自学教程：C++ H5Pset_fapl_mpio函数代码示例

/* * Create the appropriate File access property list */hid_tcreate_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type,                     hbool_t use_gpfs){    hid_t ret_pl = -1;    herr_t ret;                 /* generic return value */    int mpi_rank;		/* mpi variables */    /* need the rank for error checking macros */    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);    ret_pl = H5Pcreate (H5P_FILE_ACCESS);    VRFY((ret_pl >= 0), "H5P_FILE_ACCESS");    if (l_facc_type == FACC_DEFAULT)        return (ret_pl);    if (l_facc_type == FACC_MPIO) {        /* set Parallel access with communicator */        ret = H5Pset_fapl_mpio(ret_pl, comm, info);        VRFY((ret >= 0), "");        return(ret_pl);    }    if (l_facc_type == (FACC_MPIO | FACC_SPLIT)) {        hid_t mpio_pl;        mpio_pl = H5Pcreate (H5P_FILE_ACCESS);        VRFY((mpio_pl >= 0), "");        /* set Parallel access with communicator */        ret = H5Pset_fapl_mpio(mpio_pl, comm, info);        VRFY((ret >= 0), "");        /* setup file access template */        ret_pl = H5Pcreate (H5P_FILE_ACCESS);        VRFY((ret_pl >= 0), "");        /* set Parallel access with communicator */        ret = H5Pset_fapl_split(ret_pl, ".meta", mpio_pl, ".raw", mpio_pl);        VRFY((ret >= 0), "H5Pset_fapl_split succeeded");        H5Pclose(mpio_pl);        return(ret_pl);    }    if (l_facc_type == FACC_MPIPOSIX) {        /* set Parallel access with communicator */        ret = H5Pset_fapl_mpiposix(ret_pl, comm, use_gpfs);        VRFY((ret >= 0), "H5Pset_fapl_mpiposix succeeded");        return(ret_pl);    }    /* unknown file access types */    return (ret_pl);}

  void hdf_archive::set_access_plist(bool use_collective, Communicate* comm)  {    access_id=H5P_DEFAULT;    if(comm && comm->size()>1) //for parallel communicator    {      if(use_collective)      {#if defined(H5_HAVE_PARALLEL) && defined(ENABLE_PHDF5)        MPI_Info info=MPI_INFO_NULL;        access_id = H5Pcreate(H5P_FILE_ACCESS);        H5Pset_fapl_mpio(access_id,comm->getMPI(),info);        xfer_plist = H5Pcreate(H5P_DATASET_XFER);        H5Pset_dxpl_mpio(xfer_plist,H5FD_MPIO_COLLECTIVE);#else        use_collective=false;//cannot use collective#endif      }      //true, if this task does not need to participate in I/O      Mode.set(IS_PARALLEL,use_collective);      Mode.set(NOIO,comm->rank()&&!use_collective);    }    else    {      Mode.set(IS_PARALLEL,false);      Mode.set(NOIO,false);    }  }

PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[]){  PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)  MPI_Info          info = MPI_INFO_NULL;#endif  hid_t             plist_id;  herr_t            herr;  PetscErrorCode    ierr;  PetscFunctionBegin;  ierr = PetscStrallocpy(name, &hdf5->filename);CHKERRQ(ierr);  /* Set up file access property list with parallel I/O access */  plist_id = H5Pcreate(H5P_FILE_ACCESS);#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)  herr = H5Pset_fapl_mpio(plist_id, PetscObjectComm((PetscObject)viewer), info);CHKERRQ(herr);#endif  /* Create or open the file collectively */  switch (hdf5->btype) {  case FILE_MODE_READ:    hdf5->file_id = H5Fopen(name, H5F_ACC_RDONLY, plist_id);    break;  case FILE_MODE_APPEND:    hdf5->file_id = H5Fopen(name, H5F_ACC_RDWR, plist_id);    break;  case FILE_MODE_WRITE:    hdf5->file_id = H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);    break;  default:    SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");  }  if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);  H5Pclose(plist_id);  PetscFunctionReturn(0);}

void _io_domain_commit(cow_domain *d){#if (COW_HDF5)  for (int n=0; n<d->n_dims; ++n) {    d->L_nint_h5[n] = d->L_nint[n]; // Selection size, target and destination    d->L_ntot_h5[n] = d->L_ntot[n]; // Memory space total size    d->L_strt_h5[n] = d->L_strt[n]; // Memory space selection start    d->G_ntot_h5[n] = d->G_ntot[n]; // Global space total size    d->G_strt_h5[n] = d->G_strt[n]; // Global space selection start  }  // Here we create the following property lists:  //  // file access property list   ........ for the call to H5Fopen  // dset creation property list ........ for the call to H5Dcreate  // dset transfer property list ........ for the call to H5Dwrite  // ---------------------------------------------------------------------------  d->fapl = H5Pcreate(H5P_FILE_ACCESS);  d->dcpl = H5Pcreate(H5P_DATASET_CREATE);  d->dxpl = H5Pcreate(H5P_DATASET_XFER);#if (COW_HDF5_MPI && COW_MPI)  if (cow_mpirunning()) {    H5Pset_fapl_mpio(d->fapl, d->mpi_cart, MPI_INFO_NULL);  }#endif // COW_HDF5_MPI && COW_MPI#endif // COW_HDF5}

OHDF5mpipp::OHDF5mpipp(std::string filename, int buf_size, nestio::Logger_type logger_type): buf_size(buf_size), RANK(2), logger_type(logger_type){	//Init HDF5 file	MPI_Comm_size(MPI_COMM_WORLD, &clientscount);		hid_t fapl_id;	fapl_id = H5Pcreate(H5P_FILE_ACCESS);	H5Pset_fapl_mpio(fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL);    /* Create _a new file. If file exists its contents will be overwritten. */	file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);			MPI_Comm_rank (MPI_COMM_WORLD, &own_id);		int num_threads=omp_get_max_threads();	if (logger_type == nestio::Buffered || logger_type == nestio::Collective) {	  	  buffer_multi = new oHDF5Buffer;	  buffer_spike = new oHDF5Buffer;	  //for (int i=0; i<num_threads;i++) {	  buffer_multi->extend(buf_size*num_threads);	  buffer_spike->extend(buf_size*num_threads);	  //}	}		H5Pclose(fapl_id);}

hid_t seissol::checkpoint::h5::Fault::initFile(int odd, const char* filename){	hid_t h5file;	if (loaded()) {		// Open the file		h5file = open(filename, false);		checkH5Err(h5file);		// Fault writer		m_h5timestepFault[odd] = H5Aopen(h5file, "timestep_fault", H5P_DEFAULT);		checkH5Err(m_h5timestepFault[odd]);		// Data		for (unsigned int i = 0; i < NUM_VARIABLES; i++) {			m_h5data[odd][i] = H5Dopen(h5file, VAR_NAMES[i], H5P_DEFAULT);			checkH5Err(m_h5data[odd][i]);		}	} else {		// Create the file		hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);		checkH5Err(h5plist);		checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));#ifdef USE_MPI		checkH5Err(H5Pset_fapl_mpio(h5plist, comm(), MPI_INFO_NULL));#endif // USE_MPI		h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);		checkH5Err(h5file);		checkH5Err(H5Pclose(h5plist));		// Create scalar dataspace for attributes		hid_t h5spaceScalar = H5Screate(H5S_SCALAR);		checkH5Err(h5spaceScalar);		// Fault writer		m_h5timestepFault[odd] = H5Acreate(h5file, "timestep_fault",				H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);		checkH5Err(m_h5timestepFault[odd]);		int t = 0;		checkH5Err(H5Awrite(m_h5timestepFault[odd], H5T_NATIVE_INT, &t));		checkH5Err(H5Sclose(h5spaceScalar));		// Variables		for (unsigned int i = 0; i < NUM_VARIABLES; i++) {			h5plist = H5Pcreate(H5P_DATASET_CREATE);			checkH5Err(h5plist);			checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));			checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));			m_h5data[odd][i] = H5Dcreate(h5file, VAR_NAMES[i], H5T_IEEE_F64LE, m_h5fSpaceData,				H5P_DEFAULT, h5plist, H5P_DEFAULT);			checkH5Err(m_h5data[odd][i]);			checkH5Err(H5Pclose(h5plist));		}	}	return h5file;}

