From de7396536285e1329a4f9d74005645f0978661d5 Mon Sep 17 00:00:00 2001 From: Ed Hartnett Date: Sat, 8 Jun 2019 05:44:12 -0600 Subject: [PATCH 1/2] fixed problem attempting to remove docs directory --- Makefile.am | 2 +- src/clib/pio.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile.am b/Makefile.am index e8ee3b0568d..8a3c509509b 100644 --- a/Makefile.am +++ b/Makefile.am @@ -14,4 +14,4 @@ SUBDIRS = src tests examples ${DOC} scripts EXTRA_DIST = CMakeLists.txt set_flags.am COPYRIGHT -CLEANFILES = docs/* docs +CLEANFILES = docs/* diff --git a/src/clib/pio.h b/src/clib/pio.h index bdde365025f..69e2a7fde81 100644 --- a/src/clib/pio.h +++ b/src/clib/pio.h @@ -4,7 +4,7 @@ * @author Jim Edwards * @date 2014 * - * @see http://code.google.com/p/parallelio/ + * @see https://github.com/NCAR/ParallelIO */ #ifndef _PIO_H_ From 31a3ca06053ab05b5d30ef6e17951b702ac1bf6b Mon Sep 17 00:00:00 2001 From: Ed Hartnett Date: Sat, 8 Jun 2019 05:45:04 -0600 Subject: [PATCH 2/2] whitespace cleanup --- src/flib/pio_types.F90 | 384 ++++++++++++++++++++--------------------- 1 file changed, 192 insertions(+), 192 deletions(-) diff --git a/src/flib/pio_types.F90 b/src/flib/pio_types.F90 index 2519844d8dc..b0bd4e05718 100644 --- a/src/flib/pio_types.F90 +++ b/src/flib/pio_types.F90 @@ -42,99 +42,99 @@ !< module pio_types - use pio_kinds - use iso_c_binding - implicit none - private - !------------------------------------------- - ! data structure to describe decomposition - !------------------------------------------- - type, public :: DecompMap_t + use pio_kinds + use iso_c_binding + implicit none + private + !------------------------------------------- + ! data structure to describe decomposition + !------------------------------------------- + type, public :: DecompMap_t #ifdef SEQUENCE - sequence + sequence #endif - integer(i4) :: start !< start - integer(i4) :: length !< length - end type + integer(i4) :: start !< start + integer(i4) :: length !< length + end type DecompMap_t - !------------------------------------ - ! a file descriptor data structure - !------------------------------------ -!> -!! @struct iosystem_desc_t -!! @brief A defined PIO system descriptor created by @ref PIO_init (see pio_types) -!< - type, public :: IOSystem_desc_t - integer(kind=c_int) :: iosysid = -1 !< iosysid - end type IOSystem_desc_t + !------------------------------------ + ! a file descriptor data structure + !------------------------------------ + !> + !! @struct iosystem_desc_t + !! @brief A defined PIO system descriptor created by @ref PIO_init (see pio_types) + !< + type, public :: IOSystem_desc_t + integer(kind=c_int) :: iosysid = -1 !< iosysid + end type IOSystem_desc_t -!> -!! @private -!! @struct io_data_list -!! @brief Linked list of buffers for pnetcdf non-blocking interface -!> -! type, public :: io_data_list -! integer :: request -! real(r4), pointer :: data_real(:) => null() -! integer(i4), pointer :: data_int(:) => null() -! real(r8), pointer :: data_double(:) => null() -! type(io_data_list), pointer :: next => null() -! end type io_data_list + !> + !! @private + !! @struct io_data_list + !! @brief Linked list of buffers for pnetcdf non-blocking interface + !> + ! type, public :: io_data_list + ! integer :: request + ! real(r4), pointer :: data_real(:) => null() + ! integer(i4), pointer :: data_int(:) => null() + ! real(r8), pointer :: data_double(:) => null() + ! type(io_data_list), pointer :: next => null() + ! end type io_data_list -!