reducegrid produces empty file
Added by Brendan DeTracey almost 4 years ago
cdo 1.9.10, Ubuntu 18.04
$ cdo --pedantic -v -O -reducegrid,mask_Omon_MRI-ESM2-0_t-grid.nc deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn.nc deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn_reduced.nc
OpenMP: num_procs=24 max_threads=1
cdo reducegrid: Processed 1 variable over 1 timestep [0.11s 77MB].
$ ncdump deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn_reduced.nc
netcdf deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn_reduced {
// global attributes:
:CDI = "Climate Data Interface version 1.9.9 (https://mpimet.mpg.de/cdi)" ;
:Conventions = "CF-1.6" ;
}Any ideas? CF checker:
CHECKING NetCDF FILE: /tmp/27024.nc ===================== Using CF Checker Version 3.1.1 Checking against CF Version CF-1.7 Using Standard Name Table Version 77 (2021-01-19T13:38:50Z) Using Area Type Table Version 10 (23 June 2020) Using Standardized Region Name Table Version 4 (18 December 2018) WARN: (7.1): Boundary var vertices_latitude should not have attribute units WARN: (7.1): Boundary var vertices_longitude should not have attribute units ------------------ Checking variable: y ------------------ ERROR: (3.1): Units are not consistent with those given in the standard_name table. ------------------ Checking variable: y_bnds ------------------ ------------------ Checking variable: x ------------------ ERROR: (3.1): Units are not consistent with those given in the standard_name table. ------------------ Checking variable: x_bnds ------------------ ------------------ Checking variable: latitude ------------------ WARN: attribute missing_value attached to wrong kind of variable ------------------ Checking variable: longitude ------------------ WARN: attribute missing_value attached to wrong kind of variable ------------------ Checking variable: vertices_latitude ------------------ WARN: (7.1): Boundary Variable vertices_latitude should not have _FillValue attribute WARN: (7.1): Boundary Variable vertices_latitude should not have missing_value attribute ------------------ Checking variable: vertices_longitude ------------------ WARN: (7.1): Boundary Variable vertices_longitude should not have _FillValue attribute WARN: (7.1): Boundary Variable vertices_longitude should not have missing_value attribute ------------------ Checking variable: deptho ------------------ INFO: attribute history is being used in a non-standard way ERRORS detected: 2 WARNINGS given: 8 INFORMATION messages: 1
Replies (3)
RE: reducegrid produces empty file - Added by Ralf Mueller almost 4 years ago
Hi Brendan!
Interesting - input files have different grids:
netcdf deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn {
dimensions:
y = 362 ;
x = 360 ;
bnds = 2 ;
vertices = 4 ;
netcdf mask_Omon_MRI-ESM2-0_t-grid {
dimensions:
x = 360 ;
y = 363 ;
vertices = 4 ;
bnds = 2 ;
130680 vs. 130320 grid points. I wonder why CDO does not exit with a normal error - thought I had implemented a proper check for this.
BTW I get a different error
cdo --pedantic -v -O -reducegrid,mask_Omon_MRI-ESM2-0_t-grid.nc deptho_Ofx_MRI-ESM2-0_historical_r1i1p1f1_gn.nc depth ─╯
OpenMP: num_procs=8 max_threads=1
cdo: cdoStream.cc:78: void CdoStream::defDatarangeList(int): Assertion `nvars > 0' failed.
zsh: abort (core dumped) cdo --pedantic -v -O -reducegrid,mask_Omon_MRI-ESM2-0_t-grid.nc depth
❯ cdo -V
Climate Data Operators version 1.9.10 (https://mpimet.mpg.de/cdo)
System: x86_64-pc-linux-gnu
CXX Compiler: g++ -g -O3 -std=c++11 -Wall -fopenmp -march=native -ftree-vectorize -mavx2 -pthread
CXX version : g++ (GCC) 10.2.0
C Compiler: gcc -g -O3 -std=gnu99 -Wall -fopenmp -march=native -ftree-vectorize -mavx2 -pthread -pthread
C version : gcc (GCC) 10.2.0
F77 Compiler: gfortran -g -O2
F77 version : GNU Fortran (GCC) 10.2.0
Features: 15GB 8threads C++11 OpenMP45 Fortran PTHREADS HDF5 NC4/HDF5 OPeNDAP SZ UDUNITS2 PROJ XML2 MAGICS CURL FFTW3 AVX2
Libraries: HDF5/1.12.0 proj/6.3.2 xml2/2.9.10 curl/7.75.0(h7.74.0)
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.10
cgribex library version : 1.9.5
ecCodes library version : 2.14.1
NetCDF library version : 4.7.4 of Apr 10 2020 23:29:06 $
hdf5 library version : 1.12.0
exse library version : 1.4.2
FILE library version : 1.9.1
RE: reducegrid produces empty file - Added by Brendan DeTracey almost 4 years ago
Thanks ralf. I did not think to check that. Looks like I'll be adding MRI-ESM2 to my garbage list for cmip6 data I am processing. Compliance is a difficult target. :(
I have written almost 100 emails this past year due to issues like this, and I am just a data user. Do I have it in me to write MRI again??? Gah! Anaconda install on Ubuntu 18.04:
$ cdo -V
Climate Data Operators version 1.9.9 (https://mpimet.mpg.de/cdo)
System: x86_64-conda-linux-gnu
CXX Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-c++ -fPIC -DPIC -g -O2 -std=c++11 -fopenmp -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/brendan/miniconda3/envs/cmip6/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/brendan/miniconda3/envs/cmip6=/usr/local/src/conda-prefix -fopenmp -pthread
CXX version : unknown
C Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-cc -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/brendan/miniconda3/envs/cmip6/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/brendan/miniconda3/envs/cmip6=/usr/local/src/conda-prefix -fopenmp -pthread -pthread
C version : unknown
F77 Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-gfortran -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/brendan/miniconda3/envs/cmip6/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/brendan/miniconda3/envs/cmip6=/usr/local/src/conda-prefix
F77 version : GNU Fortran (crosstool-NG 1.24.0.133_b0863d8_dirty) 9.3.0
Features: 62GB 24threads C++11 OpenMP45 Fortran PTHREADS HDF5 NC4/HDF5/threadsafe OPeNDAP UDUNITS2 PROJ XML2 CURL FFTW3 SSE3
Libraries: HDF5/1.10.6 proj/7.2.0 xml2/2.9.10 curl/7.71.1
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.9
cgribex library version : 1.9.5
ecCodes library version : 2.19.1
NetCDF library version : 4.7.4 of Oct 21 2020 19:55:48 $
hdf5 library version : 1.10.6 threadsafe
exse library version : 1.4.1
FILE library version : 1.9.1I am a version behind until cdo gets updated on conda-forge.Edit: All my fault because MRI ocean model is on Arakawa B-grid, so deptho on cell velocity points not cell mass/tracer points.
RE: reducegrid produces empty file - Added by Ralf Mueller almost 4 years ago
ah, you are right, I need to update conda-forge - thx for the hint.
man, I feel you - cmip6 compliance can be a pain