/**
* Read a field from a file to the IO library.
*
* @param ncid identifies the netCDF file
* @param varid the variable ID to be read
* @param ioid: the I/O description ID as passed back by
* PIOc_InitDecomp().
* @param arraylen: the length of the array to be read. This
* is the length of the distrubited array. That is, the length of
* the portion of the data that is on the processor.
* @param array: pointer to the data to be read. This is a
* pointer to the distributed portion of the array that is on this
* processor.
* @return 0 for success, error code otherwise.
* @ingroup PIO_read_darray
* @author Jim Edwards, Ed Hartnett
*/
int PIOc_read_darray(int ncid, int varid, int ioid, PIO_Offset arraylen,
void *array)
{
iosystem_desc_t *ios; /* Pointer to io system information. */
file_desc_t *file; /* Pointer to file information. */
io_desc_t *iodesc; /* Pointer to IO description information. */
void *iobuf = NULL; /* holds the data as read on the io node. */
size_t rlen = 0; /* the length of data in iobuf. */
int ierr; /* Return code. */
/* Get the file info. */
if ((ierr = pio_get_file(ncid, &file)))
return pio_err(NULL, NULL, PIO_EBADID, __FILE__, __LINE__);
ios = file->iosystem;
/* Get the iodesc. */
if (!(iodesc = pio_get_iodesc_from_id(ioid)))
return pio_err(ios, file, PIO_EBADID, __FILE__, __LINE__);
pioassert(iodesc->rearranger == PIO_REARR_BOX || iodesc->rearranger == PIO_REARR_SUBSET,
"unknown rearranger", __FILE__, __LINE__);
/* ??? */
if (ios->iomaster == MPI_ROOT)
rlen = iodesc->maxiobuflen;
else
rlen = iodesc->llen;
/* Allocate a buffer for one record. */
if (ios->ioproc && rlen > 0)
if (!(iobuf = bget(iodesc->mpitype_size * rlen)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
/* Call the correct darray read function based on iotype. */
switch (file->iotype)
{
case PIO_IOTYPE_NETCDF:
case PIO_IOTYPE_NETCDF4C:
if ((ierr = pio_read_darray_nc_serial(file, iodesc, varid, iobuf)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
case PIO_IOTYPE_PNETCDF:
case PIO_IOTYPE_NETCDF4P:
if ((ierr = pio_read_darray_nc(file, iodesc, varid, iobuf)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
default:
return pio_err(NULL, NULL, PIO_EBADIOTYPE, __FILE__, __LINE__);
}
/* Rearrange the data. */
if ((ierr = rearrange_io2comp(ios, iodesc, iobuf, array)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
/* Free the buffer. */
if (rlen > 0)
brel(iobuf);
return PIO_NOERR;
}
/**
* Test the decomp read/write functionality.
*
* @param iosysid the IO system ID.
* @param ioid the ID of the decomposition.
* @param num_flavors the number of IOTYPES available in this build.
* @param flavor array of available iotypes.
* @param my_rank rank of this task.
* @param rearranger the rearranger to use (PIO_REARR_BOX or
* PIO_REARR_SUBSET).
* @param test_comm the MPI communicator for this test.
* @returns 0 for success, error code otherwise.
