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Cube I/O: Add input option to disable MPI I/O

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svn-origin-rev: 18601
This commit is contained in:
Holmberg Nico 2018-09-10 12:01:05 +00:00
parent b854a8527b
commit ff817ca511
8 changed files with 106 additions and 30 deletions
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37
src/cp_realspace_grid_cube.F
View file

@ -9,10 +9,12 @@
! **************************************************************************************************
MODULE cp_realspace_grid_cube
USE atomic_kind_types, ONLY: get_atomic_kind
USE cp_output_handling, ONLY: cp_mpi_io_get
USE kinds, ONLY: dp
USE particle_list_types, ONLY: particle_list_type
USE pw_types, ONLY: pw_type
USE realspace_grid_cube, ONLY: pw_to_cube,&
USE realspace_grid_cube, ONLY: cube_to_pw,&
pw_to_cube,&
pw_to_simple_volumetric
#include "./base/base_uses.f90"
@ -20,7 +22,7 @@ MODULE cp_realspace_grid_cube
PRIVATE
PUBLIC :: cp_pw_to_cube, cp_pw_to_simple_volumetric
PUBLIC :: cp_pw_to_cube, cp_pw_to_simple_volumetric, cp_cube_to_pw
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cp_realspace_grid_cube'
@ -94,4 +96,35 @@ CONTAINS
END SUBROUTINE cp_pw_to_simple_volumetric
! **************************************************************************************************
!> \brief Thin wrapper around routine cube_to_pw
!> \param grid pw to read from cube file
!> \param filename name of cube file
!> \param scaling scale values before storing
!> \par History
!> Created [Nico Holmberg] (09.2018)
! **************************************************************************************************
SUBROUTINE cp_cube_to_pw(grid, filename, scaling)
TYPE(pw_type), POINTER :: grid
CHARACTER(len=*), INTENT(in) :: filename
REAL(kind=dp), INTENT(in) :: scaling
CHARACTER(len=*), PARAMETER :: routineN = 'cp_cube_to_pw', routineP = moduleN//':'//routineN
LOGICAL :: parallel_read
! Determine whether to use MPI I/O for reading cube filename
parallel_read = .TRUE.
! Parallel routine falls back to stream read in serial mode,
! but it has slight overhead compared to sequential read
! Therefore, we use sequential version in serial mode
IF (grid%pw_grid%para%group_size == 1) parallel_read = .FALSE.
! Check if MPI I/O was disabled in GLOBAL section
IF (.NOT. cp_mpi_io_get()) parallel_read = .FALSE.
CALL cube_to_pw(grid, filename, scaling, parallel_read)
END SUBROUTINE cp_cube_to_pw
END MODULE cp_realspace_grid_cube

10
src/environment.F
View file

@ -31,7 +31,8 @@ MODULE environment
cp_add_default_logger, cp_get_default_logger, cp_logger_create, &
cp_logger_get_default_unit_nr, cp_logger_release, cp_logger_set, cp_logger_type, &
cp_rm_default_logger, cp_to_string
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
USE cp_output_handling, ONLY: cp_mpi_io_set,&
cp_print_key_finished_output,&
cp_print_key_unit_nr,&
debug_print_level,&
high_print_level,&
@ -496,7 +497,8 @@ CONTAINS
SReclaimable_avr, SReclaimable_max, SReclaimable_min
INTEGER, DIMENSION(:), POINTER :: i_force_eval
LOGICAL :: ata, do_echo_all_hosts, efl, explicit, &
report_maxloc, trace, trace_master
flag, report_maxloc, trace, &
trace_master
TYPE(cp_logger_type), POINTER :: logger
TYPE(enumeration_type), POINTER :: enum1, enum2
TYPE(keyword_type), POINTER :: keyword
@ -512,6 +514,8 @@ CONTAINS
CALL section_vals_val_get(global_section, "BLACS_GRID", i_val=globenv%blacs_grid_layout)
CALL section_vals_val_get(global_section, "BLACS_REPEATABLE", l_val=globenv%blacs_repeatable)
CALL section_vals_val_get(global_section, "PREFERRED_DIAG_LIBRARY", i_val=i_diag)
CALL section_vals_val_get(global_section, "ENABLE_MPI_IO", l_val=flag)
CALL cp_mpi_io_set(flag)
CALL section_vals_val_get(global_section, "ELPA_KERNEL", i_val=globenv%k_elpa)
CALL section_vals_val_get(global_section, "ELPA_QR", l_val=globenv%elpa_qr)
CALL section_vals_val_get(global_section, "ELPA_QR_UNSAFE", l_val=globenv%elpa_qr_unsafe)
@ -772,6 +776,8 @@ CONTAINS
WRITE (UNIT=output_unit, FMT="(T2,A,T75,A6)") &
start_section_label//"| Global print level", print_level_string
WRITE (UNIT=output_unit, FMT="(T2,A,T75,L6)") &
start_section_label//"| MPI I/O enabled", flag
WRITE (UNIT=output_unit, FMT="(T2,A,T75,I6)") &
start_section_label//"| Total number of message passing processes", &
para_env%num_pe, &

