425 lines
15 KiB
C
Executable File
425 lines
15 KiB
C
Executable File
/* -*- mode: c; c-basic-offset: 8; indent-tabs-mode: nil; -*-
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* vim:expandtab:shiftwidth=8:tabstop=8:
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*/
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/******************************************************************************\
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* *
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* Copyright (c) 2003, The Regents of the University of California *
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* See the file COPYRIGHT for a complete copyright notice and license. *
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* *
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********************************************************************************
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*
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* Implement abstract I/O interface for Parallel NetCDF (NCMPI).
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*
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\******************************************************************************/
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#ifdef HAVE_CONFIG_H
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#include "config.h"
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#endif
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#include <stdio.h>
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#include <stdlib.h>
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#include <sys/stat.h>
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#include <pnetcdf.h>
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#include "ior.h"
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#include "iordef.h"
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#include "aiori.h"
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#include "utilities.h"
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#define NUM_DIMS 3 /* number of dimensions to data set */
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/*
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* NCMPI_CHECK will display a custom error message and then exit the program
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*/
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#define NCMPI_CHECK(NCMPI_RETURN, MSG) do { \
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\
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if (NCMPI_RETURN < 0) { \
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fprintf(stdout, "** error **\n"); \
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fprintf(stdout, "ERROR in %s (line %d): %s.\n", \
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__FILE__, __LINE__, MSG); \
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fprintf(stdout, "ERROR: %s.\n", ncmpi_strerror(NCMPI_RETURN)); \
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fprintf(stdout, "** exiting **\n"); \
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exit(-1); \
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} \
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} while(0)
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/**************************** P R O T O T Y P E S *****************************/
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static int GetFileMode(int flags);
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static aiori_fd_t *NCMPI_Create(char *, int iorflags, aiori_mod_opt_t *);
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static aiori_fd_t *NCMPI_Open(char *, int iorflags, aiori_mod_opt_t *);
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static IOR_offset_t NCMPI_Xfer(int, aiori_fd_t *, IOR_size_t *,
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IOR_offset_t, IOR_offset_t, aiori_mod_opt_t *);
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static void NCMPI_Close(aiori_fd_t *, aiori_mod_opt_t *);
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static void NCMPI_Delete(char *, aiori_mod_opt_t *);
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static char *NCMPI_GetVersion();
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static void NCMPI_Fsync(aiori_fd_t *, aiori_mod_opt_t *);
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static IOR_offset_t NCMPI_GetFileSize(aiori_mod_opt_t *, char *);
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static int NCMPI_Access(const char *, int, aiori_mod_opt_t *);
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/************************** D E C L A R A T I O N S ***************************/
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static aiori_xfer_hint_t * hints = NULL;
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static void NCMPI_xfer_hints(aiori_xfer_hint_t * params){
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hints = params;
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MPIIO_xfer_hints(params);
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}
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typedef struct {
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int showHints; /* show hints */
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char * hintsFileName; /* full name for hints file */
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/* runtime variables */
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int var_id; /* variable id handle for data set */
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int firstReadCheck;
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int startDataSet;
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} ncmpi_options_t;
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static option_help * NCMPI_options(aiori_mod_opt_t ** init_backend_options, aiori_mod_opt_t * init_values){
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ncmpi_options_t * o = malloc(sizeof(ncmpi_options_t));
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if (init_values != NULL){
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memcpy(o, init_values, sizeof(ncmpi_options_t));
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}else{
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memset(o, 0, sizeof(ncmpi_options_t));
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}
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*init_backend_options = (aiori_mod_opt_t*) o;
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option_help h [] = {
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{0, "mpiio.hintsFileName","Full name for hints file", OPTION_OPTIONAL_ARGUMENT, 's', & o->hintsFileName},
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{0, "mpiio.showHints", "Show MPI hints", OPTION_FLAG, 'd', & o->showHints},
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LAST_OPTION
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};
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option_help * help = malloc(sizeof(h));
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memcpy(help, h, sizeof(h));
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return help;
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}
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ior_aiori_t ncmpi_aiori = {
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.name = "NCMPI",
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.name_legacy = NULL,
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.create = NCMPI_Create,
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.open = NCMPI_Open,
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.xfer = NCMPI_Xfer,
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.close = NCMPI_Close,
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.delete = NCMPI_Delete,
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.get_version = NCMPI_GetVersion,
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.fsync = NCMPI_Fsync,
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.get_file_size = NCMPI_GetFileSize,
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.statfs = aiori_posix_statfs,
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.mkdir = aiori_posix_mkdir,
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.rmdir = aiori_posix_rmdir,
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.access = NCMPI_Access,
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.stat = aiori_posix_stat,
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.get_options = NCMPI_options,
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.xfer_hints = NCMPI_xfer_hints,
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};
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/***************************** F U N C T I O N S ******************************/
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/*
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* Create and open a file through the NCMPI interface.