/* ------- begin -------------------------- readConvergence.c  --- */void readConvergence(void) {  /* This is a self-contained function to read the convergence matrix,     written by RH. */  const char routineName[] = "readConvergence";  char *atmosID;  int ncid, ncid_mpi, nx, ny;  size_t attr_size;  hid_t plist;  H5T_class_t type_class;  mpi.rh_converged = matrix_int(mpi.nx, mpi.ny);  /* --- Open the inputdata file --- */  if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);  if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);  if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)    HERR(routineName);  if (( H5Pclose(plist) ) < 0) HERR(routineName);  /* Get ncid of the MPI group */  if (( ncid_mpi = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0) HERR(routineName);  /* --- Consistency checks --- */  /* Check that atmosID is the same */  if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,                               &attr_size) ) < 0) HERR(routineName);  atmosID = (char *) malloc(attr_size + 1);  if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)    HERR(routineName);  if (!strstr(atmosID, atmos.ID)) {    sprintf(messageStr,       "Indata file was calculated for different atmosphere (%s) than current",	     atmosID);    Error(WARNING, routineName, messageStr);    }  free(atmosID);  /* Check that dimension sizes match */  if (( H5LTget_attribute_int(ncid, "/", "nx", &nx) ) < 0) HERR(routineName);  if (nx != mpi.nx) {    sprintf(messageStr,	    "Number of x points mismatch: expected %d, found %d.",	    mpi.nx, (int)nx);    Error(WARNING, routineName, messageStr);  }  if (( H5LTget_attribute_int(ncid, "/", "ny", &ny) ) < 0) HERR(routineName);  if (ny != mpi.ny) {    sprintf(messageStr,	    "Number of y points mismatch: expected %d, found %d.",	    mpi.ny, (int)ny);    Error(WARNING, routineName, messageStr);  }  /* --- Read variable --- */  if (( H5LTread_dataset_int(ncid_mpi, CONV_NAME,                             mpi.rh_converged[0]) ) < 0) HERR(routineName);  /* --- Close inputdata file --- */  if (( H5Gclose(ncid_mpi) ) < 0) HERR(routineName);  if (( H5Fclose(ncid) ) < 0) HERR(routineName);  return;}

/* * parse the command line options */static intparse_options(int argc, char **argv){    while (--argc){  if (**(++argv) != '-'){      break;  }else{      switch(*(*argv+1)){    case 'v':   if (*((*argv+1)+1))        ParseTestVerbosity((*argv+1)+1);          else        SetTestVerbosity(VERBO_MED);          break;    case 'f':   if (--argc < 1) {        nerrors++;        return(1);          }          if (**(++argv) == '-') {        nerrors++;        return(1);          }          paraprefix = *argv;          break;    case 'h':   /* print help message--return with nerrors set */          return(1);    default:    nerrors++;          return(1);      }  }    } /*while*/    /* compose the test filenames */    {  int i, n;  hid_t plist;  plist = H5Pcreate (H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist, MPI_COMM_WORLD, MPI_INFO_NULL);  n = sizeof(FILENAME)/sizeof(FILENAME[0]) - 1;  /* exclude the NULL */  for (i=0; i < n; i++)      if (h5_fixname(FILENAME[i],plist,filenames[i],sizeof(filenames[i]))    == NULL){    printf("h5_fixname failed/n");    nerrors++;    return(1);      }  H5Pclose(plist);  if (VERBOSE_MED){      printf("Test filenames are:/n");      for (i=0; i < n; i++)    printf("    %s/n", filenames[i]);  }    }    return(0);}

void BigArray<T>::loadNC(const std::string &fileName){    dataFileName = fileName;    connection.disconnect();    connection = releaseSignal().connect(boost::bind(&gurls::BigArray<T>::close, this));    std::string errorString = "Error opening file " + fileName + ":";    // Set up file access property list with parallel I/O access    plist_id = H5Pcreate(H5P_FILE_ACCESS);    if(plist_id == -1)        throw gException(errorString);    herr_t status;#ifdef USE_MPIIO    status = H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPI_INFO_NULL);#else    status = H5Pset_fapl_mpiposix(plist_id, MPI_COMM_WORLD, false);#endif    CHECK_HDF5_ERR(status, errorString)    // Create a new file collectively and release property list identifier.    file_id = H5Fopen(fileName.c_str(), H5F_ACC_RDWR, plist_id);    CHECK_HDF5_ERR(file_id, errorString)    status = H5Pclose(plist_id);    CHECK_HDF5_ERR(status, errorString)    dset_id =  H5Dopen(file_id, "mat", H5P_DEFAULT);    CHECK_HDF5_ERR(dset_id, errorString)    hid_t filespace = H5Dget_space( dset_id );    CHECK_HDF5_ERR(filespace, errorString)    hsize_t dims[2], maxDims[2];    status = H5Sget_simple_extent_dims(filespace, dims, maxDims);    CHECK_HDF5_ERR(status, errorString)    status = H5Sclose(filespace);    CHECK_HDF5_ERR(status, errorString)    this->numrows = static_cast<unsigned long>(dims[1]);    this->numcols = static_cast<unsigned long>(dims[0]);    // Create property list for collective dataset write.    plist_id = H5Pcreate(H5P_DATASET_XFER);    if(plist_id == -1)        throw gException(errorString);    status = H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT);    CHECK_HDF5_ERR(status, errorString)}

void pHdf5IoDataModel::fileOpen(const QString &file_name, FileMode mode){    //if file is already open tell it to the user and return    if(!d->file_is_open) {        //if we didn't set the communicator error        if(d->comm==nullptr) {            dtkError() << __func__ << "communicator not set";        }        // H5P_FILE_ACCESS applies to H5Fcreate and H5Fopen        d->prop_list_id = H5Pcreate(H5P_FILE_ACCESS);        MPI_Info info = MPI_INFO_NULL;        MPI_Comm comm = *static_cast<MPI_Comm *>(d->comm->data());        H5Pset_fapl_mpio(d->prop_list_id, comm, info);        switch (mode) {        case dtkIoDataModel::Trunc:            d->file_id = H5Fcreate (file_name.toUtf8().constData(), H5F_ACC_TRUNC,                                   H5P_DEFAULT, d->prop_list_id);            break;        case dtkIoDataModel::NotExisting:            d->file_id = H5Fcreate(file_name.toUtf8().constData(), H5F_ACC_EXCL,                                   H5P_DEFAULT, d->prop_list_id);            break;        case dtkIoDataModel::ReadOnly:            d->file_id = H5Fopen(file_name.toUtf8().constData(), H5F_ACC_RDONLY,                                 d->prop_list_id);            break;        case dtkIoDataModel::ReadWrite:            d->file_id = H5Fopen(file_name.toUtf8().constData(), H5F_ACC_RDWR,                                 d->prop_list_id);            break;        default:            dtkError() << "unsupported fileMode";        };        //close the property list for file        H5Pclose(d->prop_list_id);        if(d->file_id<0) {            dtkError() << "error in fileOpen for file_name " << file_name;        }        else {            //if the file is correctly open, create a propery list to collectively write datasets            d->file_is_open = true;            d->prop_list_id = H5Pcreate(H5P_DATASET_XFER);            H5Pset_dxpl_mpio(d->prop_list_id, H5FD_MPIO_COLLECTIVE);        }    }    else {        qDebug() << "File" << file_name << "is already open, please close it before opening a new one";    }}