> -!! @public -!! @struct file_desc_t -!! @brief File descriptor returned by \ref PIO_openfile or \ref PIO_createfile (see pio_types) -!! -!> - type, public :: File_desc_t - integer(kind=c_int) :: fh !< file handle - type(iosystem_desc_t), pointer :: iosystem => null() !< iosystem - end type File_desc_t + !> + !! @public + !! @struct file_desc_t + !! @brief File descriptor returned by \ref PIO_openfile or \ref PIO_createfile (see pio_types) + !! + !> + type, public :: File_desc_t + integer(kind=c_int) :: fh !< file handle + type(iosystem_desc_t), pointer :: iosystem => null() !< iosystem + end type File_desc_t -!> -!! @public -!! @struct io_desc_t -!! @brief An io descriptor handle that is generated in @ref PIO_initdecomp -!! (see pio_types) -!< - type, public :: io_desc_t + !> + !! @public + !! @struct io_desc_t + !! @brief An io descriptor handle that is generated in @ref PIO_initdecomp + !! (see pio_types) + !< + type, public :: io_desc_t #ifdef SEQUENCE - sequence + sequence #endif - integer(i4) :: ioid !< decomposition id - end type + integer(i4) :: ioid !< decomposition id + end type io_desc_t -!> -!! @public -!! @struct var_desc_t -!! @brief A variable descriptor returned from @ref PIO_def_var (see pio_types) -!< - type, public :: Var_desc_t + !> + !! @public + !! @struct var_desc_t + !! @brief A variable descriptor returned from @ref PIO_def_var (see pio_types) + !< + type, public :: Var_desc_t #ifdef SEQUENCE - sequence + sequence #endif - integer(i4) :: varID !< variable id - integer(i4) :: ncid !< file id - end type Var_desc_t + integer(i4) :: varID !< variable id + integer(i4) :: ncid !< file id + end type Var_desc_t - integer(i4), public, parameter :: & - PIO_iotype_pnetcdf = 1, & !< parallel read/write of pNetCDF files - PIO_iotype_netcdf = 2, & !< serial read/write of NetCDF file using 'base_node' - PIO_iotype_netcdf4c = 3, & !< netcdf4 (hdf5 format) file opened for compression (serial write access only) - PIO_iotype_netcdf4p = 4 !< netcdf4 (hdf5 format) file opened in parallel (all netcdf4 files for read will be opened this way) + integer(i4), public, parameter :: & + PIO_iotype_pnetcdf = 1, & !< parallel read/write of pNetCDF files + PIO_iotype_netcdf = 2, & !< serial read/write of NetCDF file using 'base_node' + PIO_iotype_netcdf4c = 3, & !< netcdf4 (hdf5 format) file opened for compression (serial write access only) + PIO_iotype_netcdf4p = 4 !< netcdf4 (hdf5 format) file opened in parallel (all netcdf4 files for read will be opened this way) -! These are for backward compatability and should not be used or expanded upon - integer(i4), public, parameter :: & - iotype_pnetcdf = PIO_iotype_pnetcdf, & !< pnetcdf iotype - iotype_netcdf = PIO_iotype_netcdf !< netcdf iotype + ! These are for backward compatability and should not be used or expanded upon + integer(i4), public, parameter :: & + iotype_pnetcdf = PIO_iotype_pnetcdf, & !< pnetcdf iotype + iotype_netcdf = PIO_iotype_netcdf !< netcdf iotype - integer(i4), public, parameter :: PIO_rearr_box = 1 !< box rearranger - integer(i4), public, parameter :: PIO_rearr_subset = 2 !< subset rearranger + integer(i4), public, parameter :: PIO_rearr_box = 1 !< box rearranger + integer(i4), public, parameter :: PIO_rearr_subset = 2 !< subset rearranger integer(i4), public, parameter :: PIO_INTERNAL_ERROR = -51 !< abort on error from any task integer(i4), public, parameter :: PIO_BCAST_ERROR = -52 !< broadcast an error @@ -142,137 +142,137 @@ module pio_types integer(i4), public, parameter :: PIO_DEFAULT = -1 !< default error handler -!