Error: NetCDF: Filter error: undefined filter encountered

[tayloj25]

I am using netcdf-c-4.9.1 with hdf5-1.12.2 and zlib-1.2.13. I am attempting to run quite a similar example to the pres_temp_4D_rd.c example on the unidata website. My dimensions are slightly different though. My code appears as below:

#include <stdio.h>
#include <string.h>
#include <netcdf.h>

/* This is the name of the data file we will read. */
#define FILE_NAME "pressure_data.nc"

#define NDIMS 4
#define NLAT 45
#define NLON 57
#define LAT_NAME "y"
#define LON_NAME "x"
#define NREC 1
#define REC_NAME "time"
#define LVL_NAME "z"
#define NLVL 1

/* Names of things. */
#define PRES_NAME "pressure"
#define UNITS "units"
#define DEGREES_EAST "degrees_east"
#define DEGREES_NORTH "degrees_north"

/* These are used to calculate the values we expect to find. */
#define SAMPLE_PRESSURE 101403.1
#define START_LAT 26.0
#define START_LON -84.0

/* For the units attributes. */
#define UNITS "units"
#define PRES_UNITS "Pa"
#define LAT_UNITS "degrees_north"
#define LON_UNITS "degrees_east"
#define MAX_ATT_LEN 80

/* Handle errors by printing an error message and exiting with a

• non-zero status. */
  #define ERR(e) {printf("Error: %s\n", nc_strerror(e)); return 2;}

int
main()
{
int ncid, pres_varid;
int lat_varid, lon_varid;

/* The start and count arrays will tell the netCDF library where to
read our data. */
size_t start[NDIMS], count[NDIMS];

/* Program variables to hold the data we will read. We will only
need enough space to hold one timestep of data; one record. */
float pres_in[NLVL][NLAT][NLON];
// float temp_in[NLVL][NLAT][NLON];

/* These program variables hold the latitudes and longitudes. */
float lats[NLAT], lons[NLON];

/* Loop indexes. */
int lvl, lat, lon, rec, i = 0;

/* Error handling. */
int retval;

/* Open the file. */
if ((retval = nc_open(FILE_NAME, NC_NOWRITE, &ncid)))
ERR(retval);

/* Get the varids of the latitude and longitude coordinate
* variables. */
if ((retval = nc_inq_varid(ncid, LAT_NAME, &lat_varid)))
ERR(retval);
if ((retval = nc_inq_varid(ncid, LON_NAME, &lon_varid)))
ERR(retval);

/* Read the coordinate variable data. */
if ((retval = nc_get_var_float(ncid, lat_varid, &lats[0])))
ERR(retval);
if ((retval = nc_get_var_float(ncid, lon_varid, &lons[0])))
ERR(retval);

/* Check the coordinate variable data. */
for (lat = 0; lat < NLAT; lat++)
if (lats[lat] != START_LAT + 5.*lat)
return 2;
for (lon = 0; lon < NLON; lon++)
if (lons[lon] != START_LON + 5.*lon)
return 2;

/* Get the varids of the pressure and temperature netCDF
* variables. */
if ((retval = nc_inq_varid(ncid, PRES_NAME, &pres_varid)))
ERR(retval);

/* Read the data. Since we know the contents of the file we know
* that the data arrays in this program are the correct size to
* hold one timestep. */
count[0] = 1;
count[1] = NLVL;
count[2] = NLAT;
count[3] = NLON;
start[1] = 0;
start[2] = 0;
start[3] = 0;

/* Read and check one record at a time. */
for (rec = 0; rec < NREC; rec++)
{
start[0] = rec;
if ((retval = nc_get_vara_float(ncid, pres_varid, start,
count, &pres_in[0][0][0])))
ERR(retval);

/* Check the data. */
   i = 0;
   for (lvl = 0; lvl < NLVL; lvl++)
                                            for (lat = 0; lat < NLAT; lat++)
                                                            for (lon = 0; lon < NLON; lon++)
                                                            {
                                                                            if (pres_in[lvl][lat][lon] != SAMPLE_PRESSURE + i)
                                                                                            return 2;
                                                                            //if (temp_in[lvl][lat][lon] != SAMPLE_TEMP + i)
                                                                            //            return 2;
                                                                            i++;
                                                            }

} /* next record */

/* Close the file. */
if ((retval = nc_close(ncid)))
                            ERR(retval);

return 0;
}

I am getting an error indicating that an undefined filter was encountered. I checked and it seems to be NC_ENOFILTER error I believe. I also believe that this error stems from the. nc_get_vara_float() function. I ran the pres_temp_4D_rd.c example with no error similar to this.

I attempted to check the filters of the .nc file with:
ncdump -h | grep FILTERS

Nothing came up for filters in the ncdump. I also tried:
ncdump -s

I did not see a "chunking" section but did see a variable like this "ChunkSizes = 1, 1, 45, 57 ; for my pressure data variable.