*/
int test_decomp_read_write(int iosysid, int ioid, int num_flavors, int *flavor, int my_rank,
int rearranger, MPI_Comm test_comm)
{
char filename[PIO_MAX_NAME + 1]; /* Name for the output files. */
int ioid2; /* ID for decomposition we will create from file. */
char title_in[PIO_MAX_NAME + 1]; /* Optional title. */
char history_in[PIO_MAX_NAME + 1]; /* Optional history. */
int fortran_order_in; /* Indicates fortran vs. c order. */
int ret; /* Return code. */
/* Use PIO to create the decomp file in each of the four
* available ways. */
for (int fmt = 0; fmt < num_flavors; fmt++)
{
/* Create the filename. */
sprintf(filename, "decomp_%s_iotype_%d.nc", TEST_NAME, flavor[fmt]);
if ((ret = PIOc_write_nc_decomp(iosysid, filename, 0, ioid, NULL, NULL, 0)))
return ret;
/* Read the data. */
if ((ret = PIOc_read_nc_decomp(iosysid, filename, &ioid2, test_comm, PIO_INT,
title_in, history_in, &fortran_order_in)))
return ret;
/* Check the results. */
{
iosystem_desc_t *ios;
io_desc_t *iodesc;
/* Get the IO system info. */
if (!(ios = pio_get_iosystem_from_id(iosysid)))
return pio_err(NULL, NULL, PIO_EBADID, __FILE__, __LINE__);
/* Get the IO desc, which describes the decomposition. */
if (!(iodesc = pio_get_iodesc_from_id(ioid2)))
return pio_err(ios, NULL, PIO_EBADID, __FILE__, __LINE__);
if (iodesc->ioid != ioid2 || iodesc->maplen != EXPECTED_MAPLEN || iodesc->ndims != NDIM3 ||
iodesc->ndof != EXPECTED_MAPLEN)
return ERR_WRONG;
if (iodesc->rearranger != rearranger || iodesc->maxregions != 1 ||
iodesc->needsfill || iodesc->mpitype != MPI_INT)
return ERR_WRONG;
for (int e = 0; e < iodesc->maplen; e++)
if (iodesc->map[e] != my_rank * iodesc->maplen + e + 1)
return ERR_WRONG;
if (iodesc->dimlen[0] != X_DIM_LEN || iodesc->dimlen[1] != Y_DIM_LEN ||
iodesc->dimlen[2] != Z_DIM_LEN)
return ERR_WRONG;
if (rearranger == PIO_REARR_SUBSET)
{
if (iodesc->nrecvs != 1 || iodesc->num_aiotasks != TARGET_NTASKS)
return ERR_WRONG;
}
else
{
/* I haven't figured out yet what these should be for
* the box rearranger. */
/* printf("iodesc->nrecv = %d iodesc->num_aiotasks = %d\n", iodesc->nrecvs, */
/* iodesc->num_aiotasks); */
}
}
/* Free the PIO decomposition. */
if ((ret = PIOc_freedecomp(iosysid, ioid2)))
ERR(ret);
}
return PIO_NOERR;
}
/**
* Write one or more arrays with the same IO decomposition to the
* file.
*
* This funciton is similar to PIOc_write_darray(), but allows the
* caller to use their own data buffering (instead of using the
* buffering implemented in PIOc_write_darray()).
*
* When the user calls PIOc_write_darray() one or more times, then
* PIO_write_darray_multi() will be called when the buffer is flushed.
*
* Internally, this function will:
* <ul>
* <li>Find info about file, decomposition, and variable.
* <li>Do a special flush for pnetcdf if needed.
* <li>Allocates a buffer big enough to hold all the data in the
* multi-buffer, for all tasks.
* <li>Calls rearrange_comp2io() to move data from compute to IO
* tasks.
* <li>For parallel iotypes (pnetcdf and netCDF-4 parallel) call
* pio_write_darray_multi_nc().
* <li>For serial iotypes (netcdf classic and netCDF-4 serial) call
* write_darray_multi_serial().
* <li>For subset rearranger, create holegrid to write missing
* data. Then call pio_write_darray_multi_nc() or
* write_darray_multi_serial() to write the holegrid.
* <li>Special buffer flush for pnetcdf.
* </ul>
*
* @param ncid identifies the netCDF file.
* @param varids an array of length nvars containing the variable ids to
* be written.
* @param ioid the I/O description ID as passed back by
* PIOc_InitDecomp().
* @param nvars the number of variables to be written with this
* call.