> -!! @struct use_PIO_kinds -!! @brief The type of variable(s) associated with this iodesc. -!! @copydoc PIO_kinds -!< + !> + !! @struct use_PIO_kinds + !! @brief The type of variable(s) associated with this iodesc. + !! @copydoc PIO_kinds + !< #ifdef _PNETCDF #include /* _EXTERNAL */ - integer, public, parameter :: PIO_global = nf_global !< global atts - integer, public, parameter :: PIO_unlimited = nf_unlimited !< unlimited dimension - integer, public, parameter :: PIO_double = nf_double !< double type - integer, public, parameter :: PIO_real = nf_real !< real type - integer, public, parameter :: PIO_int = nf_int !< int type - integer, public, parameter :: PIO_char = nf_char !< char type - integer, public, parameter :: PIO_noerr = nf_noerr !< no error - integer, public, parameter :: PIO_WRITE = nf_write !< read-write - integer, public, parameter :: PIO_nowrite = nf_nowrite !< read-only - integer, public, parameter :: PIO_CLOBBER = nf_clobber !< clobber existing file - integer, public, parameter :: PIO_NOCLOBBER = nf_NOclobber !< do not clobber existing file - integer, public, parameter :: PIO_NOFILL = nf_nofill !< do not use fill values - integer, public, parameter :: PIO_MAX_NAME = nf_max_name !< max name len - integer, public, parameter :: PIO_MAX_VAR_DIMS = min(6,nf_max_var_dims) !< max dims for a var - integer, public, parameter :: PIO_64BIT_OFFSET = nf_64bit_offset !< 64bit offset format - integer, public, parameter :: PIO_64BIT_DATA = nf_64bit_data !< CDF5 format - integer, public, parameter :: PIO_FILL_INT = nf_fill_int; !< int fill value - real, public, parameter :: PIO_FILL_FLOAT = nf_fill_float; !< float fill value - double precision, public, parameter :: PIO_FILL_DOUBLE = nf_fill_double; !< double fill value + integer, public, parameter :: PIO_global = nf_global !< global atts + integer, public, parameter :: PIO_unlimited = nf_unlimited !< unlimited dimension + integer, public, parameter :: PIO_double = nf_double !< double type + integer, public, parameter :: PIO_real = nf_real !< real type + integer, public, parameter :: PIO_int = nf_int !< int type + integer, public, parameter :: PIO_char = nf_char !< char type + integer, public, parameter :: PIO_noerr = nf_noerr !< no error + integer, public, parameter :: PIO_WRITE = nf_write !< read-write + integer, public, parameter :: PIO_nowrite = nf_nowrite !< read-only + integer, public, parameter :: PIO_CLOBBER = nf_clobber !< clobber existing file + integer, public, parameter :: PIO_NOCLOBBER = nf_NOclobber !< do not clobber existing file + integer, public, parameter :: PIO_NOFILL = nf_nofill !< do not use fill values + integer, public, parameter :: PIO_MAX_NAME = nf_max_name !< max name len + integer, public, parameter :: PIO_MAX_VAR_DIMS = min(6,nf_max_var_dims) !< max dims for a var + integer, public, parameter :: PIO_64BIT_OFFSET = nf_64bit_offset !< 64bit offset format + integer, public, parameter :: PIO_64BIT_DATA = nf_64bit_data !< CDF5 format + integer, public, parameter :: PIO_FILL_INT = nf_fill_int; !< int fill value + real, public, parameter :: PIO_FILL_FLOAT = nf_fill_float; !< float fill value + double precision, public, parameter :: PIO_FILL_DOUBLE = nf_fill_double; !< double fill value #else #ifdef _NETCDF #include /* _EXTERNAL */ - integer, public, parameter :: PIO_global = nf_global !< global atts - integer, public, parameter :: PIO_unlimited = nf_unlimited !< unlimited dimension - integer, public, parameter :: PIO_double = nf_double !< double type - integer, public, parameter :: PIO_real = nf_real !