37
src/input/cp_output_handling.F
View file

@ -108,6 +108,11 @@ MODULE cp_output_handling
cp_out_store_each = IBSET(0, cp_p_store_each), &
cp_out_default = cp_out_file_if
! Flag determining if MPI I/O should be enabled for functions that support it
LOGICAL, PRIVATE, SAVE :: enable_mpi_io = .FALSE.
! Public functions to set/get the flags
PUBLIC :: cp_mpi_io_set, cp_mpi_io_get
! **************************************************************************************************
!> \brief stores the flags_env controlling the output of properties
!> \param ref_count reference count (see doc/ReferenceCounting.html)
@ -875,7 +880,7 @@ CONTAINS
IF (PRESENT(is_new_file)) is_new_file = .FALSE.
IF (PRESENT(mpi_io)) THEN
#if defined(__parallel)
IF (logger%para_env%num_pe > 1 .AND. mpi_io) THEN
IF (cp_mpi_io_get() .AND. logger%para_env%num_pe > 1 .AND. mpi_io) THEN
my_mpi_io = .TRUE.
ELSE
my_mpi_io = .FALSE.
@ -1083,5 +1088,35 @@ CONTAINS
unit_nr = -1
END SUBROUTINE cp_print_key_finished_output
! **************************************************************************************************
!> \brief Sets flag which determines whether or not to use MPI I/O for I/O routines that
!> have been parallized with MPI
!> \param flag ...
!> \par History
!> 09.2018 created [Nico Holmberg]
! **************************************************************************************************
SUBROUTINE cp_mpi_io_set(flag)
LOGICAL, INTENT(IN) :: flag
CHARACTER(len=*), PARAMETER :: routineN = 'cp_mpi_io_set', routineP = moduleN//':'//routineN
enable_mpi_io = flag
END SUBROUTINE cp_mpi_io_set
! **************************************************************************************************
!> \brief Gets flag which determines whether or not to use MPI I/O for I/O routines that
!> have been parallized with MPI
!> \return ...
!> \par History
!> 09.2018 created [Nico Holmberg]
! **************************************************************************************************
FUNCTION cp_mpi_io_get() RESULT(flag)
LOGICAL :: flag
CHARACTER(len=*), PARAMETER :: routineN = 'cp_mpi_io_get', routineP = moduleN//':'//routineN
flag = enable_mpi_io
END FUNCTION cp_mpi_io_get
END MODULE cp_output_handling

8
src/input_cp2k_global.F
View file

@ -351,6 +351,14 @@ CONTAINS
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, name="ENABLE_MPI_IO", &
description="Enable MPI parallelization for all supported I/O routines "// &
"Currently, only cube file writer/reader routines use MPI I/O. Disabling "// &
"this flag might speed up calculations dominated by I/O.", &
usage="ENABLE_MPI_IO FALSE", default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, name="TRACE", &
description="If a debug trace of the execution of the program should be written ", &
usage="TRACE", &

