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v. 1.45.2
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@sakov
sakov committed Aug 18, 2016
1 parent a767340 commit e44c37c
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Showing 7 changed files with 308 additions and 47 deletions.
12 changes: 11 additions & 1 deletion enkf/CHANGELOG
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Original file line number Diff line number Diff line change
@@ -1,4 +1,14 @@
v. 1.46.1
v. 1.45.2
PS 18082016
-- Slightly modified update_HE() and update_Hx() to fix a once-in-a-lifetime
round-off error occuring after writing and reading `fi' to observations.nc
as a float.
-- Changed `id_orig' in observations.nc to correspond to the observation
number as read from data files rather than to the id in
observations-orig.nc (that is, after compacting).
-- Changed the type of fields `type', `product' and `instrument' of struct
observation from int to short int.
v. 1.45.1
PS 17082016
-- Changed enkfprm_check() so that no unnecessary parameters are demanded
when calculating ensemble spread only.
Expand Down
18 changes: 17 additions & 1 deletion enkf/calc/ensobs.c
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Original file line number Diff line number Diff line change
Expand Up @@ -803,7 +803,11 @@ static void das_sortobs_byid(dasystem* das)
das->sort_mode = OBS_SORTMODE_ID;
}

/** Updates ensemble observations by applying X5
/** Updates ensemble observations by applying X5.
*
* Both update_HE() and update_Hx() only use the transforms calculated for the
* (int) fj, (int) fi node of the grid. This might be improved in the future to
* yield probably a bit more precise (and better) analysis stats.
*/
static void update_HE(dasystem* das)
{
Expand Down Expand Up @@ -976,6 +980,12 @@ static void update_HE(dasystem* das)
* HE(i, :) = HE(i, :) * X5
*/
i = (int) (obs->data[o].fi);
if (i == mni)
/*
* (this can happen once in a lifetime because of the
* round-off due to writing and reading fi as a float)
*/
i--;
for (e = 0; e < nmem; ++e)
HEi_f[e] = das->S[e][o];
sgemv_(&do_T, &nmem, &nmem, &alpha, X5j[i], &nmem, HEi_f, &inc, &beta, HEi_a, &inc);
Expand Down Expand Up @@ -1210,6 +1220,12 @@ static void update_Hx(dasystem* das)
Hx /= (double) nmem;

i = (int) (obs->data[o].fi);
if (i == mni)
/*
* (this can happen once in a lifetime because of the
* round-off due to writing and reading fi as a float)
*/
i--;
/*
* HE(i, :) += HA(i, :) * b * 1'
*/
Expand Down
228 changes: 220 additions & 8 deletions enkf/common/ncw.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
#include <errno.h>
#include "ncw.h"

const char ncw_version[] = "1.01";
const char ncw_version[] = "1.03";

/* This macro is substituted in error messages instead of the name of a
* variable in cases when the name could not be found by the variable id.
Expand All @@ -46,7 +46,7 @@ static void quit_def(char* format, ...)

fflush(stdout);

fprintf(stderr, "\nerror: libncw: ");
fprintf(stderr, "\n error: libncw: ");
va_start(args, format);
vfprintf(stderr, format, args);
va_end(args);
Expand Down Expand Up @@ -425,15 +425,15 @@ void ncw_rename_var(const char fname[], int ncid, const char oldname[], const ch
quit("\"%s\": nc_rename_var(): failed for varid = %d (oldname = \"%s\", newname = \"%s\"): %s\n", fname, varid, oldname, newname, nc_strerror(status));
}

void ncw_put_var_int(const char fname[], int ncid, int varid, const int v[])
void ncw_def_var_deflate(const char fname[], int ncid, int varid, int shuffle, int deflate, int deflate_level)
{
int status = nc_put_var_int(ncid, varid, v);
int status = nc_def_var_deflate(ncid, varid, shuffle, deflate, deflate_level);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;
char varname[NC_MAX_NAME] = "STR_UNKNOWN";

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_put_var_int(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
_ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": ncw_def_var_deflate(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