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*/
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static aiori_fd_t *NCMPI_Create(char *testFileName, int iorflags, aiori_mod_opt_t * param)
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{
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int *fd;
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int fd_mode;
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MPI_Info mpiHints = MPI_INFO_NULL;
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ncmpi_options_t * o = (ncmpi_options_t*) param;
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/* read and set MPI file hints from hintsFile */
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SetHints(&mpiHints, o->hintsFileName);
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if (rank == 0 && o->showHints) {
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fprintf(stdout, "\nhints passed to MPI_File_open() {\n");
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ShowHints(&mpiHints);
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fprintf(stdout, "}\n");
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}
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fd = (int *)malloc(sizeof(int));
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if (fd == NULL)
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ERR("malloc() failed");
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fd_mode = GetFileMode(iorflags);
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NCMPI_CHECK(ncmpi_create(testComm, testFileName, fd_mode,
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mpiHints, fd), "cannot create file");
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/* free up the mpiHints object */
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if (mpiHints != MPI_INFO_NULL)
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MPI_CHECK(MPI_Info_free(&mpiHints), "cannot free file info");
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#if defined(PNETCDF_VERSION_MAJOR) && (PNETCDF_VERSION_MAJOR > 1 || PNETCDF_VERSION_MINOR >= 2)
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/* ncmpi_get_file_info is first available in 1.2.0 */
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if (rank == 0 && o->showHints) {
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MPI_Info info_used;
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MPI_CHECK(ncmpi_get_file_info(*fd, &info_used),
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"cannot inquire file info");
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/* print the MPI file hints currently used */
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fprintf(stdout, "\nhints returned from opened file {\n");
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ShowHints(&info_used);
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fprintf(stdout, "}\n");
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MPI_CHECK(MPI_Info_free(&info_used), "cannot free file info");
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}
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#endif
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return (aiori_fd_t*)(fd);
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}
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/*
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* Open a file through the NCMPI interface.
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*/
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static aiori_fd_t *NCMPI_Open(char *testFileName, int iorflags, aiori_mod_opt_t * param)
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{
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int *fd;
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int fd_mode;
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MPI_Info mpiHints = MPI_INFO_NULL;
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ncmpi_options_t * o = (ncmpi_options_t*) param;
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/* read and set MPI file hints from hintsFile */
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SetHints(&mpiHints, o->hintsFileName);
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if (rank == 0 && o->showHints) {
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fprintf(stdout, "\nhints passed to MPI_File_open() {\n");
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ShowHints(&mpiHints);
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fprintf(stdout, "}\n");
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}
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fd = (int *)malloc(sizeof(int));
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if (fd == NULL)
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ERR("malloc() failed");
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fd_mode = GetFileMode(iorflags);
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NCMPI_CHECK(ncmpi_open(testComm, testFileName, fd_mode,
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mpiHints, fd), "cannot open file");
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/* free up the mpiHints object */
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if (mpiHints != MPI_INFO_NULL)
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MPI_CHECK(MPI_Info_free(&mpiHints), "cannot free file info");
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#if defined(PNETCDF_VERSION_MAJOR) && (PNETCDF_VERSION_MAJOR > 1 || PNETCDF_VERSION_MINOR >= 2)
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/* ncmpi_get_file_info is first available in 1.2.0 */
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if (rank == 0 && o->showHints) {
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MPI_Info info_used;
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MPI_CHECK(ncmpi_get_file_info(*fd, &info_used),
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"cannot inquire file info");
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/* print the MPI file hints currently used */
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fprintf(stdout, "\nhints returned from opened file {\n");
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ShowHints(&info_used);
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fprintf(stdout, "}\n");
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MPI_CHECK(MPI_Info_free(&info_used), "cannot free file info");
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}
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#endif
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return (aiori_fd_t*)(fd);
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}
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/*
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* Write or read access to file using the NCMPI interface.