8
src/optimize_embedding_potential.F
View file

@ -36,7 +36,8 @@ MODULE optimize_embedding_potential
cp_print_key_should_output,&
cp_print_key_unit_nr
USE cp_para_types, ONLY: cp_para_env_type
USE cp_realspace_grid_cube, ONLY: cp_pw_to_cube,&
USE cp_realspace_grid_cube, ONLY: cp_cube_to_pw,&
cp_pw_to_cube,&
cp_pw_to_simple_volumetric
USE dbcsr_api, ONLY: dbcsr_p_type
USE embed_types, ONLY: opt_embed_pot_type
@ -93,7 +94,6 @@ MODULE optimize_embedding_potential
USE qs_neighbor_list_types, ONLY: neighbor_list_set_p_type
USE qs_subsys_types, ONLY: qs_subsys_get,&
qs_subsys_type
USE realspace_grid_cube, ONLY: cube_to_pw
#include "./base/base_uses.f90"
IMPLICIT NONE
@ -657,7 +657,7 @@ CONTAINS
CPABORT("Embedding cube file not found. ")
scaling_factor = 1.0_dp
CALL cube_to_pw(embed_pot%pw, filename, scaling_factor)
CALL cp_cube_to_pw(embed_pot%pw, filename, scaling_factor)
! Spin-dependent part of the potential
IF (open_shell_embed) THEN
@ -668,7 +668,7 @@ CONTAINS
CPABORT("Embedding spin cube file not found. ")
scaling_factor = 1.0_dp
CALL cube_to_pw(spin_embed_pot%pw, filename, scaling_factor)
CALL cp_cube_to_pw(spin_embed_pot%pw, filename, scaling_factor)
ENDIF
END SUBROUTINE read_embed_pot_cube

12
src/pw/realspace_grid_cube.F
View file

@ -220,15 +220,17 @@ CONTAINS
!> \param grid pw to read from cube file
!> \param filename name of cube file
!> \param scaling scale values before storing
!> \param parallel_read ...
!> \par History
!> Created [M.Watkins] (01.2014)
!> Use blocking, collective MPI read for parallel simulations [Nico Holmberg] (05.2017)
! **************************************************************************************************
SUBROUTINE cube_to_pw(grid, filename, scaling)
SUBROUTINE cube_to_pw(grid, filename, scaling, parallel_read)
TYPE(pw_type), POINTER :: grid
CHARACTER(len=*), INTENT(in) :: filename
REAL(kind=dp), INTENT(in) :: scaling
LOGICAL, INTENT(in) :: parallel_read
CHARACTER(len=*), PARAMETER :: routineN = 'cube_to_pw', routineP = moduleN//':'//routineN
INTEGER, PARAMETER :: entry_len = 13, num_entries_line = 6
@ -239,7 +241,6 @@ CONTAINS
size_of_z, tag
INTEGER, DIMENSION(3) :: lbounds, lbounds_local, npoints, &
npoints_local, ubounds, ubounds_local
LOGICAL :: parallel_read
REAL(kind=dp), ALLOCATABLE, DIMENSION(:) :: buffer
REAL(kind=dp), DIMENSION(3) :: dr, rdum
@ -247,19 +248,12 @@ CONTAINS
CALL timeset(routineN, handle)
parallel_read = .TRUE.
!get rs grids and parallel envnment
gid = grid%pw_grid%para%group
my_rank = grid%pw_grid%para%my_pos
num_pe = grid%pw_grid%para%group_size
tag = 1
! Parallel routine falls back to stream read in serial mode,
! but it has slight overhead compared to sequential read
! Therefore, we use sequential version in serial mode
IF (num_pe == 1) parallel_read = .FALSE.
lbounds_local = grid%pw_grid%bounds_local(1, :)
ubounds_local = grid%pw_grid%bounds_local(2, :)
size_of_z = ubounds_local(3)-lbounds_local(3)+1