* @param arraylen the length of the array to be written. This is the
* length of the distrubited array. That is, the length of the portion
* of the data that is on the processor. The same arraylen is used for
* all variables in the call.
* @param array pointer to the data to be written. This is a pointer
* to an array of arrays with the distributed portion of the array
* that is on this processor. There are nvars arrays of data, and each
* array of data contains one record worth of data for that variable.
* @param frame an array of length nvars with the frame or record
* dimension for each of the nvars variables in IOBUF. NULL if this
* iodesc contains non-record vars.
* @param fillvalue pointer an array (of length nvars) of pointers to
* the fill value to be used for missing data.
* @param flushtodisk non-zero to cause buffers to be flushed to disk.
* @return 0 for success, error code otherwise.
* @ingroup PIO_write_darray
* @author Jim Edwards, Ed Hartnett
*/
int PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
PIO_Offset arraylen, void *array, const int *frame,
void **fillvalue, bool flushtodisk)
{
iosystem_desc_t *ios; /* Pointer to io system information. */
file_desc_t *file; /* Pointer to file information. */
io_desc_t *iodesc; /* Pointer to IO description information. */
int rlen; /* Total data buffer size. */
var_desc_t *vdesc0; /* First entry in array of var_desc structure for each var. */
int fndims; /* Number of dims in the var in the file. */
int mpierr = MPI_SUCCESS, mpierr2; /* Return code from MPI function calls. */
int ierr; /* Return code. */
/* Get the file info. */
if ((ierr = pio_get_file(ncid, &file)))
return pio_err(NULL, NULL, PIO_EBADID, __FILE__, __LINE__);
ios = file->iosystem;
/* Check inputs. */
if (nvars <= 0 || !varids)
return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
LOG((1, "PIOc_write_darray_multi ncid = %d ioid = %d nvars = %d arraylen = %ld "
"flushtodisk = %d",
ncid, ioid, nvars, arraylen, flushtodisk));
/* Check that we can write to this file. */
if (!file->writable)
return pio_err(ios, file, PIO_EPERM, __FILE__, __LINE__);
/* Get iodesc. */
if (!(iodesc = pio_get_iodesc_from_id(ioid)))
return pio_err(ios, file, PIO_EBADID, __FILE__, __LINE__);
pioassert(iodesc->rearranger == PIO_REARR_BOX || iodesc->rearranger == PIO_REARR_SUBSET,
"unknown rearranger", __FILE__, __LINE__);
/* Check the types of all the vars. They must match the type of
* the decomposition. */
for (int v = 0; v < nvars; v++)
{
var_desc_t *vdesc;
if ((ierr = get_var_desc(varids[v], &file->varlist, &vdesc)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
if (vdesc->pio_type != iodesc->piotype)
return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
}
/* Get a pointer to the variable info for the first variable. */
if ((ierr = get_var_desc(varids[0], &file->varlist, &vdesc0)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
/* Run these on all tasks if async is not in use, but only on
* non-IO tasks if async is in use. */
if (!ios->async || !ios->ioproc)
{
/* Get the number of dims for this var. */
LOG((3, "about to call PIOc_inq_varndims varids[0] = %d", varids[0]));
if ((ierr = PIOc_inq_varndims(file->pio_ncid, varids[0], &fndims)))
return check_netcdf(file, ierr, __FILE__, __LINE__);
LOG((3, "called PIOc_inq_varndims varids[0] = %d fndims = %d", varids[0], fndims));
}
/* If async is in use, and this is not an IO task, bcast the parameters. */
if (ios->async)
{
if (!ios->ioproc)
{
int msg = PIO_MSG_WRITEDARRAYMULTI;
char frame_present = frame ? true : false; /* Is frame non-NULL? */
char fillvalue_present = fillvalue ? true : false; /* Is fillvalue non-NULL? */
