mirror of
https://github.com/LCPQ/quantum_package
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mmap works for integrals
This commit is contained in:
parent
20ad57e8c6
commit
39366f7ec1
72
plugins/Mmap/fortran_mmap.c
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72
plugins/Mmap/fortran_mmap.c
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@ -0,0 +1,72 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <sys/types.h>
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#include <sys/stat.h>
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#include <unistd.h>
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#include <fcntl.h>
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#include <sys/mman.h>
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void* mmap_fortran(char* filename, size_t bytes, int* file_descr, int read_only)
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{
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int i;
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int fd;
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int result;
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void* map;
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if (read_only == 1)
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{
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fd = open(filename, O_RDONLY, (mode_t)0600);
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if (fd == -1) {
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printf("%s:\n", filename);
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perror("Error opening mmap file for reading");
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exit(EXIT_FAILURE);
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}
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map = mmap(0, bytes, PROT_READ, MAP_SHARED, fd, 0);
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}
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else
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{
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fd = open(filename, O_RDWR | O_CREAT, (mode_t)0600);
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if (fd == -1) {
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printf("%s:\n", filename);
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perror("Error opening mmap file for writing");
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exit(EXIT_FAILURE);
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}
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result = lseek(fd, bytes, SEEK_SET);
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if (result == -1) {
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close(fd);
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printf("%s:\n", filename);
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perror("Error calling lseek() to stretch the file");
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exit(EXIT_FAILURE);
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}
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result = write(fd, "", 1);
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if (result != 1) {
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close(fd);
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printf("%s:\n", filename);
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perror("Error writing last byte of the file");
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exit(EXIT_FAILURE);
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}
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map = mmap(0, bytes, PROT_READ | PROT_WRITE, MAP_SHARED, fd, 0);
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}
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if (map == MAP_FAILED) {
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close(fd);
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printf("%s:\n", filename);
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perror("Error mmapping the file");
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exit(EXIT_FAILURE);
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}
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*file_descr = fd;
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return map;
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}
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void munmap_fortran(size_t bytes, int fd, void* map)
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{
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if (munmap(map, bytes) == -1) {
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perror("Error un-mmapping the file");
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}
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close(fd);
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}
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69
plugins/Mmap/mmap.f90
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69
plugins/Mmap/mmap.f90
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@ -0,0 +1,69 @@
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module mmap_module
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use iso_c_binding
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interface
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! File descriptors
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! ----------------
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type(c_ptr) function c_mmap_fortran(filename, length, fd, read_only) bind(c,name='mmap_fortran')
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use iso_c_binding
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character(c_char), intent(in) :: filename(*)
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integer(c_size_t), intent(in), value :: length
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integer(c_int), intent(out) :: fd
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integer(c_int), intent(in), value :: read_only
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end function
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subroutine c_munmap(length, fd, map) bind(c,name='munmap_fortran')
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use iso_c_binding
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integer(c_size_t), intent(in), value :: length
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integer(c_int), intent(in), value :: fd
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type(c_ptr), intent(in), value :: map
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end subroutine
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end interface
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contains
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subroutine mmap(filename, shape, bytes, fd, read_only, map)
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use iso_c_binding
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implicit none
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character*(*), intent(in) :: filename ! Name of the mapped file
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integer*8, intent(in) :: shape(:) ! Shape of the array to map
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integer, intent(in) :: bytes ! Number of bytes per element
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logical, intent(in) :: read_only ! If true, mmap is read-only
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integer, intent(out) :: fd ! File descriptor
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type(c_ptr), intent(out) :: map ! C Pointer
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integer(c_long) :: length
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integer(c_int) :: fd_
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length = PRODUCT( shape(:) ) * bytes
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if (read_only) then
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map = c_mmap_fortran( trim(filename)//char(0), length, fd_, 1)
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else
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map = c_mmap_fortran( trim(filename)//char(0), length, fd_, 0)
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endif
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fd = fd_
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end subroutine
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subroutine munmap(shape, bytes, fd, map)
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use iso_c_binding
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implicit none
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integer*8, intent(in) :: shape(:) ! Shape of the array to map
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integer, intent(in) :: bytes ! Number of bytes per element
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integer, intent(in) :: fd ! File descriptor
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type(c_ptr), intent(in) :: map ! C pointer
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integer(c_long) :: length
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integer(c_int) :: fd_
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length = PRODUCT( shape(:) ) * bytes
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fd_ = fd
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call c_munmap( length, fd_, map)
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end
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end module mmap_module
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@ -1 +1,2 @@
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Pseudo Bitmask ZMQ
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Pseudo Bitmask ZMQ Mmap
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@ -353,11 +353,10 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
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if (read_ao_integrals) then
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integer :: load_ao_integrals
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print*,'Reading the AO integrals'
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if (load_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin') == 0) then
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call map_load_from_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
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print*, 'AO integrals provided'
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ao_bielec_integrals_in_map = .True.