hid_t ASDF_create_new_file(const char *filename, MPI_Comm comm) {  hid_t plist_id, file_id;  CHK_H5(plist_id = H5Pcreate(H5P_FILE_ACCESS));  CHK_H5(H5Pset_fapl_mpio(plist_id, comm, MPI_INFO_NULL));  /* Create the file collectively.*/  CHK_H5(file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id));  CHK_H5(H5Pclose(plist_id));  return file_id;}

/*------------------------------------------------------------------------- * Function:	main * * Purpose:	Part 2 of a two-part H5Fflush() test. * * Return:	Success:	0 * *		Failure:	1 * * Programmer:	Robb Matzke *              Friday, October 23, 1998 * * Modifications: * 		Leon Arber * 		Sept. 26, 2006, expand to check for case where the was file not flushed. * *------------------------------------------------------------------------- */intmain(int argc, char* argv[]){    hid_t fapl1, fapl2;    H5E_auto2_t func;    char	name[1024];    const char *envval = NULL;    int mpi_size, mpi_rank;    MPI_Comm comm  = MPI_COMM_WORLD;    MPI_Info info  = MPI_INFO_NULL;    MPI_Init(&argc, &argv);    MPI_Comm_size(comm, &mpi_size);    MPI_Comm_rank(comm, &mpi_rank);    fapl1 = H5Pcreate(H5P_FILE_ACCESS);    H5Pset_fapl_mpio(fapl1, comm, info);    fapl2 = H5Pcreate(H5P_FILE_ACCESS);    H5Pset_fapl_mpio(fapl2, comm, info);    if(mpi_rank == 0)	TESTING("H5Fflush (part2 with flush)");    /* Don't run this test using the core or split file drivers */    envval = HDgetenv("HDF5_DRIVER");    if (envval == NULL)        envval = "nomatch";    if (HDstrcmp(envval, "core") && HDstrcmp(envval, "split")) {	/* Check the case where the file was flushed */	h5_fixname(FILENAME[0], fapl1, name, sizeof name);	if(check_file(name, fapl1))	{	    H5_FAILED()	    goto error;	}	else if(mpi_rank == 0)

/* * test file access by communicator besides COMM_WORLD. * Split COMM_WORLD into two, one (even_comm) contains the original * processes of even ranks.  The other (odd_comm) contains the original * processes of odd ranks.  Processes in even_comm creates a file, then * cloose it, using even_comm.  Processes in old_comm just do a barrier * using odd_comm.  Then they all do a barrier using COMM_WORLD. * If the file creation and cloose does not do correct collective action * according to the communicator argument, the processes will freeze up * sooner or later due to barrier mixed up. */voidtest_split_comm_access(char filenames[][PATH_MAX]){    MPI_Comm comm;    MPI_Info info = MPI_INFO_NULL;    int color, mrc;    int newrank, newprocs;    hid_t fid;			/* file IDs */    hid_t acc_tpl;		/* File access properties */    herr_t ret;			/* generic return value */    if (verbose)	printf("Independent write test on file %s %s/n",	    filenames[0], filenames[1]);    color = mpi_rank%2;    mrc = MPI_Comm_split (MPI_COMM_WORLD, color, mpi_rank, &comm);    assert(mrc==MPI_SUCCESS);    MPI_Comm_size(comm,&newprocs);    MPI_Comm_rank(comm,&newrank);    if (color){	/* odd-rank processes */	mrc = MPI_Barrier(comm);	assert(mrc==MPI_SUCCESS);    }else{	/* even-rank processes */	/* setup file access template */	acc_tpl = H5Pcreate (H5P_FILE_ACCESS);	assert(acc_tpl != FAIL);	/* set Parallel access with communicator */	ret = H5Pset_fapl_mpio(acc_tpl, comm, info);	assert(ret != FAIL);	/* create the file collectively */	fid=H5Fcreate(filenames[color],H5F_ACC_TRUNC,H5P_DEFAULT,acc_tpl);	assert(fid != FAIL);	MESG("H5Fcreate succeed");	/* Release file-access template */	ret=H5Pclose(acc_tpl);	assert(ret != FAIL);	ret=H5Fclose(fid);	assert(ret != FAIL);    }    if (mpi_rank == 0){	mrc = MPI_File_delete(filenames[color], info);	assert(mrc==MPI_SUCCESS);    }}

/*** /brief Opens an HDF file at the given path* /param[in]  path    Path to the HDF file to open* /param[out] file_id Pointer to an hid_t* /returns Status code* /retval 1 Failure* /retval 0 Success* /sa ch5_close*/int ch5_open(const char *path, hid_t *file_id) {  hid_t plist = H5P_DEFAULT;#ifdef HAVE_MPIIO  hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPIO_INFO_NULL);#endif  hid_t id = H5Fopen(path, H5F_ACC_RDWR, plist);#ifdef HAVE_MPIIO  H5Pclose(plist_id);#endif  if (id < 0) return 1;  *file_id = id;  return 0;}

/*** /brief Creates a new HDF file at the given path* /note Will overwrite/truncate an existing file at the given path* /param[in]  path    Path to the HDF file to create* /param[out] file_id Pointer to an hid_t* /returns Status code* /retval 1 Failure* /retval 0 Success* /sa ch5_close*/int ch5_create(const char *path, hid_t *file_id) {  hid_t plist = H5P_DEFAULT;#ifdef HAVE_MPIIO  hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist_id, MPI_COMM_WORLD, MPIO_INFO_NULL);#endif  hid_t id = H5Fcreate(path, H5F_ACC_TRUNC, H5P_DEFAULT, plist);#ifdef HAVE_MPIIO  H5Pclose(plist_id);#endif  if (id < 0) return 1;  *file_id = id;  ch5_meta_set_name( *file_id, path );  return 0;}

op_set op_decl_set_hdf5(char const *file, char const *name){  //create new communicator  int my_rank, comm_size;  MPI_Comm_dup(MPI_COMM_WORLD, &OP_MPI_HDF5_WORLD);  MPI_Comm_rank(OP_MPI_HDF5_WORLD, &my_rank);  MPI_Comm_size(OP_MPI_HDF5_WORLD, &comm_size);  //MPI variables  MPI_Info info  = MPI_INFO_NULL;  //HDF5 APIs definitions  hid_t       file_id; //file identifier  hid_t plist_id;  //property list identifier  hid_t dset_id; //dataset identifier  //Set up file access property list with parallel I/O access  plist_id = H5Pcreate(H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist_id, OP_MPI_HDF5_WORLD, info);  file_id = H5Fopen(file, H5F_ACC_RDONLY, plist_id );  H5Pclose(plist_id);  //Create the dataset with default properties and close dataspace.  dset_id = H5Dopen(file_id, name, H5P_DEFAULT);  //Create property list for collective dataset write.  plist_id = H5Pcreate(H5P_DATASET_XFER);  H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);  int g_size = 0;  //read data  H5Dread(dset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, plist_id, &g_size);  H5Pclose(plist_id);  H5Dclose(dset_id);  H5Fclose(file_id);  //calculate local size of set for this mpi process  int l_size = compute_local_size (g_size, comm_size, my_rank);  MPI_Comm_free(&OP_MPI_HDF5_WORLD);  return op_decl_set(l_size,  name);}