int flushtodisk_int = flushtodisk; /* Need this to be int not boolean. */
if (ios->compmaster == MPI_ROOT)
mpierr = MPI_Send(&msg, 1, MPI_INT, ios->ioroot, 1, ios->union_comm);
/* Send the function parameters and associated informaiton
* to the msg handler. */
if (!mpierr)
mpierr = MPI_Bcast(&ncid, 1, MPI_INT, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&nvars, 1, MPI_INT, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast((void *)varids, nvars, MPI_INT, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&ioid, 1, MPI_INT, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&arraylen, 1, MPI_OFFSET, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(array, arraylen * iodesc->piotype_size, MPI_CHAR, ios->compmaster,
ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&frame_present, 1, MPI_CHAR, ios->compmaster, ios->intercomm);
if (!mpierr && frame_present)
mpierr = MPI_Bcast((void *)frame, nvars, MPI_INT, ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&fillvalue_present, 1, MPI_CHAR, ios->compmaster, ios->intercomm);
if (!mpierr && fillvalue_present)
mpierr = MPI_Bcast((void *)fillvalue, nvars * iodesc->piotype_size, MPI_CHAR,
ios->compmaster, ios->intercomm);
if (!mpierr)
mpierr = MPI_Bcast(&flushtodisk_int, 1, MPI_INT, ios->compmaster, ios->intercomm);
LOG((2, "PIOc_write_darray_multi file->pio_ncid = %d nvars = %d ioid = %d arraylen = %d "
"frame_present = %d fillvalue_present = %d flushtodisk = %d", file->pio_ncid, nvars,
ioid, arraylen, frame_present, fillvalue_present, flushtodisk));
}
/* Handle MPI errors. */
if ((mpierr2 = MPI_Bcast(&mpierr, 1, MPI_INT, ios->comproot, ios->my_comm)))
return check_mpi(file, mpierr2, __FILE__, __LINE__);
if (mpierr)
return check_mpi(file, mpierr, __FILE__, __LINE__);
/* Share results known only on computation tasks with IO tasks. */
if ((mpierr = MPI_Bcast(&fndims, 1, MPI_INT, ios->comproot, ios->my_comm)))
check_mpi(file, mpierr, __FILE__, __LINE__);
LOG((3, "shared fndims = %d", fndims));
}
/* if the buffer is already in use in pnetcdf we need to flush first */
if (file->iotype == PIO_IOTYPE_PNETCDF && file->iobuf)
if ((ierr = flush_output_buffer(file, 1, 0)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
pioassert(!file->iobuf, "buffer overwrite",__FILE__, __LINE__);
/* Determine total size of aggregated data (all vars/records).
* For netcdf serial writes we collect the data on io nodes and
* then move that data one node at a time to the io master node
* and write (or read). The buffer size on io task 0 must be as
* large as the largest used to accommodate this serial io
* method. */
rlen = 0;
if (iodesc->llen > 0)
rlen = iodesc->maxiobuflen * nvars;
/* Allocate iobuf. */
if (rlen > 0)
{
/* Allocate memory for the buffer for all vars/records. */
if (!(file->iobuf = bget(iodesc->mpitype_size * (size_t)rlen)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
LOG((3, "allocated %lld bytes for variable buffer", (size_t)rlen * iodesc->mpitype_size));
/* If fill values are desired, and we're using the BOX
* rearranger, insert fill values. */
if (iodesc->needsfill && iodesc->rearranger == PIO_REARR_BOX)
{
LOG((3, "inerting fill values iodesc->maxiobuflen = %d", iodesc->maxiobuflen));
for (int nv = 0; nv < nvars; nv++)
for (int i = 0; i < iodesc->maxiobuflen; i++)
memcpy(&((char *)file->iobuf)[iodesc->mpitype_size * (i + nv * iodesc->maxiobuflen)],
&((char *)fillvalue)[nv * iodesc->mpitype_size], iodesc->mpitype_size);
}
}
else if (file->iotype == PIO_IOTYPE_PNETCDF && ios->ioproc)
{
/* this assures that iobuf is allocated on all iotasks thus
assuring that the flush_output_buffer call above is called
