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Code Issues Releases Wiki Activity

mmap works for integrals

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This commit is contained in:
Anthony Scemama 2016-06-14 13:59:05 +02:00
parent 20ad57e8c6
commit 39366f7ec1
7 changed files with 279 additions and 17 deletions
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72
plugins/Mmap/fortran_mmap.c Normal file
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@ -0,0 +1,72 @@
#include <stdio.h>
#include <stdlib.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/mman.h>
void* mmap_fortran(char* filename, size_t bytes, int* file_descr, int read_only)
{
int i;
int fd;
int result;
void* map;
if (read_only == 1)
{
fd = open(filename, O_RDONLY, (mode_t)0600);
if (fd == -1) {
printf("%s:\n", filename);
perror("Error opening mmap file for reading");
exit(EXIT_FAILURE);
}
map = mmap(0, bytes, PROT_READ, MAP_SHARED, fd, 0);
}
else
{
fd = open(filename, O_RDWR | O_CREAT, (mode_t)0600);
if (fd == -1) {
printf("%s:\n", filename);
perror("Error opening mmap file for writing");
exit(EXIT_FAILURE);
}
result = lseek(fd, bytes, SEEK_SET);
if (result == -1) {
close(fd);
printf("%s:\n", filename);
perror("Error calling lseek() to stretch the file");
exit(EXIT_FAILURE);
}
result = write(fd, "", 1);
if (result != 1) {
close(fd);
printf("%s:\n", filename);
perror("Error writing last byte of the file");
exit(EXIT_FAILURE);
}
map = mmap(0, bytes, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
}
if (map == MAP_FAILED) {
close(fd);
printf("%s:\n", filename);
perror("Error mmapping the file");
exit(EXIT_FAILURE);
}
*file_descr = fd;
return map;
}
void munmap_fortran(size_t bytes, int fd, void* map)
{
if (munmap(map, bytes) == -1) {
perror("Error un-mmapping the file");
}
close(fd);
}

69
plugins/Mmap/mmap.f90 Normal file
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@ -0,0 +1,69 @@
module mmap_module
use iso_c_binding
interface
! File descriptors
! ----------------
type(c_ptr) function c_mmap_fortran(filename, length, fd, read_only) bind(c,name='mmap_fortran')
use iso_c_binding
character(c_char), intent(in) :: filename(*)
integer(c_size_t), intent(in), value :: length
integer(c_int), intent(out) :: fd
integer(c_int), intent(in), value :: read_only
end function
subroutine c_munmap(length, fd, map) bind(c,name='munmap_fortran')
use iso_c_binding
integer(c_size_t), intent(in), value :: length
integer(c_int), intent(in), value :: fd
type(c_ptr), intent(in), value :: map
end subroutine
end interface
contains
subroutine mmap(filename, shape, bytes, fd, read_only, map)
use iso_c_binding
implicit none
character*(*), intent(in) :: filename ! Name of the mapped file
integer*8, intent(in) :: shape(:) ! Shape of the array to map
integer, intent(in) :: bytes ! Number of bytes per element
logical, intent(in) :: read_only ! If true, mmap is read-only
integer, intent(out) :: fd ! File descriptor
type(c_ptr), intent(out) :: map ! C Pointer
integer(c_long) :: length
integer(c_int) :: fd_
length = PRODUCT( shape(:) ) * bytes
if (read_only) then
map = c_mmap_fortran( trim(filename)//char(0), length, fd_, 1)
else
map = c_mmap_fortran( trim(filename)//char(0), length, fd_, 0)
endif
fd = fd_
end subroutine
subroutine munmap(shape, bytes, fd, map)
use iso_c_binding
implicit none
integer*8, intent(in) :: shape(:) ! Shape of the array to map
integer, intent(in) :: bytes ! Number of bytes per element
integer, intent(in) :: fd ! File descriptor
type(c_ptr), intent(in) :: map ! C pointer
integer(c_long) :: length
integer(c_int) :: fd_
length = PRODUCT( shape(:) ) * bytes
fd_ = fd
call c_munmap( length, fd_, map)
end
end module mmap_module

3
src/Integrals_Bielec/NEEDED_CHILDREN_MODULES
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@ -1 +1,2 @@
Pseudo Bitmask ZMQ
Pseudo Bitmask ZMQ Mmap

7
src/Integrals_Bielec/ao_bi_integrals.irp.f
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@ -353,11 +353,10 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
if (read_ao_integrals) then
integer :: load_ao_integrals
print*,'Reading the AO integrals'
if (load_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin') == 0) then
call map_load_from_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
print*, 'AO integrals provided'
ao_bielec_integrals_in_map = .True.
return
endif
endif
print*, 'Providing the AO integrals'
@ -402,8 +401,10 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
print*, ' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
ao_bielec_integrals_in_map = .True.
if (write_ao_integrals) then
call dump_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin')
call ezfio_set_work_empty(.False.)
call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
call ezfio_set_integrals_bielec_disk_access_ao_integrals("Read")
endif

10
src/Integrals_Bielec/mo_bi_integrals.irp.f
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@ -30,10 +30,9 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ]
if (read_mo_integrals) then
integer :: load_mo_integrals
print*,'Reading the MO integrals'
if (load_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin') == 0) then
print*, 'MO integrals provided'
return
endif
call map_load_from_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
print*, 'MO integrals provided'
return
endif
call add_integrals_to_map(full_ijkl_bitmask_4)
@ -299,7 +298,8 @@ subroutine add_integrals_to_map(mask_ijkl)
print*,' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
if (write_mo_integrals) then
call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')
call ezfio_set_work_empty(.False.)
call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
call ezfio_set_integrals_bielec_disk_access_mo_integrals("Read")
endif