  int mpi_mesh_grdecl::open_file_mpi_hdf5(const char *file_name)  {    //Set up file access property list with parallel I/O access    hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS); // Creates a new property as an instance of a property li_startt class.    //Each process of the MPI communicator creates an access template and sets i_end up wi_endh MPI parallel access information. Thi_start i_start2 done wi_endh the H5Pcreate call to obtain the file access property li_startt and the H5Pset_fapl_mpio call to set up parallel I/O access.    H5Pset_fapl_mpio(plist_id, mpi_comm, mpi_info);    // Open a new file and release property list identifier    hid_t file_id = H5Fopen (file_name, H5F_ACC_RDONLY, H5P_DEFAULT); // H5F_ACC_RDONLY - Allow read-only access to file.    if (file_id < 0)      {        printf("Error: Can't open file %s!/n", file_name);        return -1;      }    H5Pclose (plist_id);    return file_id;  }

/*---------------------------------------------------------------------------- * Name:        h5pset_fapl_mpio_c * Purpose:     Call H5Pset_fapl_mpio to set mode for parallel I/O and the user *              supplied communicator and info object * Inputs:      prp_id - property list identifier *              comm   - MPI communicator *              info   - MPI info object * Returns:     0 on success, -1 on failure * Programmer:  Elena Pourmal *              Thursday, October 26, 2000 * Modifications: *---------------------------------------------------------------------------*/int_fnh5pset_fapl_mpio_c(hid_t_f *prp_id, int_f* comm, int_f* info){     int ret_value = -1;     hid_t c_prp_id;     herr_t ret;     MPI_Comm c_comm;     MPI_Info c_info;     c_comm = MPI_Comm_f2c(*comm);     c_info = MPI_Info_f2c(*info);     /*      * Call H5Pset_mpi function.      */     c_prp_id = *prp_id;     ret = H5Pset_fapl_mpio(c_prp_id, c_comm, c_info);     if (ret < 0) return ret_value;     ret_value = 0;     return ret_value;}

void saveParticleComp_Int(int *data,char *fileName,char *dataName,int totalCnt,int cnt,int offSet){  int i,j,k;  int myrank, nTasks;  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);  MPI_Comm_size(MPI_COMM_WORLD, &nTasks);  hid_t file_id,dset_id,plist_id,tic_id;  herr_t status;  hid_t total_file_space,subfilespace,filespace,memspace,ticspace;  hsize_t dimsf[1],count[1],offset[1];  plist_id=H5Pcreate(H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist_id,MPI_COMM_WORLD,MPI_INFO_NULL);//    H5Pset_fclose_degree(plist_id,H5F_CLOSE_SEMI);//    MPI_Barrier(MPI_COMM_WORLD);  file_id=H5Fopen(fileName,H5F_ACC_RDWR,plist_id);  H5Pclose(plist_id);  dimsf[0]=totalCnt;  filespace=H5Screate_simple(1,dimsf,NULL);  count[0]=cnt;  offset[0]=offSet;  memspace=H5Screate_simple(1,count,NULL);  dset_id=H5Dcreate2(file_id,dataName,H5T_NATIVE_INT,filespace,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);  subfilespace=H5Dget_space(dset_id);  H5Sselect_hyperslab(subfilespace,H5S_SELECT_SET,offset,NULL,count,NULL);  plist_id=H5Pcreate(H5P_DATASET_XFER);  H5Pset_dxpl_mpio(plist_id,H5FD_MPIO_INDEPENDENT);  status = H5Dwrite(dset_id, H5T_NATIVE_INT,memspace,subfilespace,plist_id,data);  H5Pclose(plist_id);  H5Sclose(subfilespace);  H5Dclose(dset_id);  H5Sclose(memspace);  H5Sclose(filespace);  H5Fclose(file_id);}

	/*!	 *	 * /brief Write a set of particle position and properties into HDF5	 *	 * /tparam Pos Vector of positions type	 * /taparam Prp Vector of properties type	 * /tparam prp list of properties to output	 *	 * /param pos Vector with the positions	 * /param prp Vector with the properties	 * /param stop size of the vector to output	 *	 */	template<typename VPos, typename VPrp, int ... prp > bool write(const std::string & file, openfpm::vector<VPos> & v_pos, openfpm::vector<VPrp> & v_prp, size_t stop)	{		Vcluster & v_cl = create_vcluster();		// Open and HDF5 file in parallel		hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);		H5Pset_fapl_mpio(plist_id, v_cl.getMPIComm(), MPI_INFO_NULL);		file_id = H5Fcreate(file.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);		H5Pclose(plist_id);		// Single coordinate positional vector		openfpm::vector<typename VPos::coord_type> x_n;		x_n.resize(stop);		//for each component, fill x_n		for (size_t i = 0 ; i < VPos::dims ; i++)		{			//			for (size_t j = 0 ; j < stop ; j++)				x_n.get(j) = v_pos.template get<0>(j)[i];			std::stringstream str;			str << "x" << i;			HDF5CreateDataSet<typename VPos::coord_type>(file_id,str.str(),x_n.getPointer(),stop*sizeof(typename VPos::coord_type));		}		// Now we write the properties		typedef typename to_boost_vmpl<prp ... >::type v_prp_seq;		H5_prop_out<openfpm::vector<VPrp>,has_attributes<VPrp>::value> f(file_id,v_prp,stop);		boost::mpl::for_each_ref<v_prp_seq>(f);		H5Fclose(file_id);		return true;	}

void restoreData(float *data,char *fileName,char *dataName,int totalCnt,int cnt,int *cntOffSet){  hid_t file_id,dset_id,plist_id,group_id;  herr_t status;  hid_t subfilespace,filespace,memspace;  hsize_t dimsf[1],count[1],offset[1];  int myrank, nTasks;      MPI_Comm_rank(MPI_COMM_WORLD, &myrank);  MPI_Comm_size(MPI_COMM_WORLD, &nTasks);  plist_id=H5Pcreate(H5P_FILE_ACCESS);  H5Pset_fapl_mpio(plist_id,MPI_COMM_WORLD,MPI_INFO_NULL);//  H5Pset_fclose_degree(plist_id,H5F_CLOSE_SEMI);//  MPI_Barrier(MPI_COMM_WORLD);  file_id=H5Fopen(fileName,H5F_ACC_RDWR,plist_id);  H5Pclose(plist_id);  dimsf[0]=totalCnt;       filespace=H5Screate_simple(1,dimsf,NULL);  count[0]=cnt;  offset[0]=cntOffSet[myrank];  memspace=H5Screate_simple(1,count,NULL);  dset_id=H5Dopen2(file_id,dataName,H5P_DEFAULT);  subfilespace=H5Dget_space(dset_id);  H5Sselect_hyperslab(subfilespace,H5S_SELECT_SET,offset,NULL,count,NULL);  plist_id=H5Pcreate(H5P_DATASET_XFER);  H5Pset_dxpl_mpio(plist_id,H5FD_MPIO_COLLECTIVE);  status = H5Dread(dset_id, H5T_NATIVE_FLOAT,memspace,subfilespace,plist_id,data);  H5Pclose(plist_id);  H5Sclose(subfilespace);  H5Dclose(dset_id);  H5Sclose(memspace);  H5Sclose(filespace);  H5Fclose(file_id);}