collectively (from all iotasks) */
if (!(file->iobuf = bget(1)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
LOG((3, "allocated token for variable buffer"));
}
/* Move data from compute to IO tasks. */
if ((ierr = rearrange_comp2io(ios, iodesc, array, file->iobuf, nvars)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
/* Write the darray based on the iotype. */
LOG((2, "about to write darray for iotype = %d", file->iotype));
switch (file->iotype)
{
case PIO_IOTYPE_NETCDF4P:
case PIO_IOTYPE_PNETCDF:
if ((ierr = write_darray_multi_par(file, nvars, fndims, varids, iodesc,
DARRAY_DATA, frame)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
case PIO_IOTYPE_NETCDF4C:
case PIO_IOTYPE_NETCDF:
if ((ierr = write_darray_multi_serial(file, nvars, fndims, varids, iodesc,
DARRAY_DATA, frame)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
default:
return pio_err(NULL, NULL, PIO_EBADIOTYPE, __FILE__, __LINE__);
}
/* For PNETCDF the iobuf is freed in flush_output_buffer() */
if (file->iotype != PIO_IOTYPE_PNETCDF)
{
/* Release resources. */
if (file->iobuf)
{
LOG((3,"freeing variable buffer in pio_darray"));
brel(file->iobuf);
file->iobuf = NULL;
}
}
/* The box rearranger will always have data (it could be fill
* data) to fill the entire array - that is the aggregate start
* and count values will completely describe one unlimited
* dimension unit of the array. For the subset method this is not
* necessarily the case, areas of missing data may never be
* written. In order to make sure that these areas are given the
* missing value a 'holegrid' is used to describe the missing
* points. This is generally faster than the netcdf method of
* filling the entire array with missing values before overwriting
* those values later. */
if (iodesc->rearranger == PIO_REARR_SUBSET && iodesc->needsfill)
{
LOG((2, "nvars = %d holegridsize = %ld iodesc->needsfill = %d\n", nvars,
iodesc->holegridsize, iodesc->needsfill));
pioassert(!vdesc0->fillbuf, "buffer overwrite",__FILE__, __LINE__);
/* Get a buffer. */
if (ios->io_rank == 0)
vdesc0->fillbuf = bget(iodesc->maxholegridsize * iodesc->mpitype_size * nvars);
else if (iodesc->holegridsize > 0)
vdesc0->fillbuf = bget(iodesc->holegridsize * iodesc->mpitype_size * nvars);
/* copying the fill value into the data buffer for the box
* rearranger. This will be overwritten with data where
* provided. */
for (int nv = 0; nv < nvars; nv++)
for (int i = 0; i < iodesc->holegridsize; i++)
memcpy(&((char *)vdesc0->fillbuf)[iodesc->mpitype_size * (i + nv * iodesc->holegridsize)],
&((char *)fillvalue)[iodesc->mpitype_size * nv], iodesc->mpitype_size);
/* Write the darray based on the iotype. */
switch (file->iotype)
{
case PIO_IOTYPE_PNETCDF:
case PIO_IOTYPE_NETCDF4P:
if ((ierr = write_darray_multi_par(file, nvars, fndims, varids, iodesc,
DARRAY_FILL, frame)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
case PIO_IOTYPE_NETCDF4C:
case PIO_IOTYPE_NETCDF:
if ((ierr = write_darray_multi_serial(file, nvars, fndims, varids, iodesc,
DARRAY_FILL, frame)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
break;
default:
return pio_err(ios, file, PIO_EBADIOTYPE, __FILE__, __LINE__);
}
/* For PNETCDF fillbuf is freed in flush_output_buffer() */
if (file->iotype != PIO_IOTYPE_PNETCDF)
{
/* Free resources. */
if (vdesc0->fillbuf)
{
brel(vdesc0->fillbuf);
vdesc0->fillbuf = NULL;
}
}
}
/* Flush data to disk for pnetcdf. */
if (ios->ioproc && file->iotype == PIO_IOTYPE_PNETCDF)
if ((ierr = flush_output_buffer(file, flushtodisk, 0)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
return PIO_NOERR;
}
/**
* Write a distributed array to the output file.