2
src/Utils/NEEDED_CHILDREN_MODULES
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@ -1 +1 @@
Mmap

133
src/Utils/map_module.f90
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@ -30,8 +30,8 @@ module map_module
integer*8, parameter :: map_mask = ibset(0_8,15)-1_8
type cache_map_type
integer(cache_key_kind), pointer :: key(:)
real(integral_kind), pointer :: value(:)
integer(cache_key_kind), pointer :: key(:)
logical :: sorted
integer(cache_map_size_kind) :: map_size
integer(cache_map_size_kind) :: n_elements
@ -39,10 +39,14 @@ module map_module
end type cache_map_type
type map_type
type(cache_map_type), allocatable :: map(:)
type(cache_map_type), pointer :: map(:)
real(integral_kind), pointer :: consolidated_value(:)
integer(cache_key_kind), pointer :: consolidated_key(:)
integer*8, pointer :: consolidated_idx(:)
logical :: sorted
logical :: consolidated
integer(map_size_kind) :: map_size
integer(map_size_kind) :: n_elements
logical :: sorted
integer(omp_lock_kind) :: lock
end type map_type
@ -92,6 +96,7 @@ subroutine map_init(map,keymax)
map%n_elements = 0_8
map%map_size = ishft(keymax,map_shift)
map%consolidated = .False.
allocate(map%map(0_8:map%map_size),stat=err)
if (err /= 0) then
@ -655,12 +660,10 @@ subroutine search_key_big_interval(key,X,sze,idx,ibegin_in,iend_in)
idx = ibegin
if (min(iend_in,sze) > ibegin+16) then
iend = ibegin+16
!DIR$ VECTOR ALIGNED
do while (cache_key > X(idx))
idx = idx+1
end do
else
!DIR$ VECTOR ALIGNED
do while (cache_key > X(idx))
idx = idx+1
if (idx /= iend) then
@ -768,13 +771,11 @@ subroutine search_key_value_big_interval(key,value,X,Y,sze,idx,ibegin_in,iend_in
value = Y(idx)
if (min(iend_in,sze) > ibegin+16) then
iend = ibegin+16
!DIR$ VECTOR ALIGNED
do while (cache_key > X(idx))
idx = idx+1
value = Y(idx)
end do
else
!DIR$ VECTOR ALIGNED
do while (cache_key > X(idx))
idx = idx+1
value = Y(idx)
@ -853,3 +854,121 @@ subroutine get_cache_map(map,map_idx,keys,values,n_elements)
enddo
end
subroutine map_save_to_disk(filename,map)
use map_module
use mmap_module
implicit none
character*(*), intent(in) :: filename
type(map_type), intent(inout) :: map
type(c_ptr) :: c_pointer(3)
integer :: fd(3)
integer*8 :: i,k
integer :: j
if (map % consolidated) then
stop 'map already consolidated'
endif
call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .False., c_pointer(1))
call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size +2_8/))
call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .False., c_pointer(2))
call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .False., c_pointer(3))
call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
if (.not.associated(map%consolidated_key)) then
stop 'cannot consolidate map : consolidated_key not associated'
endif
if (.not.associated(map%consolidated_value)) then
stop 'cannot consolidate map : consolidated_value not associated'
endif
if (.not.associated(map%consolidated_idx)) then
stop 'cannot consolidate map : consolidated_idx not associated'
endif
call map_sort(map)
k = 1_8
do i=0_8, map % map_size
map % consolidated_idx (i+1) = k
do j=1, map % map(i) % n_elements
map % consolidated_value(k) = map % map(i) % value(j)
map % consolidated_key (k) = map % map(i) % key(j)
k = k+1_8
enddo
deallocate(map % map(i) % value)
deallocate(map % map(i) % key)
map % map(i) % value => map % consolidated_value ( map % consolidated_idx (i+1) :)
map % map(i) % key => map % consolidated_key ( map % consolidated_idx (i+1) :)
enddo
map % consolidated_idx (map % map_size + 2_8) = k
map % consolidated = .True.
call munmap( (/ map % map_size + 2_8 /), 8, fd(1), c_pointer(1))
call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .True., c_pointer(1))
call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size +2_8/))
call munmap( (/ map % n_elements /), cache_key_kind, fd(2), c_pointer(2))
call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .True., c_pointer(2))
call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
call munmap( (/ map % n_elements /), integral_kind, fd(3), c_pointer(3))
call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .True., c_pointer(3))
call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
end
subroutine map_load_from_disk(filename,map)
use map_module
use mmap_module
implicit none
character*(*), intent(in) :: filename
type(map_type), intent(inout) :: map
type(c_ptr) :: c_pointer(3)
integer :: fd(3)
integer*8 :: i,k
integer :: n_elements
if (map % consolidated) then
stop 'map already consolidated'
endif
call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .True., c_pointer(1))
call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size + 2_8/))
map% n_elements = map % consolidated_idx (map % map_size+2_8)-1
call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .True., c_pointer(2))
call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .True., c_pointer(3))
call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
k = 1_8
do i=0_8, map % map_size
deallocate(map % map(i) % value)
deallocate(map % map(i) % key)
map % map(i) % value => map % consolidated_value ( map % consolidated_idx (i+1) :)
map % map(i) % key => map % consolidated_key ( map % consolidated_idx (i+1) :)
map % map(i) % sorted = .True.
n_elements = map % consolidated_idx (i+2) - k
k = map % consolidated_idx (i+2)
map % map(i) % map_size = n_elements
map % map(i) % n_elements = n_elements
enddo
map % n_elements = k-1
map % sorted = .True.
map % consolidated = .True.
end