void LifeV::HDF5IO::openFile (const std::string& fileName,                              const commPtr_Type& comm,                              const bool& existing){    hid_t plistId;    MPI_Comm mpiComm = comm->Comm();    MPI_Info info = MPI_INFO_NULL;    // Set up file access property list with parallel I/O access    plistId = H5Pcreate (H5P_FILE_ACCESS);    H5Pset_fapl_mpio (plistId, mpiComm, info);    // Create/open a file collectively and release property list identifier.    if (existing)    {        M_fileId = H5Fopen (fileName.c_str(), H5F_ACC_RDONLY, plistId);    }    else    {        M_fileId = H5Fcreate (fileName.c_str(), H5F_ACC_TRUNC,                              H5P_DEFAULT, plistId);    }    H5Pclose (plistId);}

void PHDF5fileClass::CreatePHDF5file(double *L, int *dglob, int *dlocl, bool bp){  hid_t   acc_t;  hid_t   Ldataspace;  hid_t   Ldataset;  hid_t   ndataspace;  hid_t   ndataset;  herr_t  status;  hsize_t d[1];  /* ---------------------------------------------- */  /* 0- Initialize the some of the class parameters */  /* ---------------------------------------------- */  bparticles  = bp;  for (int i=0; i<ndim; i++){    LxLyLz[i]    = L[i];    dim[i]       = (hsize_t)dglob[i];    chdim[i]     = (hsize_t)dlocl[i];  }  /* ----------------------------------------------------- */  /* 1- Set the access template for the parallel HDF5 file */  /* ----------------------------------------------------- */  acc_t = H5Pcreate(H5P_FILE_ACCESS);  /* --------------------------------------- */  /* 2- Tell HDF5 that we want to use MPI-IO */  /* --------------------------------------- */  H5Pset_fapl_mpio(acc_t, comm, MPI_INFO_NULL);  /* ------------------------------------------------------- */  /* 3- Load file identifier and release the access template */  /* ------------------------------------------------------- */  file_id = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, acc_t);  H5Pclose(acc_t);  /* -------------------- */  /* 4- Set up the groups */  /* -------------------- */  for (int i=0; i<ngrp; i++){    if (!(grpnames[i]=="Particles"&&!bparticles)){      hid_t grp;      grp = H5Gcreate2(file_id, grpnames[i].c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);      H5Gclose(grp);    }  }  /* -------------------------------------- */  /* Create and fill the Parameters dataset */  /* -------------------------------------- */  d[0] = 3;  status = H5LTmake_dataset(file_id, "/Parameters/LxLyLz", 1, d, H5T_NATIVE_DOUBLE, LxLyLz);  status = H5LTmake_dataset(file_id, "/Parameters/ncell" , 1, d, H5T_NATIVE_INT   , dglob);}

/*-------------------------------------------------------------------------*/int FTI_RecoverHDF5(FTIT_configuration* FTI_Conf, FTIT_execution* FTI_Exec, FTIT_checkpoint* FTI_Ckpt,                   FTIT_dataset* FTI_Data){    char str[FTI_BUFS], fn[FTI_BUFS];    snprintf(fn, FTI_BUFS, "%s/%s", FTI_Ckpt[FTI_Exec->ckptLvel].dir, FTI_Exec->meta[FTI_Exec->ckptLvel].ckptFile);    if( FTI_Exec->h5SingleFile ) {        snprintf( fn, FTI_BUFS, "%s/%s-ID%08d.h5", FTI_Conf->h5SingleFileDir, FTI_Conf->h5SingleFilePrefix, FTI_Exec->ckptID );    }    sprintf(str, "Trying to load FTI checkpoint file (%s)...", fn);    FTI_Print(str, FTI_DBUG);        hid_t file_id;        //Open hdf5 file    if( FTI_Exec->h5SingleFile ) {         hid_t plid = H5Pcreate( H5P_FILE_ACCESS );        H5Pset_fapl_mpio( plid, FTI_COMM_WORLD, MPI_INFO_NULL );        file_id = H5Fopen( fn, H5F_ACC_RDONLY, plid );        H5Pclose( plid );    } else {        file_id = H5Fopen(fn, H5F_ACC_RDONLY, H5P_DEFAULT);    }    if (file_id < 0) {        FTI_Print("Could not open FTI checkpoint file.", FTI_EROR);        return FTI_NREC;    }    FTI_Exec->H5groups[0]->h5groupID = file_id;    FTIT_H5Group* rootGroup = FTI_Exec->H5groups[0];    int i;    for (i = 0; i < FTI_Exec->H5groups[0]->childrenNo; i++) {        FTI_OpenGroup(FTI_Exec->H5groups[rootGroup->childrenID[i]], file_id, FTI_Exec->H5groups);    }        for (i = 0; i < FTI_Exec->nbVar; i++) {        FTI_CreateComplexType(FTI_Data[i].type, FTI_Exec->FTI_Type);    }        if( FTI_Exec->h5SingleFile ) {         FTI_OpenGlobalDatasets( FTI_Exec );    }    for (i = 0; i < FTI_Exec->nbVar; i++) {        herr_t res;        if( FTI_Exec->h5SingleFile ) {             res = FTI_ReadSharedFileData( FTI_Data[i] );        } else {            res = FTI_ReadHDF5Var(&FTI_Data[i]);        }        if (res < 0) {            FTI_Print("Could not read FTI checkpoint file.", FTI_EROR);            int j;            for (j = 0; j < FTI_Exec->H5groups[0]->childrenNo; j++) {                FTI_CloseGroup(FTI_Exec->H5groups[rootGroup->childrenID[j]], FTI_Exec->H5groups);            }            H5Fclose(file_id);            return FTI_NREC;        }    }    for (i = 0; i < FTI_Exec->nbVar; i++) {        FTI_CloseComplexType(FTI_Data[i].type, FTI_Exec->FTI_Type);    }    int j;    for (j = 0; j < FTI_Exec->H5groups[0]->childrenNo; j++) {        FTI_CloseGroup(FTI_Exec->H5groups[rootGroup->childrenID[j]], FTI_Exec->H5groups);    }        if( FTI_Exec->h5SingleFile ) {         FTI_CloseGlobalDatasets( FTI_Exec );    }    FTI_Exec->H5groups[0]->h5groupID = -1;    if (H5Fclose(file_id) < 0) {        FTI_Print("Could not close FTI checkpoint file.", FTI_EROR);        return FTI_NREC;    }    FTI_Exec->reco = 0;    return FTI_SCES;}