< real type - integer, public, parameter :: PIO_int = nf_int !< int type - integer, public, parameter :: PIO_char = nf_char !< char type - integer, public, parameter :: PIO_noerr = nf_noerr !< no error - integer, public, parameter :: PIO_WRITE = nf_write !< read-write - integer, public, parameter :: PIO_nowrite = nf_nowrite !< read-only - integer, public, parameter :: PIO_CLOBBER = nf_clobber !< clobber existing file - integer, public, parameter :: PIO_NOCLOBBER = nf_NOclobber !< do not clobber existing file - integer, public, parameter :: PIO_NOFILL = nf_nofill !< do not use fill values - integer, public, parameter :: PIO_MAX_NAME = nf_max_name !< max name len - integer, public, parameter :: PIO_MAX_VAR_DIMS = min(6,nf_max_var_dims) !< max dims for a var - integer, public, parameter :: PIO_64BIT_OFFSET = nf_64bit_offset !< 64bit offset format - integer, public, parameter :: PIO_64BIT_DATA = 0 !< CDF5 format - integer, public, parameter :: PIO_FILL_INT = nf_fill_int; !< int fill value - real, public, parameter :: PIO_FILL_FLOAT = nf_fill_float; !< float fill value - double precision, public, parameter :: PIO_FILL_DOUBLE = nf_fill_double; !< double fill value + integer, public, parameter :: PIO_global = nf_global !< global atts + integer, public, parameter :: PIO_unlimited = nf_unlimited !< unlimited dimension + integer, public, parameter :: PIO_double = nf_double !< double type + integer, public, parameter :: PIO_real = nf_real !< real type + integer, public, parameter :: PIO_int = nf_int !< int type + integer, public, parameter :: PIO_char = nf_char !< char type + integer, public, parameter :: PIO_noerr = nf_noerr !< no error + integer, public, parameter :: PIO_WRITE = nf_write !< read-write + integer, public, parameter :: PIO_nowrite = nf_nowrite !< read-only + integer, public, parameter :: PIO_CLOBBER = nf_clobber !< clobber existing file + integer, public, parameter :: PIO_NOCLOBBER = nf_NOclobber !< do not clobber existing file + integer, public, parameter :: PIO_NOFILL = nf_nofill !< do not use fill values + integer, public, parameter :: PIO_MAX_NAME = nf_max_name !< max name len + integer, public, parameter :: PIO_MAX_VAR_DIMS = min(6,nf_max_var_dims) !< max dims for a var + integer, public, parameter :: PIO_64BIT_OFFSET = nf_64bit_offset !< 64bit offset format + integer, public, parameter :: PIO_64BIT_DATA = 0 !< CDF5 format + integer, public, parameter :: PIO_FILL_INT = nf_fill_int; !< int fill value + real, public, parameter :: PIO_FILL_FLOAT = nf_fill_float; !< float fill value + double precision, public, parameter :: PIO_FILL_DOUBLE = nf_fill_double; !< double fill value #else - integer, public, parameter :: PIO_global = 0 !< global atts - integer, public, parameter :: PIO_double = 6 !< double type - integer, public, parameter :: PIO_real = 5 !< real type - integer, public, parameter :: PIO_int = 4 !< int type - integer, public, parameter :: PIO_char = 2 !< char type - integer, public, parameter :: PIO_noerr = 0 !< no error - integer, public, parameter :: PIO_MAX_NAME = 25 !< max name len - integer, public, parameter :: PIO_MAX_VAR_DIMS = 6 !< max dims for a var - integer, public, parameter :: PIO_CLOBBER = 10 !< clobber existing file - integer, public, parameter :: PIO_NOCLOBBER = 11 !< do not clobber existing file - integer, public, parameter :: PIO_WRITE = 20 !< read-write - integer, public, parameter :: PIO_NOWRITE = 21 !< read-only - integer, public, parameter :: PIO_64BIT_OFFSET = 0 !