Any reason that this is happening ? Can't seem to find much info on this issue.

[DennisHeimbigner]

Try this: ncdump -hs <filename> | fgrep -i filter

…

On 2/22/2023 11:14 PM, tayloj25 wrote: I am using netcdf-c-4.9.1 with hdf5-1.12.2 and zlib-1.2.13. I am attempting to run quite a similar example to the pres_temp_4D_rd.c example on the unidata website. My dimensions are slightly different though. My code appears as below: #include <stdio.h> #include <string.h> #include <netcdf.h> /* This is the name of the data file we will read. */ #define FILE_NAME "pressure_data.nc" #define NDIMS 4 #define NLAT 45 #define NLON 57 #define LAT_NAME "y" #define LON_NAME "x" #define NREC 1 #define REC_NAME "time" #define LVL_NAME "z" #define NLVL 1 /* Names of things. */ #define PRES_NAME "pressure" #define UNITS "units" #define DEGREES_EAST "degrees_east" #define DEGREES_NORTH "degrees_north" /* These are used to calculate the values we expect to find. */ #define SAMPLE_PRESSURE 101403.1 #define START_LAT 26.0 #define START_LON -84.0 /* For the units attributes. */ #define UNITS "units" #define PRES_UNITS "Pa" #define LAT_UNITS "degrees_north" #define LON_UNITS "degrees_east" #define MAX_ATT_LEN 80 /* Handle errors by printing an error message and exiting with a * non-zero status. */ #define ERR(e) {printf("Error: %s\n", nc_strerror(e)); return 2;} int main() { int ncid, pres_varid; int lat_varid, lon_varid; /* The start and count arrays will tell the netCDF library where to read our data. */ size_t start[NDIMS], count[NDIMS]; /* Program variables to hold the data we will read. We will only need enough space to hold one timestep of data; one record. */ float pres_in[NLVL][NLAT][NLON]; // float temp_in[NLVL][NLAT][NLON]; /* These program variables hold the latitudes and longitudes. */ float lats[NLAT], lons[NLON]; /* Loop indexes. */ int lvl, lat, lon, rec, i = 0; /* Error handling. */ int retval; /* Open the file. */ if ((retval = nc_open(FILE_NAME, NC_NOWRITE, &ncid))) ERR(retval); /* Get the varids of the latitude and longitude coordinate * variables. */ if ((retval = nc_inq_varid(ncid, LAT_NAME, &lat_varid))) ERR(retval); if ((retval = nc_inq_varid(ncid, LON_NAME, &lon_varid))) ERR(retval); /* Read the coordinate variable data. */ if ((retval = nc_get_var_float(ncid, lat_varid, &lats[0]))) ERR(retval); if ((retval = nc_get_var_float(ncid, lon_varid, &lons[0]))) ERR(retval); /* Check the coordinate variable data. */ for (lat = 0; lat < NLAT; lat++) if (lats[lat] != START_LAT + 5.*lat) return 2; for (lon = 0; lon < NLON; lon++) if (lons[lon] != START_LON + 5.*lon) return 2; /* Get the varids of the pressure and temperature netCDF * variables. */ if ((retval = nc_inq_varid(ncid, PRES_NAME, &pres_varid))) ERR(retval); /* Read the data. Since we know the contents of the file we know * that the data arrays in this program are the correct size to * hold one timestep. */ count[0] = 1; count[1] = NLVL; count[2] = NLAT; count[3] = NLON; start[1] = 0; start[2] = 0; start[3] = 0; /* Read and check one record at a time. */ for (rec = 0; rec < NREC; rec++) { start[0] = rec; if ((retval = nc_get_vara_float(ncid, pres_varid, start, count, &pres_in[0][0][0]))) ERR(retval); |/* Check the data. */ i = 0; for (lvl = 0; lvl < NLVL; lvl++) for (lat = 0; lat < NLAT; lat++) for (lon = 0; lon < NLON; lon++) { if (pres_in[lvl][lat][lon] != SAMPLE_PRESSURE + i) return 2; //if (temp_in[lvl][lat][lon] != SAMPLE_TEMP + i) // return 2; i++; } } /* next record */ /* Close the file. */ if ((retval = nc_close(ncid))) ERR(retval); | return 0; } I am getting an error indicating that an undefined filter was encountered. I checked and it seems to be NC_ENOFILTER error I believe. I also believe that this error stems from the. nc_get_vara_float() function. I ran the pres_temp_4D_rd.c example with no error similar to this. I attempted to check the filters of the .nc file with: ncdump -h | grep FILTERS Nothing came up for filters in the ncdump. I also tried: ncdump -s I did not see a "chunking" section but did see a variable like this "ChunkSizes = 1, 1, 45, 57 ; for my pressure data variable. Any reason that this is happening ? Can't seem to find much info on this issue. — Reply to this email directly, view it on GitHub <#2636>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG47W2TVRGMZ562M2IH7W3WY3525ANCNFSM6AAAAAAVFGLL2E>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[tayloj25]