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*/
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static IOR_offset_t NCMPI_Xfer(int access, aiori_fd_t *fd, IOR_size_t * buffer, IOR_offset_t transferSize, IOR_offset_t offset, aiori_mod_opt_t * param)
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{
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signed char *bufferPtr = (signed char *)buffer;
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ncmpi_options_t * o = (ncmpi_options_t*) param;
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int var_id, dim_id[NUM_DIMS];
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MPI_Offset bufSize[NUM_DIMS], offsets[NUM_DIMS];
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IOR_offset_t segmentPosition;
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int segmentNum, transferNum;
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/* determine by offset if need to start data set */
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if (hints->filePerProc == TRUE) {
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segmentPosition = (IOR_offset_t) 0;
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} else {
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segmentPosition = (IOR_offset_t) ((rank + rankOffset) % hints->numTasks) * hints->blockSize;
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}
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if ((int)(offset - segmentPosition) == 0) {
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o->startDataSet = TRUE;
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/*
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* this toggle is for the read check operation, which passes through
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* this function twice; note that this function will open a data set
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* only on the first read check and close only on the second
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*/
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if (access == READCHECK) {
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o->firstReadCheck = ! o->firstReadCheck;
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}
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}
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if (o->startDataSet == TRUE &&
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(access != READCHECK || o->firstReadCheck == TRUE)) {
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if (access == WRITE) {
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int numTransfers = hints->blockSize / hints->transferSize;
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/* reshape 1D array to 3D array:
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[segmentCount*numTasks][numTransfers][transferSize]
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Requirement: none of these dimensions should be > 4G,
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*/
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NCMPI_CHECK(ncmpi_def_dim
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(*(int *)fd, "segments_times_np",
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NC_UNLIMITED, &dim_id[0]),
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"cannot define data set dimensions");
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NCMPI_CHECK(ncmpi_def_dim
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(*(int *)fd, "number_of_transfers",
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numTransfers, &dim_id[1]),
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"cannot define data set dimensions");
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NCMPI_CHECK(ncmpi_def_dim
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(*(int *)fd, "transfer_size",
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hints->transferSize, &dim_id[2]),
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"cannot define data set dimensions");
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NCMPI_CHECK(ncmpi_def_var
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(*(int *)fd, "data_var", NC_BYTE, NUM_DIMS,
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dim_id, &var_id),
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"cannot define data set variables");
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NCMPI_CHECK(ncmpi_enddef(*(int *)fd),
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"cannot close data set define mode");
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} else {
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NCMPI_CHECK(ncmpi_inq_varid
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(*(int *)fd, "data_var", &var_id),
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"cannot retrieve data set variable");
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}
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if (hints->collective == FALSE) {
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NCMPI_CHECK(ncmpi_begin_indep_data(*(int *)fd),
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"cannot enable independent data mode");
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}
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o->var_id = var_id;
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o->startDataSet = FALSE;
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}
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var_id = o->var_id;
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/* calculate the segment number */
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segmentNum = offset / (hints->numTasks * hints->blockSize);
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/* calculate the transfer number in each block */
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transferNum = offset % hints->blockSize / hints->transferSize;
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/* read/write the 3rd dim of the dataset, each is of
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amount param->transferSize */
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bufSize[0] = 1;
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bufSize[1] = 1;
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bufSize[2] = transferSize;
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offsets[0] = segmentNum * hints->numTasks + rank;
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offsets[1] = transferNum;
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offsets[2] = 0;
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/* access the file */
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if (access == WRITE) { /* WRITE */
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if (hints->collective) {
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NCMPI_CHECK(ncmpi_put_vara_schar_all
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(*(int *)fd, var_id, offsets, bufSize, bufferPtr),
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"cannot write to data set");
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} else {
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NCMPI_CHECK(ncmpi_put_vara_schar
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(*(int *)fd, var_id, offsets, bufSize, bufferPtr),