Expand Down Expand Up @@ -461,6 +461,42 @@ void ncw_put_var_short(const char fname[], int ncid, int varid, const short v[])
}
}

void ncw_put_var_ushort(const char fname[], int ncid, int varid, const unsigned short v[])
{
int status = nc_put_var_ushort(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_put_var_ushort(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_put_var_int(const char fname[], int ncid, int varid, const int v[])
{
int status = nc_put_var_int(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_put_var_int(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_put_var_uint(const char fname[], int ncid, int varid, const unsigned int v[])
{
int status = nc_put_var_uint(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_put_var_uint(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_put_var_float(const char fname[], int ncid, int varid, const float v[])
{
int status = nc_put_var_float(ncid, varid, v);
Expand Down Expand Up @@ -497,6 +533,18 @@ void ncw_get_var_text(const char fname[], int ncid, int varid, char v[])
}
}

void ncw_get_var_schar(const char fname[], int ncid, int varid, signed char v[])
{
int status = nc_get_var_schar(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_get_var_schar(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_get_var_short(const char fname[], int ncid, int varid, short int v[])
{
int status = nc_get_var_short(ncid, varid, v);
Expand All @@ -509,6 +557,18 @@ void ncw_get_var_short(const char fname[], int ncid, int varid, short int v[])
}
}

void ncw_get_var_ushort(const char fname[], int ncid, int varid, unsigned short int v[])
{
int status = nc_get_var_ushort(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_get_var_ushort(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_get_var_int(const char fname[], int ncid, int varid, int v[])
{
int status = nc_get_var_int(ncid, varid, v);
Expand All @@ -521,6 +581,18 @@ void ncw_get_var_int(const char fname[], int ncid, int varid, int v[])
}
}

void ncw_get_var_uint(const char fname[], int ncid, int varid, unsigned int v[])
{
int status = nc_get_var_uint(ncid, varid, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_get_var_uint(): failed for varid = %d (varname = \"%s\"): %s\n", fname, varid, varname, nc_strerror(status));
}
}

void ncw_get_var_float(const char fname[], int ncid, int varid, float v[])
{
int status = nc_get_var_float(ncid, varid, v);
Expand Down Expand Up @@ -585,6 +657,20 @@ void ncw_put_vara_short(const char fname[], int ncid, int varid, const size_t st
}
}

void ncw_put_vara_ushort(const char fname[], int ncid, int varid, const size_t start[], const size_t count[], const unsigned short int v[])
{
int status = nc_put_vara_ushort(ncid, varid, start, count, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;
int ndims = 0;

ncw_inq_varname(fname, ncid, varid, varname);
ncw_inq_varndims(fname, ncid, varid, &ndims);
quit("\"%s\": ncw_put_vara_ushort(): failed for varid = %d (varname = \"%s\"), start = %s, count = %s: %s\n", fname, varid, varname, uint2str(ndims, (unsigned int*) start), uint2str(ndims, (unsigned int*) count), nc_strerror(status));
}
}

void ncw_put_vara_int(const char fname[], int ncid, int varid, const size_t start[], const size_t count[], const int v[])
{
int status = nc_put_vara_int(ncid, varid, start, count, v);
Expand All @@ -599,6 +685,20 @@ void ncw_put_vara_int(const char fname[], int ncid, int varid, const size_t star
}
}

void ncw_put_vara_uint(const char fname[], int ncid, int varid, const size_t start[], const size_t count[], const unsigned int v[])
{
int status = nc_put_vara_uint(ncid, varid, start, count, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;
int ndims = 0;

ncw_inq_varname(fname, ncid, varid, varname);
ncw_inq_varndims(fname, ncid, varid, &ndims);
quit("\"%s\": ncw_put_vara_uint(): failed for varid = %d (varname = \"%s\"), start = %s, count = %s: %s\n", fname, varid, varname, uint2str(ndims, (unsigned int*) start), uint2str(ndims, (unsigned int*) count), nc_strerror(status));
}
}

void ncw_put_vara_float(const char fname[], int ncid, int varid, const size_t start[], const size_t count[], const float v[])
{
int status = nc_put_vara_float(ncid, varid, start, count, v);
Expand Down Expand Up @@ -861,6 +961,31 @@ void ncw_get_att_text(const char fname[], int ncid, int varid, const char attnam
}
}

void ncw_get_att_short(const char fname[], int ncid, int varid, const char attname[], short int v[])
{
nc_type xtype;
size_t len;
int status;

ncw_inq_att(fname, ncid, varid, attname, &xtype, &len);

if (xtype != NC_SHORT) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

_ncw_inq_varname(fname, ncid, varid, varname);
quit("ncw_get_att_short(): failed for varid = %d (varname = \"%s\"), attname = \"%s\": the attribute is of %s type\n", fname, varid, varname, attname, ncw_nctype2str(xtype));
}

status = nc_get_att_short(ncid, varid, attname, v);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

_ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_get_att_short(): failed for varid = %d (varname = \"%s\"), attname = \"%s\": %s\n", fname, varid, varname, attname, nc_strerror(status));
}
}

void ncw_get_att_int(const char fname[], int ncid, int varid, const char attname[], int v[])
{
nc_type xtype;
Expand Down Expand Up @@ -1017,6 +1142,29 @@ void ncw_copy_dims(const char* fname_src, int ncid_src, const char* fname_dst, i
}
}