/*-------------------------------------------------------------------------*/int FTI_WriteHDF5(FTIT_configuration* FTI_Conf, FTIT_execution* FTI_Exec,        FTIT_topology* FTI_Topo, FTIT_checkpoint* FTI_Ckpt,        FTIT_dataset* FTI_Data){    FTI_Print("I/O mode: HDF5.", FTI_DBUG);    char str[FTI_BUFS], fn[FTI_BUFS];    int level = FTI_Exec->ckptLvel;    if (level == 4 && FTI_Ckpt[4].isInline) { //If inline L4 save directly to global directory        snprintf(fn, FTI_BUFS, "%s/%s", FTI_Conf->gTmpDir, FTI_Exec->meta[0].ckptFile);    }    else {        snprintf(fn, FTI_BUFS, "%s/%s", FTI_Conf->lTmpDir, FTI_Exec->meta[0].ckptFile);    }    if( FTI_Exec->h5SingleFile ) {        snprintf( fn, FTI_BUFS, "%s/%s-ID%08d.h5", FTI_Conf->h5SingleFileDir, FTI_Conf->h5SingleFilePrefix, FTI_Exec->ckptID );    }    hid_t file_id;        //Creating new hdf5 file    if( FTI_Exec->h5SingleFile ) {         hid_t plid = H5Pcreate( H5P_FILE_ACCESS );        H5Pset_fapl_mpio(plid, FTI_COMM_WORLD, MPI_INFO_NULL);        file_id = H5Fcreate(fn, H5F_ACC_TRUNC, H5P_DEFAULT, plid);               H5Pclose( plid );    } else {        file_id = H5Fcreate(fn, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);    }    if (file_id < 0) {        sprintf(str, "FTI checkpoint file (%s) could not be opened.", fn);        FTI_Print(str, FTI_EROR);        return FTI_NSCS;    }    FTI_Exec->H5groups[0]->h5groupID = file_id;    FTIT_H5Group* rootGroup = FTI_Exec->H5groups[0];    int i;    for (i = 0; i < rootGroup->childrenNo; i++) {        FTI_CreateGroup(FTI_Exec->H5groups[rootGroup->childrenID[i]], file_id, FTI_Exec->H5groups);    }    // write data into ckpt file    // create datatypes    for (i = 0; i < FTI_Exec->nbVar; i++) {        int toCommit = 0;        if (FTI_Data[i].type->h5datatype < 0) {            toCommit = 1;        }        sprintf(str, "Calling CreateComplexType [%d] with hid_t %ld", FTI_Data[i].type->id, (long)FTI_Data[i].type->h5datatype);        FTI_Print(str, FTI_DBUG);        FTI_CreateComplexType(FTI_Data[i].type, FTI_Exec->FTI_Type);        if (toCommit == 1) {            char name[FTI_BUFS];            if (FTI_Data[i].type->structure == NULL) {                //this is the array of bytes with no name                sprintf(name, "Type%d", FTI_Data[i].type->id);            } else {                strncpy(name, FTI_Data[i].type->structure->name, FTI_BUFS);            }            herr_t res = H5Tcommit(FTI_Data[i].type->h5group->h5groupID, name, FTI_Data[i].type->h5datatype, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);            if (res < 0) {                sprintf(str, "Datatype #%d could not be commited", FTI_Data[i].id);                FTI_Print(str, FTI_EROR);                int j;                for (j = 0; j < FTI_Exec->H5groups[0]->childrenNo; j++) {                    FTI_CloseGroup(FTI_Exec->H5groups[rootGroup->childrenID[j]], FTI_Exec->H5groups);                }                H5Fclose(file_id);                return FTI_NSCS;            }        }    }    if( FTI_Exec->h5SingleFile ) {         FTI_CreateGlobalDatasets( FTI_Exec );    }    // write data    for (i = 0; i < FTI_Exec->nbVar; i++) {        int res;        if( FTI_Exec->h5SingleFile ) {             res = FTI_WriteSharedFileData( FTI_Data[i] );        } else {            res = FTI_WriteHDF5Var(&FTI_Data[i]);         }        if ( res != FTI_SCES ) {            sprintf(str, "Dataset #%d could not be written", FTI_Data[i].id);            FTI_Print(str, FTI_EROR);            int j;            for (j = 0; j < FTI_Exec->H5groups[0]->childrenNo; j++) {                FTI_CloseGroup(FTI_Exec->H5groups[rootGroup->childrenID[j]], FTI_Exec->H5groups);            }            H5Fclose(file_id);            return FTI_NSCS;        }    }    //.........这里部分代码省略.........

/* * Open a file through the HDF5 interface. */static void *HDF5_Open(char *testFileName, IOR_param_t * param){        hid_t accessPropList, createPropList;        hsize_t memStart[NUM_DIMS],            dataSetDims[NUM_DIMS],            memStride[NUM_DIMS],            memCount[NUM_DIMS], memBlock[NUM_DIMS], memDataSpaceDims[NUM_DIMS];        int tasksPerDataSet;        unsigned fd_mode = (unsigned)0;        hid_t *fd;        MPI_Comm comm;        MPI_Info mpiHints = MPI_INFO_NULL;        fd = (hid_t *) malloc(sizeof(hid_t));        if (fd == NULL)                ERR("malloc() failed");        /*         * HDF5 uses different flags than those for POSIX/MPIIO         */        if (param->open == WRITE) {     /* WRITE flags */                param->openFlags = IOR_TRUNC;        } else {                /* READ or check WRITE/READ flags */                param->openFlags = IOR_RDONLY;        }        /* set IOR file flags to HDF5 flags */        /* -- file open flags -- */        if (param->openFlags & IOR_RDONLY) {                fd_mode |= H5F_ACC_RDONLY;        }        if (param->openFlags & IOR_WRONLY) {                fprintf(stdout, "File write only not implemented in HDF5/n");        }        if (param->openFlags & IOR_RDWR) {                fd_mode |= H5F_ACC_RDWR;        }        if (param->openFlags & IOR_APPEND) {                fprintf(stdout, "File append not implemented in HDF5/n");        }        if (param->openFlags & IOR_CREAT) {                fd_mode |= H5F_ACC_CREAT;        }        if (param->openFlags & IOR_EXCL) {                fd_mode |= H5F_ACC_EXCL;        }        if (param->openFlags & IOR_TRUNC) {                fd_mode |= H5F_ACC_TRUNC;        }        if (param->openFlags & IOR_DIRECT) {                fprintf(stdout, "O_DIRECT not implemented in HDF5/n");        }        /* set up file creation property list */        createPropList = H5Pcreate(H5P_FILE_CREATE);        HDF5_CHECK(createPropList, "cannot create file creation property list");        /* set size of offset and length used to address HDF5 objects */        HDF5_CHECK(H5Pset_sizes                   (createPropList, sizeof(hsize_t), sizeof(hsize_t)),                   "cannot set property list properly");        /* set up file access property list */        accessPropList = H5Pcreate(H5P_FILE_ACCESS);        HDF5_CHECK(accessPropList, "cannot create file access property list");        /*         * someday HDF5 implementation will allow subsets of MPI_COMM_WORLD         */        /* store MPI communicator info for the file access property list */        if (param->filePerProc) {                comm = MPI_COMM_SELF;        } else {                comm = testComm;        }        SetHints(&mpiHints, param->hintsFileName);        /*         * note that with MP_HINTS_FILTERED=no, all key/value pairs will         * be in the info object.  The info object that is attached to         * the file during MPI_File_open() will only contain those pairs         * deemed valid by the implementation.         */        /* show hints passed to file */        if (rank == 0 && param->showHints) {                fprintf(stdout, "/nhints passed to access property list {/n");                ShowHints(&mpiHints);                fprintf(stdout, "}/n");        }        HDF5_CHECK(H5Pset_fapl_mpio(accessPropList, comm, mpiHints),                   "cannot set file access property list");        /* set alignment */        HDF5_CHECK(H5Pset_alignment(accessPropList, param->setAlignment,                                    param->setAlignment),                   "cannot set alignment");        /* open file */        if (param->open == WRITE) {     /* WRITE *///.........这里部分代码省略.........