Nothing comes from fgrep -I filter, omitting this, I get this:

netcdf pressure_data {
dimensions:
time = 1 ;
z = 1 ;
y = 45 ;
x = 57 ;
variables:
float pressure(time, z, y, x) ;
pressure:valid_min = 94849.89f ;
pressure:valid_max = 107875.9f ;
pressure:_FillValue = -9999.f ;
pressure:long_name = "Pressure reduced to MSL" ;
pressure:units = "Pa" ;
pressure:grid_mapping = "grid_mapping" ;
pressure:_Storage = "chunked" ;
pressure:_ChunkSizes = 1, 1, 45, 57 ;
pressure:_DeflateLevel = 5 ;
pressure:_Endianness = "little" ;
double forecast_period(time) ;
forecast_period:standard_name = "forecast_period" ;
forecast_period:long_name = "time interval between the forecast reference time and the valid time" ;
forecast_period:units = "seconds" ;
forecast_period:_Storage = "contiguous" ;
forecast_period:_Endianness = "little" ;
double forecast_reference_time ;
forecast_reference_time:standard_name = "forecast_reference_time" ;
forecast_reference_time:long_name = "the time of the analysis from which the forecast was made" ;
forecast_reference_time:units = "seconds since 1970-01-01T00:00:00Z" ;
forecast_reference_time:calendar = "gregorian" ;
forecast_reference_time:reference_date = "2021-04-09T06:00:00Z" ;
forecast_reference_time:_Storage = "contiguous" ;
forecast_reference_time:_Endianness = "little" ;
int grid_mapping ;
grid_mapping:earth_radius = 6371229.f ;
grid_mapping:grid_mapping_name = "latitude_longitude" ;
grid_mapping:_Storage = "contiguous" ;
grid_mapping:_Endianness = "little" ;
double time(time) ;
time:standard_name = "time" ;
time:long_name = "data valid time" ;
time:units = "seconds since 1970-01-01T00:00:00Z" ;
time:calendar = "gregorian" ;
time:axis = "T" ;
time:reference_date = "2021-04-09T07:00:00Z" ;
time:_Storage = "contiguous" ;
time:_Endianness = "little" ;
float x(x) ;
x:standard_name = "longitude" ;
x:long_name = "longitude" ;
x:units = "degrees_east" ;
x:axis = "X" ;
x:_Storage = "contiguous" ;
x:_Endianness = "little" ;
float y(y) ;
y:standard_name = "latitude" ;
y:long_name = "latitude" ;
y:units = "degrees_north" ;
y:axis = "Y" ;
y:_Storage = "contiguous" ;
y:_Endianness = "little" ;
float z(z) ;
z:long_name = "Mean sea level" ;
z:axis = "Z" ;
z:_Storage = "contiguous" ;
z:_Endianness = "little" ;

// global attributes:
:Conventions = "CF-1.6" ;
:source = "US NWS - NCEP" ;
:title = "Global Forecast System Model" ;
:history = "Tue Apr 13 15:33:28 2021: ncks -d x,384,496,2 -d y,464,552,2 PRESSURE_DATA.nc pressure_data.nc\n",
"Converted to NetCDF from Grib2 with Grib2toNc, V1.25, from NCAR-RAL." ;
:NCO = "4.7.2" ;
:_NCProperties = "version=1|netcdflibversion=4.6.0|hdf5libversion=1.10.0" ;
:_SuperblockVersion = 0 ;
:_IsNetcdf4 = 0 ;
:_Format = "netCDF-4 classic model" ;
}

[DennisHeimbigner]

The key is this line: pressure:_DeflateLevel = 5 ; It means you are using the zlib compressor. You might try installing zlib and see if that fixes the problem.

…

On 2/23/2023 12:28 PM, tayloj25 wrote: pressure:_DeflateLevel = 5 ;

[tayloj25]

I thought that I had already installed zlib.
I ran "nc-config --all" and got:

This netCDF 4.9.1 has been built with the following features:

--cc -> gcc
--cflags -> -I/usr/local/include -I/usr/local/include
--libs -> -L/usr/local/lib -lnetcdf
--static -> -lhdf5_hl -lhdf5 -lm -lz -ldl -lxml2 -lcurl

--has-c++ -> no
--cxx ->

--has-c++4 -> no
--cxx4 ->

--has-fortran -> no
--has-dap -> no
--has-dap2 -> no
--has-dap4 -> no
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-logging -> no
--has-pnetcdf -> no
--has-szlib -> no
--has-cdf5 -> yes
--has-parallel4 -> no
--has-parallel -> no
--has-nczarr -> yes
--has-zstd -> no
--has-benchmarks -> no
--has-multifilters -> yes
--has-stdfilters -> deflate bz2
--has-quantize -> yes

--prefix -> /usr/local
--includedir -> /usr/local/include
--libdir -> /usr/local/lib
--plugindir ->
--version -> netCDF 4.9.1

Does the -lz in static mean that is included or do I need to add something else to these options?