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"cannot write to data set");
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}
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} else { /* READ or CHECK */
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if (hints->collective == TRUE) {
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NCMPI_CHECK(ncmpi_get_vara_schar_all
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(*(int *)fd, var_id, offsets, bufSize, bufferPtr),
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"cannot read from data set");
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} else {
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NCMPI_CHECK(ncmpi_get_vara_schar
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(*(int *)fd, var_id, offsets, bufSize, bufferPtr),
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"cannot read from data set");
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}
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}
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return (transferSize);
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}
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/*
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* Perform fsync().
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*/
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static void NCMPI_Fsync(aiori_fd_t *fd, aiori_mod_opt_t * param)
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{
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}
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/*
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* Close a file through the NCMPI interface.
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*/
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static void NCMPI_Close(aiori_fd_t *fd, aiori_mod_opt_t * param)
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{
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if (hints->collective == FALSE) {
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NCMPI_CHECK(ncmpi_end_indep_data(*(int *)fd),
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"cannot disable independent data mode");
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}
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NCMPI_CHECK(ncmpi_close(*(int *)fd), "cannot close file");
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free(fd);
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}
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/*
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* Delete a file through the NCMPI interface.
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*/
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static void NCMPI_Delete(char *testFileName, aiori_mod_opt_t * param)
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{
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return(MPIIO_Delete(testFileName, param));
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}
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/*
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* Determine api version.
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*/
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static char* NCMPI_GetVersion()
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{
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return (char *)ncmpi_inq_libvers();
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}
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/*
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* Return the correct file mode for NCMPI.
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*/
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static int GetFileMode(int flags)
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{
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int fd_mode = 0;
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/* set IOR file flags to NCMPI flags */
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/* -- file open flags -- */
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if (flags & IOR_RDONLY) {
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fd_mode |= NC_NOWRITE;
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}
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if (flags & IOR_WRONLY) {
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WARN("File write only not implemented in NCMPI");
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}
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if (flags & IOR_RDWR) {
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fd_mode |= NC_WRITE;
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}
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if (flags & IOR_APPEND) {
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WARN("File append not implemented in NCMPI");
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}
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if (flags & IOR_CREAT) {
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fd_mode |= NC_CLOBBER;
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}
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if (flags & IOR_EXCL) {
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WARN("Exclusive access not implemented in NCMPI");
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}
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if (flags & IOR_TRUNC) {
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WARN("File truncation not implemented in NCMPI");
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}
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if (flags & IOR_DIRECT) {
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WARN("O_DIRECT not implemented in NCMPI");
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}
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/* to enable > 4GB file size */
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fd_mode |= NC_64BIT_OFFSET;
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return (fd_mode);
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}
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/*
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* Use MPIIO call to get file size.
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*/
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static IOR_offset_t NCMPI_GetFileSize(aiori_mod_opt_t * opt,
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char *testFileName)
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{
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return(MPIIO_GetFileSize(opt, testFileName));
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}
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/*
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* Use MPIIO call to check for access.
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*/
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static int NCMPI_Access(const char *path, int mode, aiori_mod_opt_t *param)
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{
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return(MPIIO_Access(path, mode, param));
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}
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