void _io_write_prim_h5mpi(const char *fname, const char **pnames, const double *data)// -----------------------------------------------------------------------------// This function uses a collective MPI-IO procedure to write the contents of// 'data' to the HDF5 file named 'fname', which is assumed to have been created// already. The dataset with name 'dname', which is being written to, must not// exist already. Chunking is enabled as per the module-wide ChunkSize variable,// and is disabled by default. Recommended chunk size is local subdomain// size. This will result in optimized read/write on the same decomposition// layout, but poor performance for different access patterns, for example the// slabs used by cluster-FFT functions.////                                   WARNING!//// All processors must define the same chunk size, the behavior of this function// is not defined otherwise. This implies that chunking should be disabled when// running on a strange number of cores, and subdomain sizes are non-uniform.// -----------------------------------------------------------------------------{  hsize_t ndp1 = n_dims + 1;  hsize_t *a_nint = (hsize_t*) malloc(ndp1*sizeof(hsize_t));  hsize_t *l_ntot = (hsize_t*) malloc(ndp1*sizeof(hsize_t));  hsize_t *l_strt = (hsize_t*) malloc(ndp1*sizeof(hsize_t));  hsize_t *stride = (hsize_t*) malloc(ndp1*sizeof(hsize_t));  int i;  for (i=0; i<n_dims; ++i) {    a_nint[i] = A_nint[i]; // Selection size, target and destination    l_ntot[i] = L_ntot[i]; // Memory space total size    l_strt[i] = L_strt[i]; // Memory space selection start    stride[i] = 1;  }  a_nint[ndp1 - 1] = 1;  l_ntot[ndp1 - 1] = n_prim;  stride[ndp1 - 1] = n_prim;  // Here we create the following property lists:  //  // file access property list   ........ for the call to H5Fopen  // dset creation property list ........ for the call to H5Dcreate  // dset transfer property list ........ for the call to H5Dwrite  // ---------------------------------------------------------------------------  hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);  hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE);  hid_t dxpl = H5Pcreate(H5P_DATASET_XFER);  // Here we define collective (MPI) access to the file with alignment  // properties optimized for the local file system, according to DiskBlockSize.  // ---------------------------------------------------------------------------  if (EnableChunking) {    H5Pset_chunk(dcpl, n_dims, ChunkSize);  }  if (EnableAlignment) {    H5Pset_alignment(fapl, AlignThreshold, DiskBlockSize);  }  H5Pset_fapl_mpio(fapl, MPI_COMM_WORLD, MPI_INFO_NULL);  H5Pset_dxpl_mpio(dxpl, H5FD_MPIO_COLLECTIVE);  hid_t file = H5Fopen(fname, H5F_ACC_RDWR, fapl);  const int overwrite = H5Lexists(file, "prim", H5P_DEFAULT);  hid_t prim = overwrite ? H5Gopen(file, "prim", H5P_DEFAULT) :    H5Gcreate(file, "prim", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);  hid_t mspc = H5Screate_simple(ndp1  , l_ntot, NULL);  hid_t fspc = H5Screate_simple(n_dims, G_ntot, NULL);  // Call signature to H5Sselect_hyperslab is (start, stride, count, chunk)  // ---------------------------------------------------------------------------  const clock_t start_all = clock();  for (i=0; i<n_prim; ++i) {    hid_t dset = overwrite ? H5Dopen(prim, pnames[i], H5P_DEFAULT) :       H5Dcreate(prim, pnames[i], H5T_NATIVE_DOUBLE, fspc,		H5P_DEFAULT, dcpl, H5P_DEFAULT);    l_strt[ndp1 - 1] = i;    H5Sselect_hyperslab(mspc, H5S_SELECT_SET, l_strt, stride, a_nint, NULL);    H5Sselect_hyperslab(fspc, H5S_SELECT_SET, G_strt,   NULL, A_nint, NULL);    H5Dwrite(dset, H5T_NATIVE_DOUBLE, mspc, fspc, dxpl, data);    H5Dclose(dset);  }  if (iolog) {    const double sec = (double)(clock() - start_all) / CLOCKS_PER_SEC;    fprintf(iolog, "[h5mpi] write to %s took %f minutes/n", fname, sec/60.0);    fflush(iolog);  }  free(a_nint);  free(l_ntot);  free(l_strt);  // Always close the hid_t handles in the reverse order they were opened in.  // ---------------------------------------------------------------------------  H5Sclose(fspc);  H5Sclose(mspc);  H5Gclose(prim);  H5Fclose(file);  H5Pclose(dxpl);  H5Pclose(dcpl);  H5Pclose(fapl);}

/*------------------------------------------------------------------------- * Function:    main * * Purpose:    Part 1 of a two-part H5Fflush() test. * * Return:    Success:    0 * *        Failure:    1 * * Programmer:    Robb Matzke *              Friday, October 23, 1998 * * Modifications: *         Leon Arber *         Sept. 26, 2006, expand test to check for failure if H5Fflush is not called. * * *------------------------------------------------------------------------- */intmain(int argc, char* argv[]){    hid_t file1, file2, fapl;    MPI_File    *mpifh_p = NULL;    char    name[1024];    const char  *envval = NULL;    int mpi_size, mpi_rank;    MPI_Comm comm  = MPI_COMM_WORLD;    MPI_Info info  = MPI_INFO_NULL;    MPI_Init(&argc, &argv);    MPI_Comm_size(comm, &mpi_size);    MPI_Comm_rank(comm, &mpi_rank);    fapl = H5Pcreate(H5P_FILE_ACCESS);    H5Pset_fapl_mpio(fapl, comm, info);    if(mpi_rank == 0)    TESTING("H5Fflush (part1)");    envval = HDgetenv("HDF5_DRIVER");    if(envval == NULL)        envval = "nomatch";    if(HDstrcmp(envval, "split")) {    /* Create the file */    h5_fixname(FILENAME[0], fapl, name, sizeof name);    file1 = create_file(name, fapl);    /* Flush and exit without closing the library */    if(H5Fflush(file1, H5F_SCOPE_GLOBAL) < 0) goto error;    /* Create the other file which will not be flushed */    h5_fixname(FILENAME[1], fapl, name, sizeof name);    file2 = create_file(name, fapl);    if(mpi_rank == 0)        PASSED();    fflush(stdout);    fflush(stderr);    } /* end if */    else {        SKIPPED();        puts("    Test not compatible with current Virtual File Driver");    } /* end else */    /*     * Some systems like AIX do not like files not closed when MPI_Finalize     * is called.  So, we need to get the MPI file handles, close them by hand.     * Then the _exit is still needed to stop at_exit from happening in some systems.     * Note that MPIO VFD returns the address of the file-handle in the VFD struct     * because MPI_File_close wants to modify the file-handle variable.     */    /* close file1 */    if(H5Fget_vfd_handle(file1, fapl, (void **)&mpifh_p) < 0) {    printf("H5Fget_vfd_handle for file1 failed/n");    goto error;    } /* end if */    if(MPI_File_close(mpifh_p) != MPI_SUCCESS) {    printf("MPI_File_close for file1 failed/n");    goto error;    } /* end if */    /* close file2 */    if(H5Fget_vfd_handle(file2, fapl, (void **)&mpifh_p) < 0) {    printf("H5Fget_vfd_handle for file2 failed/n");    goto error;    } /* end if */    if(MPI_File_close(mpifh_p) != MPI_SUCCESS) {    printf("MPI_File_close for file2 failed/n");    goto error;    } /* end if */    fflush(stdout);    fflush(stderr);    HD_exit(0);error:    fflush(stdout);    fflush(stderr);    HD_exit(1);}