[DennisHeimbigner]

No idea at the moment why this is failing. After you build the netcdf-c library did you run 'make check'?

…

On 2/23/2023 1:46 PM, tayloj25 wrote: I thought that I had already installed zlib. I ran "nc-config --all" and got: This netCDF 4.9.1 has been built with the following features: --cc -> gcc --cflags -> -I/usr/local/include -I/usr/local/include --libs -> -L/usr/local/lib -lnetcdf --static -> -lhdf5_hl -lhdf5 -lm -lz -ldl -lxml2 -lcurl --has-c++ -> no --cxx -> --has-c++4 -> no --cxx4 -> --has-fortran -> no --has-dap -> no --has-dap2 -> no --has-dap4 -> no --has-nc2 -> yes --has-nc4 -> yes --has-hdf5 -> yes --has-hdf4 -> no --has-logging -> no --has-pnetcdf -> no --has-szlib -> no --has-cdf5 -> yes --has-parallel4 -> no --has-parallel -> no --has-nczarr -> yes --has-zstd -> no --has-benchmarks -> no --has-multifilters -> yes --has-stdfilters -> deflate bz2 --has-quantize -> yes --prefix -> /usr/local --includedir -> /usr/local/include --libdir -> /usr/local/lib --plugindir -> --version -> netCDF 4.9.1 Does the -lz in static mean that is included or do I need to add something else to these options? — Reply to this email directly, view it on GitHub <#2636 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG47W44IPAKICAKFL3CJPLWY7EAVANCNFSM6AAAAAAVFGLL2E>. You are receiving this because you commented.Message ID: ***@***.***>

[tayloj25]

I thought I had, but I just ran it again and encountered failure with:
tst_netcdf4.sh
tst_ncgen4.sh
tst_netcdf4_4.sh
tst_nccopy4.sh
tst_nccopy5.sh

I have attached the test-suite.log below:

netCDF 4.9.1: ncdump/test-suite.log

TOTAL: 47

PASS: 42

SKIP: 0

XFAIL: 0

FAIL: 5

XPASS: 0

ERROR: 0

.. contents:: :depth: 2

FAIL: tst_netcdf4

*** Testing ncgen and ncdump for netCDF-4 format.
*** Creating test output tst_netcdf4_c0.nc.
*** Testing that program tst_h_rdc0 can read tst_netcdf4_c0.nc.

*** Checking HDF5 file c0.nc.
*** Checking HDF5 objcts...ok.
*** Tests successful!
*** Running tst_create_files.c to create test files.

*** Creating test files for ncdump.
*** creating nested group file tst_solar_1.nc...ok.
*** checking nested group file tst_solar_1.nc...ok.
*** creating file with VLEN tst_solar_2.nc...ok.
*** creating file with compound type tst_solar_cmp.nc...ok.
*** Tests successful!
*** Testing tst_create_files output for netCDF-4 features.
*** Running tst_group_data.c to create test files.

*** Testing groups.
*** creating nested group file tst_group_data.nc...ok.
*** Tests successful!
*** Testing -v option with absolute name and groups...
*** Testing -v option with relative name and groups...
*** Running tst_enum_data.c to create test files.

*** Testing enums.
*** creating enum test file tst_enum_data.nc...ok.
*** Tests successful!
*** Running tst_enum_undef.c to create test files.

*** Testing enum undefined identifier.
*** creating enum test file tst_enum_undef.nc...ok.
*** Tests successful!
*** Running tst_opaque_data.c to create test files.

*** Testing opaque types.
*** creating opaque test file tst_opaque_data.nc...ok.
*** Tests successful!
*** Running tst_comp.c to create test files.

*** Testing compound types.
*** creating compound test file tst_comp.nc...ok.
*** Tests successful!
*** Running tst_nans.c to create test files.

*** Testing NaN
*** creating NaN test file tst_nans.nc...ok.
*** Tests successful!
*** Running tst_special_atts.c to create test files.

