NCMPI ported to current ADIO. Fixed autoconf #303.
parent
eb883f533a
commit
21bf5a5a12
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@ -160,8 +160,10 @@ AC_ARG_WITH([ncmpi],
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[],
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[with_ncmpi=no])
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AM_CONDITIONAL([USE_NCMPI_AIORI], [test x$with_ncmpi = xyes])
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AM_COND_IF([USE_NCMPI_AIORI],[
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AC_DEFINE([USE_NCMPI_AIORI], [], [Build NCMPI backend AIORI])
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AS_IF([test "x$with_ncmpi" = xyes ], [
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AC_CHECK_HEADERS([pnetcdf.h], [AC_DEFINE([USE_NCMPI_AIORI], [], [PNetCDF available])], [
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AC_MSG_FAILURE([--with-ncmpi was given but pnetcdf.h not found])
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])
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])
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# MMAP IO support
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@ -45,20 +45,57 @@
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/**************************** P R O T O T Y P E S *****************************/
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static int GetFileMode(IOR_param_t *);
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static int GetFileMode(int flags);
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static void *NCMPI_Create(char *, IOR_param_t *);
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static void *NCMPI_Open(char *, IOR_param_t *);
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static IOR_offset_t NCMPI_Xfer(int, void *, IOR_size_t *,
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IOR_offset_t, IOR_param_t *);
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static void NCMPI_Close(void *, IOR_param_t *);
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static void NCMPI_Delete(char *, IOR_param_t *);
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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(void *, IOR_param_t *);
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static IOR_offset_t NCMPI_GetFileSize(IOR_param_t *, MPI_Comm, char *);
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static int NCMPI_Access(const char *, int, IOR_param_t *);
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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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@ -76,6 +113,8 @@ ior_aiori_t ncmpi_aiori = {
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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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@ -83,15 +122,16 @@ ior_aiori_t ncmpi_aiori = {
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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 void *NCMPI_Create(char *testFileName, IOR_param_t * param)
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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, param->hintsFileName);
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if (rank == 0 && param->showHints) {
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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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@ -101,7 +141,7 @@ static void *NCMPI_Create(char *testFileName, IOR_param_t * param)
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if (fd == NULL)
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ERR("malloc() failed");
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fd_mode = GetFileMode(param);
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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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@ -111,7 +151,7 @@ static void *NCMPI_Create(char *testFileName, IOR_param_t * param)
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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 && param->showHints) {
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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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@ -123,21 +163,22 @@ static void *NCMPI_Create(char *testFileName, IOR_param_t * param)
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}
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#endif
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return (fd);
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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 void *NCMPI_Open(char *testFileName, IOR_param_t * param)
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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, param->hintsFileName);
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if (rank == 0 && param->showHints) {
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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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@ -147,7 +188,7 @@ static void *NCMPI_Open(char *testFileName, IOR_param_t * param)
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if (fd == NULL)
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ERR("malloc() failed");
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fd_mode = GetFileMode(param);
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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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@ -157,7 +198,7 @@ static void *NCMPI_Open(char *testFileName, IOR_param_t * param)
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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 && param->showHints) {
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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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@ -169,51 +210,43 @@ static void *NCMPI_Open(char *testFileName, IOR_param_t * param)
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}
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#endif
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return (fd);
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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, void *fd, IOR_size_t * buffer,
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IOR_offset_t length, IOR_param_t * param)
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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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static int firstReadCheck = FALSE, startDataSet;
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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], offset[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 (param->filePerProc == TRUE) {
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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 =
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(IOR_offset_t) ((rank + rankOffset) % param->numTasks)
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* param->blockSize;
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segmentPosition = (IOR_offset_t) ((rank + rankOffset) % hints->numTasks) * hints->blockSize;
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}
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if ((int)(param->offset - segmentPosition) == 0) {
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startDataSet = TRUE;
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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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if (firstReadCheck == TRUE) {
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firstReadCheck = FALSE;
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} else {
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firstReadCheck = TRUE;
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}
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o->firstReadCheck = ! o->firstReadCheck;
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}
