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Merge branch 'master' into ejh_uthash_include
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@edhartnett
edhartnett authored Jul 5, 2019
2 parents ffd5b57 + a29a28c commit 1b08a2b
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Showing 24 changed files with 1,090 additions and 1,090 deletions.
8 changes: 4 additions & 4 deletions src/clib/bget.c
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Original file line number Diff line number Diff line change
Expand Up @@ -564,12 +564,12 @@ static bufsize pool_len = 0; /* 0: no bpool calls have been made
/* added for PIO so that a bpool can be freed and another allocated */
void bpoolrelease()
{
LOG((2, "bpoolrelease"));
PLOG((2, "bpoolrelease"));
freelist.bh.prevfree=0;
freelist.bh.bsize=0;
freelist.ql.flink=&freelist;
freelist.ql.blink=&freelist;
LOG((2, "bpoolrelease"));
PLOG((2, "bpoolrelease"));

#ifdef BufStats
totalloc = 0; /* Total space currently allocated */
Expand All @@ -583,7 +583,7 @@ void bpoolrelease()
numdrel = 0; /* Number of direct gets and rels */
#endif /* BECtl */
#endif /* BufStats */
LOG((2, "bpoolrelease"));
PLOG((2, "bpoolrelease"));

#ifdef BECtl
/* Automatic expansion block management functions */
Expand All @@ -593,7 +593,7 @@ void bpoolrelease()
exp_incr = 0;
pool_len = 0;
#endif
LOG((2, "bpoolrelease"));
PLOG((2, "bpoolrelease"));

}

Expand Down
90 changes: 45 additions & 45 deletions src/clib/pio_darray.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -147,9 +147,9 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
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));
PLOG((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)
Expand Down Expand Up @@ -181,10 +181,10 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
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]));
PLOG((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));
PLOG((3, "called PIOc_inq_varndims varids[0] = %d fndims = %d", varids[0], fndims));
for (int v=1; v < nvars; v++){
if ((ierr = PIOc_inq_varndims(file->pio_ncid, varids[v], &fndims2)))
return check_netcdf(file, ierr, __FILE__, __LINE__);
Expand Down Expand Up @@ -234,9 +234,9 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
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));
PLOG((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. */
Expand All @@ -248,7 +248,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
/* 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(NULL, file, mpierr, __FILE__, __LINE__);
LOG((3, "shared fndims = %d", fndims));
PLOG((3, "shared fndims = %d", fndims));
}

/* if the buffer is already in use in pnetcdf we need to flush first */
Expand All @@ -274,13 +274,13 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
/* 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));
PLOG((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 && fillvalue)
{
LOG((3, "inerting fill values iodesc->maxiobuflen = %d", iodesc->maxiobuflen));
PLOG((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)],
Expand All @@ -294,7 +294,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
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"));
PLOG((3, "allocated token for variable buffer"));
}
if (iodesc->needssort)
{
Expand All @@ -312,7 +312,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int 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));
PLOG((2, "about to write darray for iotype = %d", file->iotype));
switch (file->iotype)
{
case PIO_IOTYPE_NETCDF4P:
Expand All @@ -338,7 +338,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
/* Release resources. */
if (file->iobuf)
{
LOG((3,"freeing variable buffer in pio_darray"));
PLOG((3,"freeing variable buffer in pio_darray"));
brel(file->iobuf);
file->iobuf = NULL;
}
Expand All @@ -356,8 +356,8 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
* 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));
PLOG((2, "nvars = %d holegridsize = %ld iodesc->needsfill = %d\n", nvars,
iodesc->holegridsize, iodesc->needsfill));

pioassert(!vdesc0->fillbuf, "buffer overwrite",__FILE__, __LINE__);

Expand Down Expand Up @@ -457,13 +457,13 @@ pio_inq_var_fill_expected(int ncid, int varid, int pio_type, PIO_Offset type_siz
/* Check inputs. */
assert(fillvalue);

LOG((2, "pio_inq_var_fill_expected ncid %d varid %d pio_type %d type_size %d",
ncid, varid, pio_type, type_size));
PLOG((2, "pio_inq_var_fill_expected ncid %d varid %d pio_type %d type_size %d",
ncid, varid, pio_type, type_size));

/* Is there a _FillValue attribute? */
ret = PIOc_inq_att_eh(ncid, varid, "_FillValue", 0, NULL, NULL);

LOG((3, "pio_inq_var_fill_expected ret %d", ret));
PLOG((3, "pio_inq_var_fill_expected ret %d", ret));

/* If there is a fill value, get it. */
if (!ret)
Expand Down Expand Up @@ -551,7 +551,7 @@ find_var_fillvalue(file_desc_t *file, int varid, var_desc_t *vdesc)
pioassert(file && file->iosystem && vdesc, "invalid input", __FILE__, __LINE__);
ios = file->iosystem;

LOG((3, "find_var_fillvalue file->pio_ncid = %d varid = %d", file->pio_ncid, varid));
PLOG((3, "find_var_fillvalue file->pio_ncid = %d varid = %d", file->pio_ncid, varid));

/* Find out PIO data type of var. */
if ((ierr = PIOc_inq_vartype(file->pio_ncid, varid, &pio_type)))
Expand All @@ -560,8 +560,8 @@ find_var_fillvalue(file_desc_t *file, int varid, var_desc_t *vdesc)
/* Find out length of type. */
if ((ierr = PIOc_inq_type(file->pio_ncid, pio_type, NULL, &type_size)))
return pio_err(ios, NULL, ierr, __FILE__, __LINE__);
LOG((3, "getting fill value for varid = %d pio_type = %d type_size = %d",
varid, pio_type, type_size));
PLOG((3, "getting fill value for varid = %d pio_type = %d type_size = %d",
varid, pio_type, type_size));