*** Testing '-s' option for special attributes.
*** creating special attributes test file tst_special_atts.nc...Sorry! Unexpected result, tst_special_atts.c, line: 130
FAIL tst_netcdf4.sh (exit status: 2)

FAIL: tst_ncgen4

*** Performing diff tests: k=3
*** Testing ncgen with -k3
*** Testing: nc_enddef
*** SUCCEED: nc_enddef
*** Testing: ref_tst_unicode
*** SUCCEED: ref_tst_unicode
*** Testing: ref_tst_utf8
*** SUCCEED: ref_tst_utf8
*** Testing: simple_xy
*** SUCCEED: simple_xy
*** Testing: small
*** SUCCEED: small
*** Testing: nc_sync
*** SUCCEED: nc_sync
*** Testing: ref_tst_small
*** SUCCEED: ref_tst_small
*** Testing: small2
*** SUCCEED: small2
*** Testing: tst_ncml
*** SUCCEED: tst_ncml
*** Testing: n3time
*** SUCCEED: n3time
*** Testing: ref_tst_chardata
*** XFAIL : ref_tst_chardata
*** Testing: ref_tst_nul3
*** SUCCEED: ref_tst_nul3
*** Testing: ref_tst_long_charconst
*** SUCCEED: ref_tst_long_charconst
*** Testing: tst_chararray
*** SUCCEED: tst_chararray
*** Testing: unlimtest1
*** SUCCEED: unlimtest1
*** Testing: ref_keyword
*** SUCCEED: ref_keyword
*** Testing: test0
*** SUCCEED: test0
*** Testing: sfc_pres_temp
*** SUCCEED: sfc_pres_temp
*** Testing: fills
*** SUCCEED: fills
*** Testing: c0
*** SUCCEED: c0
*** Testing: example_good
*** SUCCEED: example_good
*** Testing: pres_temp_4D
*** SUCCEED: pres_temp_4D
*** Testing: ref_nctst
*** SUCCEED: ref_nctst
*** Testing: ref_nctst_64bit_offset
*** SUCCEED: ref_nctst_64bit_offset
*** Testing: ref_ctest1_nc4
*** SUCCEED: ref_ctest1_nc4
*** Testing: ref_ctest1_nc4c
*** SUCCEED: ref_ctest1_nc4c
*** Testing: ref_nctst_netcdf4
*** SUCCEED: ref_nctst_netcdf4
*** Testing: ref_nctst_netcdf4_classic
*** SUCCEED: ref_nctst_netcdf4_classic
*** Testing: ref_tst_unlim2
*** XFAIL : ref_tst_unlim2
*** Testing: ref_tst_names
*** SUCCEED: ref_tst_names
*** Testing: ref_dimscope
*** SUCCEED: ref_dimscope
*** Testing: ref_typescope
*** SUCCEED: ref_typescope
*** Testing: ref_tst_string_data
*** SUCCEED: ref_tst_string_data
*** Testing: ref_tst_comp
*** SUCCEED: ref_tst_comp
*** Testing: ref_tst_comp2
*** SUCCEED: ref_tst_comp2
*** Testing: ref_tst_comp3
*** SUCCEED: ref_tst_comp3
*** Testing: ref_tst_group_data
*** SUCCEED: ref_tst_group_data
*** Testing: ref_tst_opaque_data
*** SUCCEED: ref_tst_opaque_data
*** Testing: ref_tst_solar_1
*** SUCCEED: ref_tst_solar_1
*** Testing: ref_tst_solar_2
*** SUCCEED: ref_tst_solar_2
*** Testing: ref_tst_enum_data
*** SUCCEED: ref_tst_enum_data
*** Testing: ref_tst_special_atts
ncgen: NetCDF: Filter error: undefined filter encountered
(genbin.c:genbin_definespecialattributes:231)
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0:
#000: H5PLint.c line 261 in H5PL_load(): search in path table failed
major: Plugin for dynamically loaded library
minor: Can't get value
#1: H5PLpath.c line 802 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error
major: Plugin for dynamically loaded library
minor: Can't get value
#2: H5PLpath.c line 855 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin
major: Plugin for dynamically loaded library
minor: Can't open directory or file
FAIL tst_ncgen4.sh (exit status: 1)

FAIL: tst_netcdf4_4

*** Running extra netcdf-4 tests.
*** running tst_string_data to create test files...

*** Testing strings.
*** creating strings test file tst_string_data.nc...ok.
*** Tests successful!
*** dumping tst_string_data.nc to tst_string_data.cdl...
*** comparing tst_string_data.cdl with ref_tst_string_data.cdl...
*** testing reference file ref_tst_compounds2.nc...
*** testing reference file ref_tst_compounds3.nc...
*** testing reference file ref_tst_compounds4.nc...
Filter id=1; filter not available
ncgen: NetCDF: Filter error: undefined filter encountered
(genbin.c:genbin_definespecialattributes:259)
HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0:
#000: H5PLint.c line 261 in H5PL_load(): search in path table failed
major: Plugin for dynamically loaded library
minor: Can't get value
#1: H5PLpath.c line 802 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error
major: Plugin for dynamically loaded library
minor: Can't get value
#2: H5PLpath.c line 855 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin
major: Plugin for dynamically loaded library
minor: Can't open directory or file
FAIL tst_netcdf4_4.sh (exit status: 1)