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}
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if (startDataSet == TRUE &&
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(access != READCHECK || firstReadCheck == TRUE)) {
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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 =
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param->blockSize / param->transferSize;
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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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"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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param->transferSize, &dim_id[2]),
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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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@ -244,77 +277,72 @@ static IOR_offset_t NCMPI_Xfer(int access, void *fd, IOR_size_t * buffer,
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"cannot retrieve data set variable");
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}
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if (param->collective == FALSE) {
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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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param->var_id = var_id;
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startDataSet = FALSE;
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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 = param->var_id;
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var_id = o->var_id;
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/* calculate the segment number */
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segmentNum = param->offset / (param->numTasks * param->blockSize);
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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 = param->offset % param->blockSize / param->transferSize;
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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] = param->transferSize;
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bufSize[2] = transferSize;
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offset[0] = segmentNum * param->numTasks + rank;
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offset[1] = transferNum;
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offset[2] = 0;
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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 (param->collective) {
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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, offset, bufSize,
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bufferPtr),
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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, offset, bufSize,
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bufferPtr),
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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 (param->collective == TRUE) {
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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, offset, bufSize,
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bufferPtr),
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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, offset, bufSize,
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bufferPtr),
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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 (length);
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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(void *fd, IOR_param_t * param)
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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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/*
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* Close a file through the NCMPI interface.
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*/
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static void NCMPI_Close(void *fd, IOR_param_t * param)
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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 (param->collective == FALSE) {
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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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@ -325,7 +353,7 @@ static void NCMPI_Close(void *fd, IOR_param_t * param)
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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, IOR_param_t * param)
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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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* Return the correct file mode for NCMPI.
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*/
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static int GetFileMode(IOR_param_t * param)
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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 (param->openFlags & IOR_RDONLY) {
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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 (param->openFlags & IOR_WRONLY) {
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fprintf(stdout, "File write only not implemented in NCMPI\n");
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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 (param->openFlags & IOR_RDWR) {
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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 (param->openFlags & IOR_APPEND) {
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fprintf(stdout, "File append not implemented in NCMPI\n");
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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 (param->openFlags & IOR_CREAT) {
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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 (param->openFlags & IOR_EXCL) {
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fprintf(stdout, "Exclusive access not implemented in NCMPI\n");
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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 (param->openFlags & IOR_TRUNC) {
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fprintf(stdout, "File truncation not implemented in NCMPI\n");
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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 (param->openFlags & IOR_DIRECT) {
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fprintf(stdout, "O_DIRECT not implemented in NCMPI\n");
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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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@ -381,16 +409,16 @@ static int GetFileMode(IOR_param_t * param)
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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(IOR_param_t * test, MPI_Comm testComm,
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static IOR_offset_t NCMPI_GetFileSize(aiori_mod_opt_t * opt,
|
||||
char *testFileName)
|
||||
{
|
||||
return(MPIIO_GetFileSize(test, testComm, testFileName));
|
||||
return(MPIIO_GetFileSize(opt, testFileName));
|
||||
}
|
||||
|
||||
/*
|
||||
* Use MPIIO call to check for access.
|
||||
*/
|
||||
static int NCMPI_Access(const char *path, int mode, IOR_param_t *param)
|
||||
static int NCMPI_Access(const char *path, int mode, aiori_mod_opt_t *param)
|
||||
{
|
||||
return(MPIIO_Access(path, mode, param));
|
||||
}
|
||||
|
|
|
@ -166,9 +166,6 @@ typedef struct
|
|||
rados_t rados_cluster; /* RADOS cluster handle */
|
||||
rados_ioctx_t rados_ioctx; /* I/O context for our pool in the RADOS cluster */
|
||||
|
||||
/* NCMPI variables */
|
||||
int var_id; /* variable id handle for data set */
|
||||
|
||||
int id; /* test's unique ID */
|
||||
int intraTestBarriers; /* barriers between open/op and op/close */
|
||||
int warningAsErrors; /* treat any warning as an error */
|
||||
|
|
Loading…
Reference in New Issue