< 64bit offset format - integer, public, parameter :: PIO_64BIT_DATA = 0 !< CDF5 format - integer, public, parameter :: PIO_FILL_INT = -2147483647; !< int fill value - real, public, parameter :: PIO_FILL_FLOAT = 9.9692099683868690e+36; !< float fill value - double precision, public, parameter :: PIO_FILL_DOUBLE = 9.9692099683868690e+36; !< double fill value + integer, public, parameter :: PIO_global = 0 !< global atts + integer, public, parameter :: PIO_double = 6 !< double type + integer, public, parameter :: PIO_real = 5 !< real type + integer, public, parameter :: PIO_int = 4 !< int type + integer, public, parameter :: PIO_char = 2 !< char type + integer, public, parameter :: PIO_noerr = 0 !< no error + integer, public, parameter :: PIO_MAX_NAME = 25 !< max name len + integer, public, parameter :: PIO_MAX_VAR_DIMS = 6 !< max dims for a var + integer, public, parameter :: PIO_CLOBBER = 10 !< clobber existing file + integer, public, parameter :: PIO_NOCLOBBER = 11 !< do not clobber existing file + integer, public, parameter :: PIO_WRITE = 20 !< read-write + integer, public, parameter :: PIO_NOWRITE = 21 !< read-only + integer, public, parameter :: PIO_64BIT_OFFSET = 0 !< 64bit offset format + integer, public, parameter :: PIO_64BIT_DATA = 0 !< CDF5 format + integer, public, parameter :: PIO_FILL_INT = -2147483647; !< int fill value + real, public, parameter :: PIO_FILL_FLOAT = 9.9692099683868690e+36; !< float fill value + double precision, public, parameter :: PIO_FILL_DOUBLE = 9.9692099683868690e+36; !< double fill value #endif #endif - integer, public, parameter :: PIO_num_OST = 16 !< num ost + integer, public, parameter :: PIO_num_OST = 16 !< num ost - enum, bind(c) - enumerator :: PIO_rearr_comm_p2p = 0 - enumerator :: PIO_rearr_comm_coll - end enum + enum, bind(c) + enumerator :: PIO_rearr_comm_p2p = 0 + enumerator :: PIO_rearr_comm_coll + end enum -!> -!! @defgroup PIO_rearr_comm_t Rearranger Communication -!! @public -!! There are two choices for rearranger communication. -!! - PIO_rearr_comm_p2p : Point to point -!! - PIO_rearr_comm_coll : Collective -!> -!> -!! @defgroup PIO_rearr_comm_dir PIO_rearr_comm_dir -!! @public -!! There are four choices for rearranger communication direction. -!! - PIO_rearr_comm_fc_2d_enable : COMM procs to IO procs and vice versa -!! - PIO_rearr_comm_fc_1d_comp2io: COMM procs to IO procs only -!! - PIO_rearr_comm_fc_1d_io2comp: IO procs to COMM procs only -!! - PIO_rearr_comm_fc_2d_disable: Disable flow control -!! -!! @defgroup PIO_rearr_comm_fc_options Rearranger Flow Control Options -!! Type that defines the PIO rearranger options. -!! - enable_hs : Enable handshake (true/false) -!! - enable_isend : Enable Isends (true/false) -!! - max_pend_req : Maximum pending requests (To indicated unlimited -!! number of requests use PIO_REARR_COMM_UNLIMITED_PEND_REQ) -!! -!! @defgroup PIO_rearr_options Rearranger Options -!! @brief Type that defines the PIO rearranger options -!! @details -!! - comm_type : @copydoc PIO_rearr_comm_t -!! - fcd : @copydoc PIO_rearr_comm_dir -!! - comm_fc_opts_comp2io : @copydoc PIO_rearr_comm_fc_options -!! - comm_fc_opts_io2comp : @copydoc PIO_rearr_comm_fc_options -!> - enum, bind(c) - enumerator :: PIO_rearr_comm_fc_2d_enable = 0 !< COMM procs to IO procs and vice versa. - enumerator :: PIO_rearr_comm_fc_1d_comp2io !< COMM procs to IO procs only. - enumerator :: PIO_rearr_comm_fc_1d_io2comp !< IO procs to COMM procs only. - enumerator :: PIO_rearr_comm_fc_2d_disable !< Disable flow control. - end enum + !