*
* This routine aggregates output on the compute nodes and only sends
* it to the IO nodes when the compute buffer is full or when a flush
* is triggered.
*
* Internally, this function will:
* <ul>
* <li>Locate info about this file, decomposition, and variable.
* <li>If we don't have a fillvalue for this variable, determine one
* and remember it for future calls.
* <li>Initialize or find the multi_buffer for this record/var.
* <li>Find out how much free space is available in the multi buffer
* and flush if needed.
* <li>Store the new user data in the mutli buffer.
* <li>If needed (only for subset rearranger), fill in gaps in data
* with fillvalue.
* <li>Remember the frame value (i.e. record number) of this data if
* there is one.
* </ul>
*
* NOTE: The write multi buffer wmulti_buffer is the cache on compute
* nodes that will collect and store multiple variables before sending
* them to the io nodes. Aggregating variables in this way leads to a
* considerable savings in communication expense. Variables in the wmb
* array must have the same decomposition and base data size and we
* also need to keep track of whether each is a recordvar (has an
* unlimited dimension) or not.
*
* @param ncid the ncid of the open netCDF file.
* @param varid the ID of the variable that these data will be written
* to.
* @param ioid the I/O description ID as passed back by
* PIOc_InitDecomp().
* @param arraylen the length of the array to be written. This should
* be at least the length of the local component of the distrubited
* array. (Any values beyond length of the local component will be
* ignored.)
* @param array pointer to an array of length arraylen with the data
* to be written. This is a pointer to the distributed portion of the
* array that is on this task.
* @param fillvalue pointer to the fill value to be used for missing
* data.
* @returns 0 for success, non-zero error code for failure.
* @ingroup PIO_write_darray
* @author Jim Edwards, Ed Hartnett
*/
int PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *array,
void *fillvalue)
{
iosystem_desc_t *ios; /* Pointer to io system information. */
file_desc_t *file; /* Info about file we are writing to. */
io_desc_t *iodesc; /* The IO description. */
var_desc_t *vdesc; /* Info about the var being written. */
void *bufptr; /* A data buffer. */
wmulti_buffer *wmb; /* The write multi buffer for one or more vars. */
int needsflush = 0; /* True if we need to flush buffer. */
#if PIO_USE_MALLOC
void *realloc_data = NULL;
#else
bufsize totfree; /* Amount of free space in the buffer. */
bufsize maxfree; /* Max amount of free space in buffer. */
#endif
int mpierr = MPI_SUCCESS; /* Return code from MPI functions. */
int ierr = PIO_NOERR; /* Return code. */
size_t io_data_size; /* potential size of data on io task */
LOG((1, "PIOc_write_darray ncid = %d varid = %d ioid = %d arraylen = %d",
ncid, varid, ioid, arraylen));
/* Get the file info. */
if ((ierr = pio_get_file(ncid, &file)))
return pio_err(NULL, NULL, PIO_EBADID, __FILE__, __LINE__);
ios = file->iosystem;
/* Can we write to this file? */
if (!file->writable)
return pio_err(ios, file, PIO_EPERM, __FILE__, __LINE__);
/* Get decomposition information. */
if (!(iodesc = pio_get_iodesc_from_id(ioid)))
return pio_err(ios, file, PIO_EBADID, __FILE__, __LINE__);
/* Check that the local size of the variable passed in matches the