/** Copies dimension from one NetCDF file to another.
*
* @param fname_src Source file name
* @param ncid_src Source file id
* @param dimname Dimension name
* @param fname_dst Destination file name
* @param ncid_dst Destination file id
*/
void ncw_copy_dim(const char* fname_src, int ncid_src, const char dimname[], const char* fname_dst, int ncid_dst)
{
int unlimdimid = -1;
int dimid;
size_t size;

ncw_inq_unlimdimid(fname_src, ncid_src, &unlimdimid);
ncw_inq_dimid(fname_src, ncid_src, dimname, &dimid);
if (dimid == unlimdimid)
size = NC_UNLIMITED;
else
ncw_inq_dimlen(fname_src, ncid_src, dimid, &size);
ncw_def_dim(fname_dst, ncid_dst, dimname, size, &dimid);
}

/** Copies definition of a specified variable from one NetCDF file to another.
*
* @param fname_src Source file name
Expand Down Expand Up @@ -1133,7 +1281,7 @@ void ncw_copy_vardata(const char* fname_src, int ncid_src, int vid_src, const ch
nc_redef(ncid_dst);
}

/** Copies definition and data for a given variable from one file to another.
/** Copies definitiona and data for a given variable from one file to another.
*
* @param fname_src Source file name
* @param ncid_src Source file id
Expand All @@ -1150,6 +1298,32 @@ void ncw_copy_var(const char* fname_src, int ncid_src, const char varname[], con
ncw_copy_vardata(fname_src, ncid_src, vid_src, fname_dst, ncid_dst);
}

/** Set deflation (compression) level for all variables in a file.
*
* @param fname NetCDF file name
* @param ncid NetCDF file id
* @param shuffle Shuffle flag, whatever it means
* @param deflate Flag, turns deflation on/off
* @param deflate_level Compression level
*/
void ncw_def_deflate(const char fname[], int ncid, int shuffle, int deflate, int deflate_level)
{
int nv = -1; /* total number of variables */
int vid;

ncw_inq_nvars(fname, ncid, &nv);
for (vid = 0; vid < nv; ++vid) {
int status = nc_def_var_deflate(ncid, vid, shuffle, deflate, deflate_level);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = "STR_UNKNOWN";

_ncw_inq_varname(fname, ncid, vid, varname);
quit("\"%s\": ncw_def_deflate(): failed for \"%s\": %s\n", fname, varname, nc_strerror(status));
}
}
}

/** Gets the id for the first dimension found to be present in a NetCDF file
* out of two dimensions specified by names. Useful for handling both new and
* old data formats.
Expand Down Expand Up @@ -1597,6 +1771,44 @@ void ncw_put_var_float_record(const char fname[], int ncid, int varid, int r, fl
}
}

/** Checks that the attribute has certain type and length
*/
void ncw_check_att(const char fname[], int ncid, int varid, const char attname[], nc_type att_type, size_t att_len)
{
nc_type type;
size_t len;
int status = nc_inq_att(ncid, varid, attname, &type, &len);

if (status != NC_NOERR) {
char varname[NC_MAX_NAME] = STR_UNKNOWN;

_ncw_inq_varname(fname, ncid, varid, varname);
quit("\"%s\": nc_inq_att(): failed for varid = %d (varname = \"%s\"), attname = \"%s\", atttype = %d: %s\n", fname, varid, varname, attname, ncw_nctype2str(type), nc_strerror(status));
}

if (type != att_type)
quit("\"%s\": ncw_check_att(): attribute \"%s\" is supposed to have type \"%s\"; the actual type is \"%s\"\n", fname, attname, ncw_nctype2str(att_type), ncw_nctype2str(type));
if (len != att_len)
quit("\"%s\": ncw_check_att(): attribute \"%s\" is supposed to have length %z; the actual length is %z\n", fname, attname, att_len, len);
}

/** Check that the dimension has certain length
*/
void ncw_check_dimlen(const char fname[], int ncid, const char dimname[], size_t dimlen)
{
size_t len;
int dimid;
int status;

ncw_inq_dimid(fname, ncid, dimname, &dimid);
status = nc_inq_dimlen(ncid, dimid, &len);

if (status != NC_NOERR)
quit("\"%s\": nc_inq_dimlen(): failed for dimid = %d (dimname = \"%s\"): %s\n", fname, dimid, dimname, nc_strerror(status));
if (len != dimlen)
quit("\"%s\": ncw_check_dimlen(): dimension \"%s\" is supposed to have length %zu; the actual length is %zu\n", fname, dimname, dimlen, len);
}

/** Sets the quit function.
*/
void ncw_set_quitfn(ncw_quit_fn quitfn)
Expand Down
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