> + !! @defgroup PIO_rearr_comm_t Rearranger Communication + !! @public + !! There are two choices for rearranger communication. + !! - PIO_rearr_comm_p2p : Point to point + !! - PIO_rearr_comm_coll : Collective + !> + !> + !! @defgroup PIO_rearr_comm_dir PIO_rearr_comm_dir + !! @public + !! There are four choices for rearranger communication direction. + !! - PIO_rearr_comm_fc_2d_enable : COMM procs to IO procs and vice versa + !! - PIO_rearr_comm_fc_1d_comp2io: COMM procs to IO procs only + !! - PIO_rearr_comm_fc_1d_io2comp: IO procs to COMM procs only + !! - PIO_rearr_comm_fc_2d_disable: Disable flow control + !! + !! @defgroup PIO_rearr_comm_fc_options Rearranger Flow Control Options + !! Type that defines the PIO rearranger options. + !! - enable_hs : Enable handshake (true/false) + !! - enable_isend : Enable Isends (true/false) + !! - max_pend_req : Maximum pending requests (To indicated unlimited + !! number of requests use PIO_REARR_COMM_UNLIMITED_PEND_REQ) + !! + !! @defgroup PIO_rearr_options Rearranger Options + !! @brief Type that defines the PIO rearranger options + !! @details + !! - comm_type : @copydoc PIO_rearr_comm_t + !! - fcd : @copydoc PIO_rearr_comm_dir + !! - comm_fc_opts_comp2io : @copydoc PIO_rearr_comm_fc_options + !! - comm_fc_opts_io2comp : @copydoc PIO_rearr_comm_fc_options + !> + enum, bind(c) + enumerator :: PIO_rearr_comm_fc_2d_enable = 0 !< COMM procs to IO procs and vice versa. + enumerator :: PIO_rearr_comm_fc_1d_comp2io !< COMM procs to IO procs only. + enumerator :: PIO_rearr_comm_fc_1d_io2comp !< IO procs to COMM procs only. + enumerator :: PIO_rearr_comm_fc_2d_disable !< Disable flow control. + end enum - type, bind(c), public :: PIO_rearr_comm_fc_opt_t - logical(c_bool) :: enable_hs !< Enable handshake. - logical(c_bool) :: enable_isend !< Enable isends. - integer(c_int) :: max_pend_req !< Maximum pending requests (PIO_REARR_COMM_UNLIMITED_PEND_REQ for unlimited). - end type PIO_rearr_comm_fc_opt_t + type, bind(c), public :: PIO_rearr_comm_fc_opt_t + logical(c_bool) :: enable_hs !< Enable handshake. + logical(c_bool) :: enable_isend !< Enable isends. + integer(c_int) :: max_pend_req !< Maximum pending requests (PIO_REARR_COMM_UNLIMITED_PEND_REQ for unlimited). + end type PIO_rearr_comm_fc_opt_t - integer, public, parameter :: PIO_REARR_COMM_UNLIMITED_PEND_REQ = -1 !< unlimited requests - type, bind(c), public :: PIO_rearr_opt_t - integer(c_int) :: comm_type !< Rearranger communication. - integer(c_int) :: fcd !< Communication direction. - type(PIO_rearr_comm_fc_opt_t) :: comm_fc_opts_comp2io !< The comp2io options. - type(PIO_rearr_comm_fc_opt_t) :: comm_fc_opts_io2comp !< The io2comp options. - end type PIO_rearr_opt_t + integer, public, parameter :: PIO_REARR_COMM_UNLIMITED_PEND_REQ = -1 !< unlimited requests + type, bind(c), public :: PIO_rearr_opt_t + integer(c_int) :: comm_type !< Rearranger communication. + integer(c_int) :: fcd !< Communication direction. + type(PIO_rearr_comm_fc_opt_t) :: comm_fc_opts_comp2io !< The comp2io options. + type(PIO_rearr_comm_fc_opt_t) :: comm_fc_opts_io2comp !< The io2comp options. + end type PIO_rearr_opt_t - public :: PIO_rearr_comm_p2p, PIO_rearr_comm_coll,& - PIO_rearr_comm_fc_2d_enable, PIO_rearr_comm_fc_1d_comp2io,& - PIO_rearr_comm_fc_1d_io2comp, PIO_rearr_comm_fc_2d_disable + public :: PIO_rearr_comm_p2p, PIO_rearr_comm_coll,& + PIO_rearr_comm_fc_2d_enable, PIO_rearr_comm_fc_1d_comp2io,& + PIO_rearr_comm_fc_1d_io2comp, PIO_rearr_comm_fc_2d_disable end module pio_types