FAIL: tst_nccopy4

*** Testing groups.
*** creating nested group file tst_group_data.nc...ok.
*** Tests successful!

*** Testing enums.
*** creating enum test file tst_enum_data.nc...ok.
*** Tests successful!

*** Testing compound types.
*** creating compound test file tst_comp.nc...ok.
*** Tests successful!

*** Testing compound types some more.
*** creating another compound test file tst_comp2.nc...ok.
*** Tests successful!

*** Testing netCDF-4 features of nccopy on ncdump/*.nc files
*** Test nccopy tst_comp.nc copy_of_tst_comp.nc ...
*** compare with copy_of_tst_comp.cdl
*** Test nccopy tst_comp2.nc copy_of_tst_comp2.nc ...
*** compare with copy_of_tst_comp2.cdl
*** Test nccopy tst_enum_data.nc copy_of_tst_enum_data.nc ...
*** compare with copy_of_tst_enum_data.cdl
*** Test nccopy tst_fillbug.nc copy_of_tst_fillbug.nc ...
*** compare with copy_of_tst_fillbug.cdl
*** Test nccopy tst_group_data.nc copy_of_tst_group_data.nc ...
*** compare with copy_of_tst_group_data.cdl
*** Test nccopy tst_nans.nc copy_of_tst_nans.nc ...
*** compare with copy_of_tst_nans.cdl
*** Test nccopy tst_opaque_data.nc copy_of_tst_opaque_data.nc ...
*** compare with copy_of_tst_opaque_data.cdl
*** Test nccopy tst_solar_1.nc copy_of_tst_solar_1.nc ...
*** compare with copy_of_tst_solar_1.cdl
*** Test nccopy tst_solar_2.nc copy_of_tst_solar_2.nc ...
*** compare with copy_of_tst_solar_2.cdl
*** Test nccopy tst_solar_cmp.nc copy_of_tst_solar_cmp.nc ...
*** compare with copy_of_tst_solar_cmp.cdl
*** Test nccopy tst_special_atts.nc copy_of_tst_special_atts.nc ...
*** compare with copy_of_tst_special_atts.cdl
*** Test nccopy tst_string_data.nc copy_of_tst_string_data.nc ...
*** compare with copy_of_tst_string_data.cdl
*** Creating compressible test files tst_inflated.nc, tst_inflated4.nc...ok.
*** Tests successful!
*** Test nccopy -d1 can compress a classic format file ...
NetCDF: Filter error: undefined filter encountered
Location: file nccopy.c; fcn copy_var_specials line 1152
FAIL tst_nccopy4.sh (exit status: 1)

FAIL: tst_nccopy5

*** Creating chunkable test file tmp_nc5_base.nc...
ok.
*** Tests successful!
*** Test nccopy -c with per-variable chunking; classic->enhanced
*** Test nccopy -c with per-variable chunking; enhanced->enhanced
*** Creating chunkable test file tst_nc5.nc...
option: deflate
Sorry! Unexpected result(0), tst_chunking.c, line: 103
1 failures
1 errors detected! Sorry!
FAIL tst_nccopy5.sh (exit status: 2)

I'm guessing that it has to do with that last error? Any ideas ?

[DennisHeimbigner]

can you send me the complete set of build options you used?