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return
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endif
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endif
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print*, 'Providing the AO integrals'
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@ -402,8 +401,10 @@ BEGIN_PROVIDER [ logical, ao_bielec_integrals_in_map ]
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print*, ' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1+tiny(1.d0)), ' )'
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ao_bielec_integrals_in_map = .True.
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if (write_ao_integrals) then
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call dump_ao_integrals(trim(ezfio_filename)//'/work/ao_integrals.bin')
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call ezfio_set_work_empty(.False.)
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call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
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call ezfio_set_integrals_bielec_disk_access_ao_integrals("Read")
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endif
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@ -30,10 +30,9 @@ BEGIN_PROVIDER [ logical, mo_bielec_integrals_in_map ]
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if (read_mo_integrals) then
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integer :: load_mo_integrals
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print*,'Reading the MO integrals'
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if (load_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin') == 0) then
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print*, 'MO integrals provided'
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return
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endif
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call map_load_from_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
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print*, 'MO integrals provided'
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return
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endif
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call add_integrals_to_map(full_ijkl_bitmask_4)
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@ -299,7 +298,8 @@ subroutine add_integrals_to_map(mask_ijkl)
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print*,' wall time :',wall_2 - wall_1, 's ( x ', (cpu_2-cpu_1)/(wall_2-wall_1), ')'
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if (write_mo_integrals) then
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call dump_mo_integrals(trim(ezfio_filename)//'/work/mo_integrals.bin')
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call ezfio_set_work_empty(.False.)
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call map_save_to_disk(trim(ezfio_filename)//'/work/mo_ints',mo_integrals_map)
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call ezfio_set_integrals_bielec_disk_access_mo_integrals("Read")
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endif
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@ -1 +1 @@
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Mmap
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@ -30,8 +30,8 @@ module map_module
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integer*8, parameter :: map_mask = ibset(0_8,15)-1_8
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type cache_map_type
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integer(cache_key_kind), pointer :: key(:)
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real(integral_kind), pointer :: value(:)
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integer(cache_key_kind), pointer :: key(:)
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logical :: sorted
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integer(cache_map_size_kind) :: map_size
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integer(cache_map_size_kind) :: n_elements
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@ -39,10 +39,14 @@ module map_module
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end type cache_map_type
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type map_type
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type(cache_map_type), allocatable :: map(:)
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type(cache_map_type), pointer :: map(:)
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real(integral_kind), pointer :: consolidated_value(:)
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integer(cache_key_kind), pointer :: consolidated_key(:)
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integer*8, pointer :: consolidated_idx(:)
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logical :: sorted
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logical :: consolidated
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integer(map_size_kind) :: map_size
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integer(map_size_kind) :: n_elements
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logical :: sorted
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integer(omp_lock_kind) :: lock
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end type map_type
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@ -92,6 +96,7 @@ subroutine map_init(map,keymax)
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map%n_elements = 0_8
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map%map_size = ishft(keymax,map_shift)
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map%consolidated = .False.