/*------------------------------------------------------------------------- * Function:    test_fapl_mpio_dup * * Purpose:     Test if fapl_mpio property list keeps a duplicate of the * 		communicator and INFO objects given when set; and returns * 		duplicates of its components when H5Pget_fapl_mpio is called. * * Return:      Success:        None * *              Failure:        Abort * * Programmer:  Albert Cheng *              January 9, 2003 * * Modifications: *------------------------------------------------------------------------- */voidtest_fapl_mpio_dup(void){    int mpi_size, mpi_rank;    MPI_Comm comm, comm_tmp;    int mpi_size_old, mpi_rank_old;    int mpi_size_tmp, mpi_rank_tmp;    MPI_Info info = MPI_INFO_NULL;    MPI_Info info_tmp = MPI_INFO_NULL;    int mrc;			/* MPI return value */    hid_t acc_pl;		/* File access properties */    herr_t ret;			/* hdf5 return value */    int nkeys, nkeys_tmp;    if (VERBOSE_MED)	printf("Verify fapl_mpio duplicates communicator and INFO objects/n");    /* set up MPI parameters */    MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);    if (VERBOSE_MED)	printf("rank/size of MPI_COMM_WORLD are %d/%d/n", mpi_rank, mpi_size);    /* Create a new communicator that has the same processes as MPI_COMM_WORLD.     * Use MPI_Comm_split because it is simplier than MPI_Comm_create     */    mrc = MPI_Comm_split(MPI_COMM_WORLD, 0, 0, &comm);    VRFY((mrc==MPI_SUCCESS), "MPI_Comm_split");    MPI_Comm_size(comm,&mpi_size_old);    MPI_Comm_rank(comm,&mpi_rank_old);    if (VERBOSE_MED)	printf("rank/size of comm are %d/%d/n", mpi_rank_old, mpi_size_old);    /* create a new INFO object with some trivial information. */    mrc = MPI_Info_create(&info);    VRFY((mrc==MPI_SUCCESS), "MPI_Info_create");    mrc = MPI_Info_set(info, "hdf_info_name", "XYZ");    VRFY((mrc==MPI_SUCCESS), "MPI_Info_set");    if (MPI_INFO_NULL != info){	mrc=MPI_Info_get_nkeys(info, &nkeys);	VRFY((mrc==MPI_SUCCESS), "MPI_Info_get_nkeys");    }    if (VERBOSE_MED)	h5_dump_info_object(info);    acc_pl = H5Pcreate (H5P_FILE_ACCESS);    VRFY((acc_pl >= 0), "H5P_FILE_ACCESS");    ret = H5Pset_fapl_mpio(acc_pl, comm, info);    VRFY((ret >= 0), "");    /* Case 1:     * Free the created communicator and INFO object.     * Check if the access property list is still valid and can return     * valid communicator and INFO object.     */    mrc = MPI_Comm_free(&comm);    VRFY((mrc==MPI_SUCCESS), "MPI_Comm_free");    if (MPI_INFO_NULL!=info){	mrc = MPI_Info_free(&info);	VRFY((mrc==MPI_SUCCESS), "MPI_Info_free");    }    ret = H5Pget_fapl_mpio(acc_pl, &comm_tmp, &info_tmp);    VRFY((ret >= 0), "H5Pget_fapl_mpio");    MPI_Comm_size(comm_tmp,&mpi_size_tmp);    MPI_Comm_rank(comm_tmp,&mpi_rank_tmp);    if (VERBOSE_MED)	printf("After H5Pget_fapl_mpio: rank/size of comm are %d/%d/n",	mpi_rank_tmp, mpi_size_tmp);    VRFY((mpi_size_tmp==mpi_size), "MPI_Comm_size");    VRFY((mpi_rank_tmp==mpi_rank), "MPI_Comm_rank");    if (MPI_INFO_NULL != info_tmp){	mrc=MPI_Info_get_nkeys(info_tmp, &nkeys_tmp);	VRFY((mrc==MPI_SUCCESS), "MPI_Info_get_nkeys");	VRFY((nkeys_tmp==nkeys), "new and old nkeys equal");    }    if (VERBOSE_MED)	h5_dump_info_object(info_tmp);    /* Case 2:     * Free the retrieved communicator and INFO object.     * Check if the access property list is still valid and can return//.........这里部分代码省略.........

hid_t seissol::checkpoint::h5::Wavefield::initFile(int odd, const char* filename){	hid_t h5file;	if (loaded()) {		// Open the old file		h5file = open(filename, false);		checkH5Err(h5file);		// Time		m_h5time[odd] = H5Aopen(h5file, "time", H5P_DEFAULT);		checkH5Err(m_h5time[odd]);		// Wavefield writer		m_h5timestepWavefield[odd] = H5Aopen(h5file, "timestep_wavefield", H5P_DEFAULT);		checkH5Err(m_h5timestepWavefield[odd]);		// Data		m_h5data[odd] = H5Dopen(h5file, "values", H5P_DEFAULT);		checkH5Err(m_h5data[odd]);	} else {		// Create the file		hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);		checkH5Err(h5plist);		checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));		hsize_t align = utils::Env::get<hsize_t>("SEISSOL_CHECKPOINT_ALIGNMENT", 0);		if (align > 0)			checkH5Err(H5Pset_alignment(h5plist, 1, align));#ifdef USE_MPI		MPIInfo info;		checkH5Err(H5Pset_fapl_mpio(h5plist, seissol::MPI::mpi.comm(), info.get()));#endif // USE_MPI		h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);		checkH5Err(h5file);		checkH5Err(H5Pclose(h5plist));		// Create scalar dataspace for attributes		hid_t h5spaceScalar = H5Screate(H5S_SCALAR);		checkH5Err(h5spaceScalar);		// Time		m_h5time[odd] = H5Acreate(h5file, "time", H5T_IEEE_F64LE, h5spaceScalar,				H5P_DEFAULT, H5P_DEFAULT);		checkH5Err(m_h5time[odd]);		// Partitions		hid_t h5partitions = H5Acreate(h5file, "partitions", H5T_STD_I32LE, h5spaceScalar,				H5P_DEFAULT, H5P_DEFAULT);		checkH5Err(h5partitions);		int p = partitions();		checkH5Err(H5Awrite(h5partitions, H5T_NATIVE_INT, &p));		checkH5Err(H5Aclose(h5partitions));		// Wavefield writer		m_h5timestepWavefield[odd] = H5Acreate(h5file, "timestep_wavefield",				H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);		checkH5Err(m_h5timestepWavefield[odd]);		int t = 0;		checkH5Err(H5Awrite(m_h5timestepWavefield[odd], H5T_NATIVE_INT, &t));		checkH5Err(H5Sclose(h5spaceScalar));		// Variable		h5plist = H5Pcreate(H5P_DATASET_CREATE);		checkH5Err(h5plist);		checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));		checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));		m_h5data[odd] = H5Dcreate(h5file, "values", H5T_IEEE_F64LE, m_h5fSpaceData,				H5P_DEFAULT, h5plist, H5P_DEFAULT);		checkH5Err(m_h5data[odd]);		checkH5Err(H5Pclose(h5plist));	}	return h5file;}