…

On 2/23/2023 2:31 PM, tayloj25 wrote: I thought I had, but I just ran it again and encountered failure with: tst_netcdf4.sh tst_ncgen4.sh tst_netcdf4_4.sh tst_nccopy4.sh tst_nccopy5.sh I have attached the test-suite.log below: netCDF 4.9.1: ncdump/test-suite.log TOTAL: 47 PASS: 42 SKIP: 0 XFAIL: 0 FAIL: 5 XPASS: 0 ERROR: 0 .. contents:: :depth: 2 FAIL: tst_netcdf4 *** Testing ncgen and ncdump for netCDF-4 format. *** Creating test output tst_netcdf4_c0.nc. *** Testing that program tst_h_rdc0 can read tst_netcdf4_c0.nc. *** Checking HDF5 file c0.nc. *** Checking HDF5 objcts...ok. *** Tests successful! *** Running tst_create_files.c to create test files. *** Creating test files for ncdump. *** creating nested group file tst_solar_1.nc...ok. *** checking nested group file tst_solar_1.nc...ok. *** creating file with VLEN tst_solar_2.nc...ok. *** creating file with compound type tst_solar_cmp.nc...ok. *** Tests successful! *** Testing tst_create_files output for netCDF-4 features. *** Running tst_group_data.c to create test files. *** Testing groups. *** creating nested group file tst_group_data.nc...ok. *** Tests successful! *** Testing -v option with absolute name and groups... *** Testing -v option with relative name and groups... *** Running tst_enum_data.c to create test files. *** Testing enums. *** creating enum test file tst_enum_data.nc...ok. *** Tests successful! *** Running tst_enum_undef.c to create test files. *** Testing enum undefined identifier. *** creating enum test file tst_enum_undef.nc...ok. *** Tests successful! *** Running tst_opaque_data.c to create test files. *** Testing opaque types. *** creating opaque test file tst_opaque_data.nc...ok. *** Tests successful! *** Running tst_comp.c to create test files. *** Testing compound types. *** creating compound test file tst_comp.nc...ok. *** Tests successful! *** Running tst_nans.c to create test files. *** Testing NaN *** creating NaN test file tst_nans.nc...ok. *** Tests successful! *** Running tst_special_atts.c to create test files. *** Testing '-s' option for special attributes. *** creating special attributes test file tst_special_atts.nc...Sorry! Unexpected result, tst_special_atts.c, line: 130 FAIL tst_netcdf4.sh (exit status: 2) FAIL: tst_ncgen4 *** Performing diff tests: k=3 *** Testing ncgen with -k3 *** Testing: nc_enddef *** SUCCEED: nc_enddef *** Testing: ref_tst_unicode *** SUCCEED: ref_tst_unicode *** Testing: ref_tst_utf8 *** SUCCEED: ref_tst_utf8 *** Testing: simple_xy *** SUCCEED: simple_xy *** Testing: small *** SUCCEED: small *** Testing: nc_sync *** SUCCEED: nc_sync *** Testing: ref_tst_small *** SUCCEED: ref_tst_small *** Testing: small2 *** SUCCEED: small2 *** Testing: tst_ncml *** SUCCEED: tst_ncml *** Testing: n3time *** SUCCEED: n3time *** Testing: ref_tst_chardata *** XFAIL : ref_tst_chardata *** Testing: ref_tst_nul3 *** SUCCEED: ref_tst_nul3 *** Testing: ref_tst_long_charconst *** SUCCEED: ref_tst_long_charconst *** Testing: tst_chararray *** SUCCEED: tst_chararray *** Testing: unlimtest1 *** SUCCEED: unlimtest1 *** Testing: ref_keyword *** SUCCEED: ref_keyword *** Testing: test0 *** SUCCEED: test0 *** Testing: sfc_pres_temp *** SUCCEED: sfc_pres_temp *** Testing: fills *** SUCCEED: fills *** Testing: c0 *** SUCCEED: c0 *** Testing: example_good *** SUCCEED: example_good *** Testing: pres_temp_4D *** SUCCEED: pres_temp_4D *** Testing: ref_nctst *** SUCCEED: ref_nctst *** Testing: ref_nctst_64bit_offset *** SUCCEED: ref_nctst_64bit_offset *** Testing: ref_ctest1_nc4 *** SUCCEED: ref_ctest1_nc4 *** Testing: ref_ctest1_nc4c *** SUCCEED: ref_ctest1_nc4c *** Testing: ref_nctst_netcdf4 *** SUCCEED: ref_nctst_netcdf4 *** Testing: ref_nctst_netcdf4_classic *** SUCCEED: ref_nctst_netcdf4_classic *** Testing: ref_tst_unlim2 *** XFAIL : ref_tst_unlim2 *** Testing: ref_tst_names *** SUCCEED: ref_tst_names *** Testing: ref_dimscope *** SUCCEED: ref_dimscope *** Testing: ref_typescope *** SUCCEED: ref_typescope *** Testing: ref_tst_string_data *** SUCCEED: ref_tst_string_data *** Testing: ref_tst_comp *** SUCCEED: ref_tst_comp *** Testing: ref_tst_comp2 *** SUCCEED: ref_tst_comp2 *** Testing: ref_tst_comp3 *** SUCCEED: ref_tst_comp3 *** Testing: ref_tst_group_data *** SUCCEED: ref_tst_group_data *** Testing: ref_tst_opaque_data *** SUCCEED: ref_tst_opaque_data *** Testing: ref_tst_solar_1 *** SUCCEED: ref_tst_solar_1 *** Testing: ref_tst_solar_2 *** SUCCEED: ref_tst_solar_2 *** Testing: ref_tst_enum_data *** SUCCEED: ref_tst_enum_data *** Testing: ref_tst_special_atts ncgen: NetCDF: Filter error: undefined filter encountered (genbin.c:genbin_definespecialattributes:231) HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0: #000: H5PLint.c line 261 in H5PL_load(): search in path table failed major: Plugin for