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allocate(map%map(0_8:map%map_size),stat=err)
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if (err /= 0) then
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@ -655,12 +660,10 @@ subroutine search_key_big_interval(key,X,sze,idx,ibegin_in,iend_in)
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idx = ibegin
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if (min(iend_in,sze) > ibegin+16) then
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iend = ibegin+16
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!DIR$ VECTOR ALIGNED
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do while (cache_key > X(idx))
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idx = idx+1
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end do
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else
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!DIR$ VECTOR ALIGNED
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do while (cache_key > X(idx))
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idx = idx+1
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if (idx /= iend) then
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@ -768,13 +771,11 @@ subroutine search_key_value_big_interval(key,value,X,Y,sze,idx,ibegin_in,iend_in
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value = Y(idx)
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if (min(iend_in,sze) > ibegin+16) then
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iend = ibegin+16
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!DIR$ VECTOR ALIGNED
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do while (cache_key > X(idx))
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idx = idx+1
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value = Y(idx)
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end do
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else
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!DIR$ VECTOR ALIGNED
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do while (cache_key > X(idx))
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idx = idx+1
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value = Y(idx)
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@ -853,3 +854,121 @@ subroutine get_cache_map(map,map_idx,keys,values,n_elements)
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enddo
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end
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subroutine map_save_to_disk(filename,map)
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use map_module
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use mmap_module
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implicit none
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character*(*), intent(in) :: filename
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type(map_type), intent(inout) :: map
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type(c_ptr) :: c_pointer(3)
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integer :: fd(3)
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integer*8 :: i,k
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integer :: j
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if (map % consolidated) then
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stop 'map already consolidated'
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endif
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call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .False., c_pointer(1))
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call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size +2_8/))
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call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .False., c_pointer(2))
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call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
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call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .False., c_pointer(3))
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call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
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if (.not.associated(map%consolidated_key)) then
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stop 'cannot consolidate map : consolidated_key not associated'
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endif
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if (.not.associated(map%consolidated_value)) then
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stop 'cannot consolidate map : consolidated_value not associated'
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endif
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if (.not.associated(map%consolidated_idx)) then
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stop 'cannot consolidate map : consolidated_idx not associated'
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endif
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call map_sort(map)
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k = 1_8
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do i=0_8, map % map_size
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map % consolidated_idx (i+1) = k
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do j=1, map % map(i) % n_elements
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map % consolidated_value(k) = map % map(i) % value(j)
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map % consolidated_key (k) = map % map(i) % key(j)
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k = k+1_8
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enddo
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deallocate(map % map(i) % value)
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deallocate(map % map(i) % key)
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map % map(i) % value => map % consolidated_value ( map % consolidated_idx (i+1) :)
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map % map(i) % key => map % consolidated_key ( map % consolidated_idx (i+1) :)
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enddo
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map % consolidated_idx (map % map_size + 2_8) = k
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map % consolidated = .True.
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call munmap( (/ map % map_size + 2_8 /), 8, fd(1), c_pointer(1))
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call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .True., c_pointer(1))
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call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size +2_8/))
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call munmap( (/ map % n_elements /), cache_key_kind, fd(2), c_pointer(2))
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call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .True., c_pointer(2))
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call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
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call munmap( (/ map % n_elements /), integral_kind, fd(3), c_pointer(3))
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call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .True., c_pointer(3))
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call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
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end
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subroutine map_load_from_disk(filename,map)
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use map_module
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use mmap_module
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implicit none
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character*(*), intent(in) :: filename
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type(map_type), intent(inout) :: map
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type(c_ptr) :: c_pointer(3)
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integer :: fd(3)
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integer*8 :: i,k
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integer :: n_elements
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if (map % consolidated) then
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stop 'map already consolidated'
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endif
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call mmap(trim(filename)//'_consolidated_idx', (/ map % map_size + 2_8 /), 8, fd(1), .True., c_pointer(1))
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call c_f_pointer(c_pointer(1),map % consolidated_idx, (/ map % map_size + 2_8/))
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map% n_elements = map % consolidated_idx (map % map_size+2_8)-1
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call mmap(trim(filename)//'_consolidated_key', (/ map % n_elements /), cache_key_kind, fd(2), .True., c_pointer(2))
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call c_f_pointer(c_pointer(2),map % consolidated_key, (/ map % n_elements /))
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call mmap(trim(filename)//'_consolidated_value', (/ map % n_elements /), integral_kind, fd(3), .True., c_pointer(3))
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call c_f_pointer(c_pointer(3),map % consolidated_value, (/ map % n_elements /))
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k = 1_8
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do i=0_8, map % map_size
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deallocate(map % map(i) % value)
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deallocate(map % map(i) % key)
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map % map(i) % value => map % consolidated_value ( map % consolidated_idx (i+1) :)
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map % map(i) % key => map % consolidated_key ( map % consolidated_idx (i+1) :)
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map % map(i) % sorted = .True.
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n_elements = map % consolidated_idx (i+2) - k
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k = map % consolidated_idx (i+2)
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map % map(i) % map_size = n_elements
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map % map(i) % n_elements = n_elements
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enddo
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map % n_elements = k-1
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map % sorted = .True.
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map % consolidated = .True.
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end
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