , value :: ldb
real (c_double ) , intent(in) , value :: beta
real (c_double ) , intent(out) :: C(ldc,*)
integer (c_int64_t) , intent(in) , value :: size_C
integer (c_int64_t) , intent(in) , value :: ldc
end function qmckl_dgemm_safe
end interface
#+end_src
** ~qmckl_matmul~
Matrix multiplication using the =qmckl_matrix= data type:
@ -1403,8 +1622,6 @@ integer function qmckl_adjugate_f(context, na, A, LDA, B, ldb, det_l) &
integer*8, intent(in) :: na
double precision, intent(inout) :: det_l
integer :: i,j
info = QMCKL_SUCCESS
if (context == QMCKL_NULL_CONTEXT) then
@ -2225,6 +2442,159 @@ qmckl_exit_code test_qmckl_adjugate(qmckl_context context);
assert(QMCKL_SUCCESS == test_qmckl_adjugate(context));
#+end_src
** ~qmckl_adjugate_safe~
"Size-safe" proxy function with the same functionality as ~qmckl_adjugate~
but with 2 additional arguments. These arguments ~size_max_M~ (where ~M~ is a matix)
are required primarily for the Python API, where compatibility with
NumPy arrays implies that sizes of the input and output arrays are provided.
#+NAME: qmckl_adjugate_safe_args
| Variable | Type | In/Out | Description |
|--------------+-----------------+--------+------------------------------------------------|
| ~context~ | ~qmckl_context~ | in | Global state |
| ~n~ | ~int64_t~ | in | Number of rows and columns of the input matrix |
| ~A~ | ~double[][lda]~ | in | Array containing the $n \times n$ matrix $A$ |
| ~size_max_A~ | ~int64_t~ | in | Size of the matrix $A$ |
| ~lda~ | ~int64_t~ | in | Leading dimension of array ~A~ |
| ~B~ | ~double[][ldb]~ | out | Adjugate of $A$ |
| ~size_max_B~ | ~int64_t~ | in | Size of the matrix $B$ |
| ~ldb~ | ~int64_t~ | in | Leading dimension of array ~B~ |
| ~det_l~ | ~double~ | inout | determinant of $A$ |
Requirements:
- ~context~ is not ~QMCKL_NULL_CONTEXT~
- ~n > 0~
- ~lda >= m~
- ~A~ is allocated with at least $m \times m \times 8$ bytes
- ~ldb >= m~
- ~B~ is allocated with at least $m \times m \times 8$ bytes
- ~size_max_A >= m * m~
- ~size_max_B >= m * m~
#+CALL: generate_c_header(table=qmckl_adjugate_safe_args,rettyp="qmckl_exit_code",fname="qmckl_adjugate_safe")
#+RESULTS:
#+BEGIN_src c :tangle (eval h_func) :comments org
qmckl_exit_code qmckl_adjugate_safe (
const qmckl_context context,
const int64_t n,
const double* A,
const int64_t size_max_A,
const int64_t lda,
double* const B,
const int64_t size_max_B,
const int64_t ldb,
double* det_l );
#+END_src
For small matrices (\le 5\times 5), we use specialized routines
for performance motivations. For larger sizes, we rely on the
LAPACK library.
#+begin_src f90 :tangle (eval f) :exports none
integer function qmckl_adjugate_safe_f(context, &
na, A, size_A, LDA, B, size_B, LDB, det_l) &
result(info)
use qmckl
implicit none
integer(qmckl_context) , intent(in) :: context
double precision, intent(in) :: A (LDA,*)
integer*8, intent(in) :: size_A
integer*8, intent(in) :: LDA
double precision, intent(out) :: B (LDB,*)
integer*8, intent(in) :: size_B
integer*8, intent(in) :: LDB
integer*8, intent(in) :: na
double precision, intent(inout) :: det_l
integer, external :: qmckl_adjugate_f
info = QMCKL_SUCCESS
if (size_A < na) then
info = QMCKL_INVALID_ARG_4
return
endif
if (size_B <= 0_8) then
info = QMCKL_INVALID_ARG_7
return
endif
info = qmckl_adjugate_f(context, na, A, LDA, B, LDB, det_l)
if (info == QMCKL_INVALID_ARG_4) then
info = QMCKL_INVALID_ARG_5
return
endif
if (info == QMCKL_INVALID_ARG_6) then
info = QMCKL_INVALID_ARG_8
return
endif
end function qmckl_adjugate_safe_f
#+end_src
*** C interface
#+CALL: generate_c_interface(table=qmckl_adjugate_safe_args,rettyp="qmckl_exit_code",fname="qmckl_adjugate_safe")
#+RESULTS:
#+begin_src f90 :tangle (eval f) :comments org :exports none
integer(c_int32_t) function qmckl_adjugate_safe &
(context, n, A, size_A, lda, B, size_B, ldb, det_l) &
bind(C) result(info)
use, intrinsic :: iso_c_binding
implicit none
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(in) , value :: n
real (c_double ) , intent(in) :: A(lda,*)
integer (c_int64_t) , intent(in) , value :: lda
integer (c_int64_t) , intent(in) , value :: size_A
real (c_double ) , intent(out) :: B(ldb,*)
integer (c_int64_t) , intent(in) , value :: ldb
integer (c_int64_t) , intent(in) , value :: size_B
real (c_double ) , intent(inout) :: det_l
integer(c_int32_t), external :: qmckl_adjugate_safe_f
info = qmckl_adjugate_safe_f &
(context, n, A, size_A, lda, B, size_B, ldb, det_l)
end function qmckl_adjugate_safe
#+end_src
#+CALL: generate_f_interface(table=qmckl_adjugate_safe_args,rettyp="qmckl_exit_code",fname="qmckl_adjugate_safe")
#+RESULTS:
#+begin_src f90 :tangle (eval fh_func) :comments org :exports none
interface
integer(c_int32_t) function qmckl_adjugate_safe &
(context, n, A, size_A, lda, B, size_B, ldb, det_l) &
bind(C)
use, intrinsic :: iso_c_binding
import
implicit none
integer (c_int64_t) , intent(in) , value :: context
integer (c_int64_t) , intent(in) , value :: n
real (c_double ) , intent(in) :: A(lda,*)
integer (c_int64_t) , intent(in) , value :: lda
integer (c_int64_t) , intent(in) , value :: size_A
real (c_double ) , intent(out) :: B(ldb,*)
integer (c_int64_t) , intent(in) , value :: ldb
integer (c_int64_t) , intent(in) , value :: size_B
real (c_double ) , intent(inout) :: det_l
end function qmckl_adjugate_safe
end interface
#+end_src
** ~qmckl_transpose~
Transposes a matrix: $A^\dagger_{ji} = A_{ij}$.
@ -2324,9 +2694,7 @@ qmckl_transpose (qmckl_context context,
assert (qmckl_context_destroy(context) == QMCKL_SUCCESS);
return 0;
}
#+end_src
# -*- mode: org -*-
# vim: syntax=c

