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Merge branch 'master' into ejh_hdf5_sep

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Ed Hartnett 2018-07-30 12:13:45 -06:00 committed by GitHub
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5 changed files with 46 additions and 61 deletions
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1
docs/all-error-codes.md
View File

@ -71,6 +71,7 @@ may occur.
#define NC_ENOTFOUND (-90) // No such file
#define NC_ECANTREMOVE (-91) // Cannot remove file
#define NC_EINTERNAL (-92) // NetCDF Library Internal Error
#define NC_EPNETCDF (-93) // Error at PnetCDF layer
~~~~
# NetCDF-4 Error Codes {#nc4-error-codes}

1
include/netcdf.h
View File

@ -426,6 +426,7 @@ by the desired type. */
#define NC_ENOTFOUND (-90) /**< No such file */
#define NC_ECANTREMOVE (-91) /**< Can't remove file */
#define NC_EINTERNAL (-92) /**< NetCDF Library Internal Error */
#define NC_EPNETCDF (-93) /**< Error at PnetCDF layer */
/* The following was added in support of netcdf-4. Make all netcdf-4
error codes < -100 so that errors can be added to netcdf-3 if

2
libdispatch/derror.c
View File

@ -196,6 +196,8 @@ const char *nc_strerror(int ncerr1)
return "NetCDF: cannot delete file";
case NC_EINTERNAL:
return "NetCDF: internal library error; Please contact Unidata support";
case NC_EPNETCDF:
return "NetCDF: PnetCDF error";
case NC_EHDFERR:
return "NetCDF: HDF error";
case NC_ECANTREAD:

96
libsrcp/ncpdispatch.c
View File

@ -15,14 +15,9 @@
typedef struct NCP_INFO
{
/* pnetcdf_file will be true if the file is created/opened with the
* parallel-netcdf library. pnetcdf_access_mode keeps track of
* whether independpent or collective mode is
* desired. pnetcdf_ndims keeps track of how many dims each var
* has, which I need to know to convert start, count, and stride
* arrays from size_t to MPI_Offset. (I can't use an inq function
* to find out the number of dims, because these are collective in
* pnetcdf.) */
/* pnetcdf_access_mode keeps track of whether independpent or collective
* mode is set currently.
*/
int pnetcdf_access_mode;
} NCP_INFO;
@ -46,8 +41,8 @@ NCP_create(const char *path, int cmode,
{
int res, default_format;
NCP_INFO* nc5;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
MPI_Comm comm;
MPI_Info info;
/* Check the cmode for only valid flags*/
if(cmode & ~LEGAL_CREATE_FLAGS)
@ -88,23 +83,9 @@ NCP_create(const char *path, int cmode,
/* Link nc5 and nc */
NCP_DATA_SET(nc,nc5);
/* Fix up the cmode by keeping only essential flags;
these are the flags that are the same in netcf.h and pnetcdf.h
*/
/* It turns out that pnetcdf.h defines a flag called
NC_64BIT_DATA (not to be confused with NC_64BIT_OFFSET).
This flag is essential to getting ncmpi_create to create
a proper pnetcdf format file.
We have set the value of NC_64BIT_DATA to be the same as in pnetcdf.h
(as of pnetcdf version 1.6.0) to avoid conflicts.
In any case, this flag must be set.
*/
/* PnetCDF recognizes the flags below for create and ignores NC_LOCK and NC_SHARE */
cmode &= (NC_WRITE | NC_NOCLOBBER | NC_SHARE | NC_64BIT_OFFSET | NC_64BIT_DATA);
res = ncmpi_create(comm, path, cmode, info, &(nc->int_ncid));
if(res && nc5 != NULL) free(nc5); /* reclaim allocated space */
if (res != NC_NOERR) free(nc5); /* reclaim allocated space */
done:
return res;
}
@ -117,36 +98,19 @@ NCP_open(const char *path, int cmode,
{
int res;
NCP_INFO* nc5;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
MPI_Comm comm;
MPI_Info info;
/* Check the cmode for only valid flags*/
if(cmode & ~LEGAL_OPEN_FLAGS)
{res = NC_EINVAL; goto done;}
/* Cannot have both MPIO flags */
if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
{res = NC_EINVAL; goto done;}
/* No MPI environment initialized */
if (mpidata == NULL)
{res = NC_ENOPAR; goto done;}
/* Appears that this comment is wrong; allow 64 bit offset*/
/* Cannot have 64 bit offset flag */
/* if(cmode & (NC_64BIT_OFFSET)) {res = NC_EINVAL; goto done;} */
if(mpidata != NULL) {
comm = ((NC_MPI_INFO *)mpidata)->comm;
info = ((NC_MPI_INFO *)mpidata)->info;
} else {
comm = MPI_COMM_WORLD;
info = MPI_INFO_NULL;
}
/* PnetCDF recognizes the flags NC_WRITE and NC_NOCLOBBER for file open
* and ignores NC_LOCK, NC_SHARE, NC_64BIT_OFFSET, and NC_64BIT_DATA.
* Ignoring the NC_64BIT_OFFSET and NC_64BIT_DATA flags is because the
* file is already in one of the CDF-formats, and setting these 2 flags
* will not change the format of that file.