20
src/qs_cdft_methods.F
View file

@ -21,7 +21,8 @@ MODULE qs_cdft_methods
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
cp_print_key_unit_nr
USE cp_para_types, ONLY: cp_para_env_type
USE cp_realspace_grid_cube, ONLY: cp_pw_to_cube
USE cp_realspace_grid_cube, ONLY: cp_cube_to_pw,&
cp_pw_to_cube
USE cube_utils, ONLY: cube_info_type
USE hirshfeld_methods, ONLY: create_shape_function
USE hirshfeld_types, ONLY: get_hirshfeld_info,&
@ -76,7 +77,6 @@ MODULE qs_cdft_methods
qs_rho_type
USE qs_subsys_types, ONLY: qs_subsys_get,&
qs_subsys_type
USE realspace_grid_cube, ONLY: cube_to_pw
USE realspace_grid_types, ONLY: &
pw2rs, realspace_grid_desc_type, realspace_grid_type, rs2pw, rs_grid_create, &
rs_grid_release, rs_grid_retain, rs_grid_zero, rs_pw_transfer
@ -923,22 +923,22 @@ CONTAINS
! Total density (rho_alpha + rho_beta)
CALL pw_pool_create_pw(auxbas_pw_pool, becke_control%fragments(1, 1)%pw, &
use_data=REALDATA3D, in_space=REALSPACE)
CALL cube_to_pw(becke_control%fragments(1, 1)%pw, &
becke_control%fragment_a_fname, 1.0_dp)
CALL cp_cube_to_pw(becke_control%fragments(1, 1)%pw, &
becke_control%fragment_a_fname, 1.0_dp)
CALL pw_pool_create_pw(auxbas_pw_pool, becke_control%fragments(1, 2)%pw, &
use_data=REALDATA3D, in_space=REALSPACE)
CALL cube_to_pw(becke_control%fragments(1, 2)%pw, &
becke_control%fragment_b_fname, 1.0_dp)
CALL cp_cube_to_pw(becke_control%fragments(1, 2)%pw, &
becke_control%fragment_b_fname, 1.0_dp)
! Spin difference density (rho_alpha - rho_beta) if needed
IF (needs_spin_density) THEN
CALL pw_pool_create_pw(auxbas_pw_pool, becke_control%fragments(2, 1)%pw, &
use_data=REALDATA3D, in_space=REALSPACE)
CALL cube_to_pw(becke_control%fragments(2, 1)%pw, &
becke_control%fragment_a_spin_fname, multiplier(1))
CALL cp_cube_to_pw(becke_control%fragments(2, 1)%pw, &
becke_control%fragment_a_spin_fname, multiplier(1))
CALL pw_pool_create_pw(auxbas_pw_pool, becke_control%fragments(2, 2)%pw, &
use_data=REALDATA3D, in_space=REALSPACE)
CALL cube_to_pw(becke_control%fragments(2, 2)%pw, &
becke_control%fragment_b_spin_fname, multiplier(2))
CALL cp_cube_to_pw(becke_control%fragments(2, 2)%pw, &
becke_control%fragment_b_spin_fname, multiplier(2))
END IF
! Sum up fragments
DO i = 1, nfrag_spins

4
src/qs_external_potential.F
View file

@ -14,6 +14,7 @@ MODULE qs_external_potential
pbc
USE cp_control_types, ONLY: dft_control_type
USE cp_log_handling, ONLY: cp_to_string
USE cp_realspace_grid_cube, ONLY: cp_cube_to_pw
USE force_fields_util, ONLY: get_generic_info
USE fparser, ONLY: evalf,&
evalfd,&
@ -37,7 +38,6 @@ MODULE qs_external_potential
USE qs_force_types, ONLY: qs_force_type
USE qs_kind_types, ONLY: get_qs_kind,&
qs_kind_type
USE realspace_grid_cube, ONLY: cube_to_pw
USE string_utilities, ONLY: compress
#include "./base/base_uses.f90"
@ -89,7 +89,7 @@ CONTAINS
IF ((.NOT. static_potential) .OR. dft_control%eval_external_potential) THEN
IF (read_from_cube) THEN
CALL section_vals_val_get(ext_pot_section, "SCALING_FACTOR", r_val=scaling_factor)
CALL cube_to_pw(v_ee%pw, 'pot.cube', scaling_factor)
CALL cp_cube_to_pw(v_ee%pw, 'pot.cube', scaling_factor)
dft_control%eval_external_potential = .FALSE.
ELSE
dr = v_ee%pw%pw_grid%dr