2
python/pyproject.toml
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@ -2,6 +2,6 @@
requires = [
"setuptools>=42",
"wheel",
"numpy>=1.17.3"
"oldest-supported-numpy"
]
build-backend = "setuptools.build_meta"

4
python/setup.py
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@ -71,5 +71,7 @@ setup(name = MODULE_NAME,
"Operating System :: MacOS"
],
python_requires = ">=3.0",
install_requires = ["numpy>=1.17.3"]
# The ABI incompatibility of numpy is a pain, for now set the
# min numpy version such that we have wheels for CPython 3.5 & 3.6
install_requires = ["numpy>=1.13.3"]
)

10
python/src/qmckl.i
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@ -20,6 +20,7 @@
%include typemaps.i
%apply int *OUTPUT { qmckl_exit_code *exit_code};
%apply double *OUTPUT { double* det_l};
/* Avoid passing file_name length as an additiona argument */
%apply (char *STRING, int LENGTH) { (const char* file_name, const int64_t size_max) };
@ -29,6 +30,9 @@
%cstring_bounded_output(char* function_name, 1024);
%cstring_bounded_output(char* message, 1024);
%cstring_bounded_output(char* const basis_type, 2);
/* Required for qmckl_last_error function to work */
%cstring_bounded_output(char* buffer, 1024);
/* This block is needed make SWIG convert NumPy arrays to/from from the C pointer and size_max argument.
NOTE: `numpy.i` interface file is not part of SWIG but it is included in the numpy distribution (under numpy/tools/swig/numpy.i)
@ -48,6 +52,12 @@ import_array();
/* Include typemaps generated by the process_header.py script */
%include "qmckl_include.i"
/* Some custom array typemaps which are not generated by process_header.py */
%apply ( double* IN_ARRAY1 , int64_t DIM1 ) { ( const double * A, const int64_t size_max_A) };
%apply ( double* IN_ARRAY1 , int64_t DIM1 ) { ( const double * B, const int64_t size_max_B) };
%apply ( double* ARGOUT_ARRAY1 , int64_t DIM1 ) { ( double* const C, const int64_t size_max_C) };
%apply ( double* ARGOUT_ARRAY1 , int64_t DIM1 ) { ( double* const B, const int64_t size_max_B) };
/* Handle properly get_point */

3
python/test/test_api.py
View File

@ -33,6 +33,9 @@ assert mo_num == 404
pq.set_electron_coord(ctx, 'T', walk_num, coord)
ao_type = pq.get_ao_basis_type(ctx)
assert 'G' in ao_type
size_max = 5*walk_num*elec_num*mo_num
mo_vgl = pq.get_mo_basis_mo_vgl(ctx, size_max)