*/
cmode &= (NC_WRITE | NC_NOCLOBBER);
comm = ((NC_MPI_INFO *)mpidata)->comm;
info = ((NC_MPI_INFO *)mpidata)->info;
/* Create our specific NCP_INFO instance */
nc5 = (NCP_INFO*)calloc(1,sizeof(NCP_INFO));
@ -158,7 +122,7 @@ NCP_open(const char *path, int cmode,
res = ncmpi_open(comm, path, cmode, info, &(nc->int_ncid));
/* Default to independent access, like netCDF-4/HDF5 files. */
if(!res) {
if (res == NC_NOERR) {
res = ncmpi_begin_indep_data(nc->int_ncid);
nc5->pnetcdf_access_mode = NC_INDEPENDENT;
}
@ -193,9 +157,8 @@ NCP__enddef(int ncid, size_t h_minfree, size_t v_align, size_t v_minfree, size_t
nc5 = NCP_DATA(nc);
assert(nc5);
/* causes implicitly defined warning; may be because of old installed pnetcdf? */
#if 1
/* In PnetCDF ncmpi__enddef() is only implemented in v1.5.0 and later */
#if (PNETCDF_VERSION_MAJOR*10000 + PNETCDF_VERSION_MINOR*100 + PNETCDF_VERSION_SUB >= 10500)
/* ncmpi__enddef() was first implemented in PnetCDF v1.5.0 */
status = ncmpi__enddef(nc->int_ncid, mpi_h_minfree, mpi_v_align,
mpi_v_minfree, mpi_r_align);
#else
@ -257,7 +220,12 @@ NCP_set_fill(int ncid, int fillmode, int *old_mode_ptr)
NC* nc;
int status = NC_check_id(ncid, &nc);
if(status != NC_NOERR) return status;
#if (PNETCDF_VERSION_MAJOR*10000 + PNETCDF_VERSION_MINOR*100 + PNETCDF_VERSION_SUB >= 10601)
/* ncmpi_set_fill was first implemented in PnetCDF 1.6.1 */
return ncmpi_set_fill(nc->int_ncid,fillmode,old_mode_ptr);
#else
return NC_EPNETCDF;
#endif
}
static int
@ -314,7 +282,7 @@ NCP_inq_type(int ncid, nc_type typeid, char* name, size_t* size)
{
/* Assert mode & NC_FORMAT_CDF5 */
if (typeid < NC_BYTE || typeid >= NC_STRING)
return NC_EBADTYPE;
return NC_EBADTYPE;
if(name)
strcpy(name, NC_atomictypename(typeid));
if(size)
@ -440,15 +408,14 @@ NCP_get_att(
{
NC* nc;
int status;
nc_type xtype;
status = NC_check_id(ncid, &nc);
if(status != NC_NOERR) return status;
status = NCP_inq_att(ncid,varid,name,&xtype,NULL);
if(status != NC_NOERR) return status;
if(memtype == NC_NAT) memtype = xtype;
if (memtype == NC_NAT) {
status = NCP_inq_att(ncid,varid,name,&memtype,NULL);
if (status != NC_NOERR) return status;
}
switch (memtype) {
case NC_CHAR:
@ -1171,7 +1138,13 @@ NCP_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
if(deflatep) *deflatep = 0;
if(fletcher32p) *fletcher32p = 0;
if(contiguousp) *contiguousp = NC_CONTIGUOUS;
#if (PNETCDF_VERSION_MAJOR*10000 + PNETCDF_VERSION_MINOR*100 + PNETCDF_VERSION_SUB >= 10601)
/* ncmpi_inq_var_fill was first implemented in PnetCDF 1.6.1 */
if(no_fill) ncmpi_inq_var_fill(nc->int_ncid, varid, no_fill, fill_valuep);
#else
/* PnetCDF 1.6.0 and priors support NC_NOFILL only */
if(no_fill) *no_fill = 1;
#endif
if(endiannessp) return NC_ENOTNC4;
if(idp) return NC_ENOTNC4;
if(nparamsp) return NC_ENOTNC4;
@ -1185,7 +1158,12 @@ NCP_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value)
NC* nc;
int status = NC_check_id(ncid, &nc);
if(status != NC_NOERR) return status;
#if (PNETCDF_VERSION_MAJOR*10000 + PNETCDF_VERSION_MINOR*100 + PNETCDF_VERSION_SUB >= 10601)
/* ncmpi_def_var_fill was first implemented in PnetCDF 1.6.1 */
return ncmpi_def_var_fill(nc->int_ncid, varid, no_fill, fill_value);
#else
return NC_EPNETCDF;
#endif
}
static int

7
nc_test/util.c
View File

@ -1284,6 +1284,8 @@ char* nc_err_code_name(int err)
case (NC_EAUTH): return "NC_EAUTH";
case (NC_ENOTFOUND): return "NC_ENOTFOUND";
case (NC_ECANTREMOVE): return "NC_ECANTREMOVE";
case (NC_EINTERNAL): return "NC_EINTERNAL";
case (NC_EPNETCDF): return "NC_EPNETCDF";
case (NC_EHDFERR): return "NC_EHDFERR";
case (NC_ECANTREAD): return "NC_ECANTREAD";
case (NC_ECANTWRITE): return "NC_ECANTWRITE";
@ -1315,8 +1317,9 @@ char* nc_err_code_name(int err)
case (NC_EDISKLESS): return "NC_EDISKLESS";
case (NC_ECANTEXTEND): return "NC_ECANTEXTEND";
case (NC_EMPI): return "NC_EMPI";
case (NC_ENULLPAD): return "NC_NULLPAD";
// case (NC_EURL): return "NC_EURL";
case (NC_ENULLPAD): return "NC_NULLPAD";
case (NC_EINMEMORY): return "NC_EINMEMORY";
// case (NC_EURL): return "NC_EURL";
// case (NC_ECONSTRAINT): return "NC_ECONSTRAINT";
#ifdef USE_PNETCDF
case (NC_ESMALL): return "NC_ESMALL";