* size expected by the io descriptor. Fail if arraylen is too
* small, just put a warning in the log if it is too big (the
* excess values will be ignored.) */
if (arraylen < iodesc->ndof)
return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
LOG((2, "%s arraylen = %d iodesc->ndof = %d",
(iodesc->ndof != arraylen) ? "WARNING: iodesc->ndof != arraylen" : "",
arraylen, iodesc->ndof));
/* Get var description. */
if ((ierr = get_var_desc(varid, &file->varlist, &vdesc)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
/* If the type of the var doesn't match the type of the
* decomposition, return an error. */
if (iodesc->piotype != vdesc->pio_type)
return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
pioassert(iodesc->mpitype_size == vdesc->mpi_type_size, "wrong mpi info",
__FILE__, __LINE__);
/* If we don't know the fill value for this var, get it. */
if (!vdesc->fillvalue)
if ((ierr = find_var_fillvalue(file, varid, vdesc)))
return pio_err(ios, file, PIO_EBADID, __FILE__, __LINE__);
/* Check that if the user passed a fill value, it is correct. */
if (fillvalue)
if (memcmp(fillvalue, vdesc->fillvalue, vdesc->pio_type_size))
return pio_err(ios, file, PIO_EINVAL, __FILE__, __LINE__);
/* Move to end of list or the entry that matches this ioid. */
for (wmb = &file->buffer; wmb->next; wmb = wmb->next)
if (wmb->ioid == ioid && wmb->recordvar == vdesc->rec_var)
break;
LOG((3, "wmb->ioid = %d wmb->recordvar = %d", wmb->ioid, wmb->recordvar));
/* If we did not find an existing wmb entry, create a new wmb. */
if (wmb->ioid != ioid || wmb->recordvar != vdesc->rec_var)
{
/* Allocate a buffer. */
if (!(wmb->next = bget((bufsize)sizeof(wmulti_buffer))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
/* Set pointer to newly allocated buffer and initialize.*/
wmb = wmb->next;
wmb->recordvar = vdesc->rec_var;
wmb->next = NULL;
wmb->ioid = ioid;
wmb->num_arrays = 0;
wmb->arraylen = arraylen;
wmb->vid = NULL;
wmb->data = NULL;
wmb->frame = NULL;
wmb->fillvalue = NULL;
}
LOG((2, "wmb->num_arrays = %d arraylen = %d vdesc->mpi_type_size = %d\n",
wmb->num_arrays, arraylen, vdesc->mpi_type_size));
#if PIO_USE_MALLOC
/* Try realloc first and call flush if realloc fails. */
if (arraylen > 0)
{
size_t data_size = (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size;
if ((realloc_data = realloc(wmb->data, data_size)))
{
needsflush = 0;
wmb->data = realloc_data;
}
else /* Failed to realloc, but wmb->data is still valid for a flush. */
{
needsflush = 1;
}
LOG((2, "realloc attempted to get %ld bytes for data, needsflush %d", data_size,
needsflush));
}
#else
/* Find out how much free, contiguous space is available. */
bfreespace(&totfree, &maxfree);
/* maxfree is the available memory. If that is < 10% greater than
* the size of the current request needsflush is true. */
if (needsflush == 0)
needsflush = (maxfree <= 1.1 * (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size);
#endif
/* the limit of data_size < INT_MAX is due to a bug in ROMIO which limits
the size of contiguous data to INT_MAX, a fix has been proposed in
https://github.com/pmodels/mpich/pull/2888 */
io_data_size = (1 + wmb->num_arrays) * iodesc->maxiobuflen * vdesc->mpi_type_size;
if(io_data_size > INT_MAX)
needsflush = 2;
/* Tell all tasks on the computation communicator whether we need
* to flush data. */
if ((mpierr = MPI_Allreduce(MPI_IN_PLACE, &needsflush, 1, MPI_INT, MPI_MAX,
ios->comp_comm)))