/* Allocate storage for the fill value. */
if (!(vdesc->fillvalue = malloc(type_size)))
Expand All @@ -572,7 +572,7 @@ find_var_fillvalue(file_desc_t *file, int varid, var_desc_t *vdesc)
if ((ierr = PIOc_inq_var_fill(file->pio_ncid, varid, &no_fill, vdesc->fillvalue)))
return pio_err(ios, NULL, ierr, __FILE__, __LINE__);
vdesc->use_fill = no_fill ? 0 : 1;
LOG((3, "vdesc->use_fill = %d", vdesc->use_fill));
PLOG((3, "vdesc->use_fill = %d", vdesc->use_fill));

/* Get the fill value one would expect, if NOFILL were not turned
* on. */
Expand Down Expand Up @@ -654,8 +654,8 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
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));
PLOG((1, "PIOc_write_darray ncid = %d varid = %d ioid = %d arraylen = %d",
ncid, varid, ioid, arraylen));
#ifdef USE_MPE
pio_start_mpe_log(DARRAY_WRITE);
#endif /* USE_MPE */
Expand All @@ -679,9 +679,9 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
* 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));
PLOG((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)))
Expand Down Expand Up @@ -710,7 +710,7 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
hashid = ioid*10 + vdesc->rec_var;
HASH_FIND_INT( file->buffer, &hashid, wmb);
if (wmb)
LOG((3, "wmb->ioid = %d wmb->recordvar = %d", wmb->ioid, wmb->recordvar));
PLOG((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)
Expand All @@ -731,8 +731,8 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
wmb->htid = hashid;
HASH_ADD_INT( file->buffer, htid, wmb );
}
LOG((2, "wmb->num_arrays = %d arraylen = %d iodesc->mpitype_size = %d\n",
wmb->num_arrays, arraylen, iodesc->mpitype_size));
PLOG((2, "wmb->num_arrays = %d arraylen = %d iodesc->mpitype_size = %d\n",
wmb->num_arrays, arraylen, iodesc->mpitype_size));
#if PIO_USE_MALLOC
/* Try realloc first and call flush if realloc fails. */
if (arraylen > 0)
Expand All @@ -748,8 +748,8 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
{
needsflush = 1;
}
LOG((2, "realloc attempted to get %ld bytes for data, needsflush %d", data_size,
needsflush));
PLOG((2, "realloc attempted to get %ld bytes for data, needsflush %d", data_size,
needsflush));
}
#else
/* Find out how much free, contiguous space is available. */
Expand All @@ -772,7 +772,7 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
if ((mpierr = MPI_Allreduce(MPI_IN_PLACE, &needsflush, 1, MPI_INT, MPI_MAX,
ios->comp_comm)))
return check_mpi(NULL, file, mpierr, __FILE__, __LINE__);
LOG((2, "needsflush = %d", needsflush));
PLOG((2, "needsflush = %d", needsflush));

/* Flush data if needed. */
if (needsflush > 0)
Expand All @@ -781,9 +781,9 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
#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 * iodesc->mpitype_size = %ld totfree = %ld\n", maxfree, wmb->num_arrays,
(1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size, totfree));
PLOG((2, "maxfree = %ld wmb->num_arrays = %d (1 + wmb->num_arrays) *"
" arraylen * iodesc->mpitype_size = %ld totfree = %ld\n", maxfree, wmb->num_arrays,
(1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size, totfree));
#endif /* PIO_ENABLE_LOGGING */
#endif /* !PIO_USE_MALLOC */

Expand All @@ -800,15 +800,15 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
{
if (!(wmb->data = realloc(wmb->data, (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_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 * iodesc->mpitype_size));
PLOG((2, "after a flush, realloc got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size));
}
#else
/* Get memory for data. */
if (arraylen > 0)
{
if (!(wmb->data = bgetr(wmb->data, (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size)))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
LOG((2, "got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size));
PLOG((2, "got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size));
}
#endif

Expand Down Expand Up @@ -840,15 +840,15 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
/* 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]));
PLOG((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 * iodesc->mpitype_size * wmb->num_arrays);
if (arraylen > 0)
{
memcpy(bufptr, array, arraylen * iodesc->mpitype_size);
LOG((3, "copied %ld bytes of user data", arraylen * iodesc->mpitype_size));
PLOG((3, "copied %ld bytes of user data", arraylen * iodesc->mpitype_size));
}

/* Add the unlimited dimension value of this variable to the frame
Expand All @@ -861,9 +861,9 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
pio_stop_mpe_log(DARRAY_WRITE, __func__);
#endif /* USE_MPE */

LOG((2, "wmb->num_arrays = %d iodesc->maxbytes / iodesc->mpitype_size = %d "
"iodesc->ndof = %d iodesc->llen = %d", wmb->num_arrays,
iodesc->maxbytes / iodesc->mpitype_size, iodesc->ndof, iodesc->llen));
PLOG((2, "wmb->num_arrays = %d iodesc->maxbytes / iodesc->mpitype_size = %d "
"iodesc->ndof = %d iodesc->llen = %d", wmb->num_arrays,
iodesc->maxbytes / iodesc->mpitype_size, iodesc->ndof, iodesc->llen));

return PIO_NOERR;
}
Expand Down
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