dynamically loaded library minor: Can't get value #1 <#1>: H5PLpath.c line 802 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error major: Plugin for dynamically loaded library minor: Can't get value #2 <#2>: H5PLpath.c line 855 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin major: Plugin for dynamically loaded library minor: Can't open directory or file FAIL tst_ncgen4.sh (exit status: 1) FAIL: tst_netcdf4_4 *** Running extra netcdf-4 tests. *** running tst_string_data to create test files... *** Testing strings. *** creating strings test file tst_string_data.nc...ok. *** Tests successful! *** dumping tst_string_data.nc to tst_string_data.cdl... *** comparing tst_string_data.cdl with ref_tst_string_data.cdl... *** testing reference file ref_tst_compounds2.nc... *** testing reference file ref_tst_compounds3.nc... *** testing reference file ref_tst_compounds4.nc... Filter id=1; filter not available ncgen: NetCDF: Filter error: undefined filter encountered (genbin.c:genbin_definespecialattributes:259) HDF5-DIAG: Error detected in HDF5 (1.12.2) thread 0: #000: H5PLint.c line 261 in H5PL_load(): search in path table failed major: Plugin for dynamically loaded library minor: Can't get value #1 <#1>: H5PLpath.c line 802 in H5PL__find_plugin_in_path_table(): search in path /usr/local/hdf5/lib/plugin encountered an error major: Plugin for dynamically loaded library minor: Can't get value #2 <#2>: H5PLpath.c line 855 in H5PL__find_plugin_in_path(): can't open directory: /usr/local/hdf5/lib/plugin major: Plugin for dynamically loaded library minor: Can't open directory or file FAIL tst_netcdf4_4.sh (exit status: 1) FAIL: tst_nccopy4 *** Testing groups. *** creating nested group file tst_group_data.nc...ok. *** Tests successful! *** Testing enums. *** creating enum test file tst_enum_data.nc...ok. *** Tests successful! *** Testing compound types. *** creating compound test file tst_comp.nc...ok. *** Tests successful! *** Testing compound types some more. *** creating another compound test file tst_comp2.nc...ok. *** Tests successful! *** Testing netCDF-4 features of nccopy on ncdump/*.nc files *** Test nccopy tst_comp.nc copy_of_tst_comp.nc ... *** compare with copy_of_tst_comp.cdl *** Test nccopy tst_comp2.nc copy_of_tst_comp2.nc ... *** compare with copy_of_tst_comp2.cdl *** Test nccopy tst_enum_data.nc copy_of_tst_enum_data.nc ... *** compare with copy_of_tst_enum_data.cdl *** Test nccopy tst_fillbug.nc copy_of_tst_fillbug.nc ... *** compare with copy_of_tst_fillbug.cdl *** Test nccopy tst_group_data.nc copy_of_tst_group_data.nc ... *** compare with copy_of_tst_group_data.cdl *** Test nccopy tst_nans.nc copy_of_tst_nans.nc ... *** compare with copy_of_tst_nans.cdl *** Test nccopy tst_opaque_data.nc copy_of_tst_opaque_data.nc ... *** compare with copy_of_tst_opaque_data.cdl *** Test nccopy tst_solar_1.nc copy_of_tst_solar_1.nc ... *** compare with copy_of_tst_solar_1.cdl *** Test nccopy tst_solar_2.nc copy_of_tst_solar_2.nc ... *** compare with copy_of_tst_solar_2.cdl *** Test nccopy tst_solar_cmp.nc copy_of_tst_solar_cmp.nc ... *** compare with copy_of_tst_solar_cmp.cdl *** Test nccopy tst_special_atts.nc copy_of_tst_special_atts.nc ... *** compare with copy_of_tst_special_atts.cdl *** Test nccopy tst_string_data.nc copy_of_tst_string_data.nc ... *** compare with copy_of_tst_string_data.cdl *** Creating compressible test files tst_inflated.nc, tst_inflated4.nc...ok. *** Tests successful! *** Test nccopy -d1 can compress a classic format file ... NetCDF: Filter error: undefined filter encountered Location: file nccopy.c; fcn copy_var_specials line 1152 FAIL tst_nccopy4.sh (exit status: 1) FAIL: tst_nccopy5 *** Creating chunkable test file tmp_nc5_base.nc... ok. *** Tests successful! *** Test nccopy -c with per-variable chunking; classic->enhanced *** Test nccopy -c with per-variable chunking; enhanced->enhanced *** Creating chunkable test file tst_nc5.nc... option: deflate Sorry! Unexpected result(0), tst_chunking.c, line: 103 1 failures 1 errors detected! Sorry! FAIL tst_nccopy5.sh (exit status: 2) I'm guessing that it has to do with that last error? Any ideas ? — Reply to this email directly, view it on GitHub <#2636 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAG47W2MCMQNQFC7RFRKOQTWY7JLDANCNFSM6AAAAAAVFGLL2E>. You are receiving this because you commented.Message ID: ***@***.***>

[tayloj25]

CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib ./configure --prefix=/usr/local --disable-dap --enable-byterange

I believe that is it... Is that what you were requesting? Is there some way to check it? I also may have added --disable-byterange at the end because I was getting a configure error: curl required for byte range support.

I installed curl and I believe that fixed the error.