return check_mpi(file, mpierr, __FILE__, __LINE__);
LOG((2, "needsflush = %d", needsflush));
/* Flush data if needed. */
if (needsflush > 0)
{
#if !PIO_USE_MALLOC
#ifdef PIO_ENABLE_LOGGING
/* Collect a debug report about buffer. */
cn_buffer_report(ios, true);
LOG((2, "maxfree = %ld wmb->num_arrays = %d (1 + wmb->num_arrays) *"
" arraylen * vdesc->mpi_type_size = %ld totfree = %ld\n", maxfree, wmb->num_arrays,
(1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size, totfree));
#endif /* PIO_ENABLE_LOGGING */
#endif /* !PIO_USE_MALLOC */
/* If needsflush == 2 flush to disk otherwise just flush to io
* node. This will cause PIOc_write_darray_multi() to be
* called. */
if ((ierr = flush_buffer(ncid, wmb, needsflush == 2)))
return pio_err(ios, file, ierr, __FILE__, __LINE__);
}
#if PIO_USE_MALLOC
/* Try realloc again if there is a flush. */
if (arraylen > 0 && needsflush > 0)
{
if (!(wmb->data = realloc(wmb->data, (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
LOG((2, "after a flush, realloc got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size));
}
#else
/* Get memory for data. */
if (arraylen > 0)
{
if (!(wmb->data = bgetr(wmb->data, (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
LOG((2, "got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * vdesc->mpi_type_size));
}
#endif
/* vid is an array of variable ids in the wmb list, grow the list
* and add the new entry. */
if (!(wmb->vid = bgetr(wmb->vid, sizeof(int) * (1 + wmb->num_arrays))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
/* wmb->frame is the record number, we assume that the variables
* in the wmb list may not all have the same unlimited dimension
* value although they usually do. */
if (vdesc->record >= 0)
if (!(wmb->frame = bgetr(wmb->frame, sizeof(int) * (1 + wmb->num_arrays))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
/* If we need a fill value, get it. If we are using the subset
* rearranger and not using the netcdf fill mode then we need to
* do an extra write to fill in the holes with the fill value. */
if (iodesc->needsfill)
{
/* Get memory to hold fill value. */
if (!(wmb->fillvalue = bgetr(wmb->fillvalue, vdesc->mpi_type_size * (1 + wmb->num_arrays))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
memcpy((char *)wmb->fillvalue + vdesc->mpi_type_size * wmb->num_arrays,
vdesc->fillvalue, vdesc->mpi_type_size);
}
/* Tell the buffer about the data it is getting. */
wmb->arraylen = arraylen;
wmb->vid[wmb->num_arrays] = varid;
LOG((3, "wmb->num_arrays = %d wmb->vid[wmb->num_arrays] = %d", wmb->num_arrays,
wmb->vid[wmb->num_arrays]));
/* Copy the user-provided data to the buffer. */
bufptr = (void *)((char *)wmb->data + arraylen * vdesc->mpi_type_size * wmb->num_arrays);
if (arraylen > 0)
{
memcpy(bufptr, array, arraylen * vdesc->mpi_type_size);
LOG((3, "copied %ld bytes of user data", arraylen * vdesc->mpi_type_size));
}
/* Add the unlimited dimension value of this variable to the frame
* array in wmb. */
if (wmb->frame)
wmb->frame[wmb->num_arrays] = vdesc->record;
wmb->num_arrays++;
LOG((2, "wmb->num_arrays = %d iodesc->maxbytes / vdesc->mpi_type_size = %d "
"iodesc->ndof = %d iodesc->llen = %d", wmb->num_arrays,
iodesc->maxbytes / vdesc->mpi_type_size, iodesc->ndof, iodesc->llen));
return PIO_NOERR;
}
int PIOc_get_local_array_size(int ioid)
{
io_desc_t *iodesc;
iodesc = pio_get_iodesc_from_id(ioid);
return(iodesc->ndof);
}
