Let netCDF Operators NCO version 5.0.2 join your stack...
http://nco.sf.net (Homepage, Mailing lists, Help)
http://github.com/nco (Source Code, Issues, Releases, Developers)
What's new?
Version 5.0.2 contains significant new features and few minor fixes.
ncclimo now splits timeseries into variables specified by regular
expressions. ncremap now supports the MOAB parallel interface to the
TempestRemap (TR) weight-generation libraries for 1D FV->FV grids.
The regridder and all quantization algorithms (including BitGroom)
have been refactored to treat NC_FILL_FLOAT/DOUBLE as the _FillValue
if no other _FillValue has been explicitly set.
Work on NCO 5.0.3 has commenced and will improve ncremap support
for MOAB, incorporate new MOAB improvements, and improve quantization
metadata and algorithms.
Enjoy,
Charlie
NEW FEATURES (full details always in ChangeLog):
A. ncclimo now expands variable lists that contain regular
expressions (RX). Previously the splitter would aggregate
all variables specified by an RX into a single timeseries file.
Now the splitter places every variable into its own file.
Thus using an RX produces the same timeseries files as explicitly
specifying every variable. There is no change in the behavior
of climo mode; it continues to put all variables in one file.
ncclimo --var_lst=_2DMS.? in*.nc
ncclimo --var_lst=_2DMS.? --var_xtr=area in*.nc
Both commands use an RX in a variable list. The second command
explicitly adds the 'area' variable to all output timeseries.
The improved functionality should be especially useful to analyze
datasets with large numbers of tracers/species.
Thanks to Qi Tang of PNNL for suggesting this feature.
B. ncremap now supports the MOAB parallel interface to the
TempestRemap (TR) weight-generation libraries for 1D FV->FV grids.
ncremap will invoke mbtempest in parallel mode whenever the user
requests a TR algorithm (e.g., --alg_typ=fv2fv_flx) and,
additionally, specifies the number of MPI tasks-per-node with
--mpi_nb=<mpi_nbr>:
ncremap --alg_typ=fv2fv_flx ... --map=map.nc # TR
ncremap --mpi_nbr=24 --alg_typ=fv2fv_flx ... --map=map.nc # MOAB
BTW, the same convention applies to MPI-enabled ERWG:
ncremap --alg_typ=aave ... --map=map.nc # ESMF
ncremap --mpi_nbr=24 --alg_typ=aave ... --map=map.nc # Parallel ESMF
ncremap automatically uses mbconvert to convert SCRIP and Exodus
gridfiles (based on their file suffix) to MOAB .h5m format.
It then uses mbpart to partition the MOAB grids, and then
calls mbtempest. Two ncremap options specific to mbtempest are
available to configure this workflow. The intersection algorithm
can be set with --nsx_alg=advfront|kdtree (default is kdtree).
Set the partition number for mbpart with --prt_nbr=<prt_nbr>.
The partition number must be a multiple of mpi_nbr and by default
prt_nbr=mpi_nbr.
ncremap --mpi_nbr=24 --nsx_alg=advfront --alg_typ=fv2fv_flx ...
ncremap --mpi_nbr=24 --prt_nbr=48 --alg_typ=fv2fv_flx ...
ncremap --mpi_nbr=24 --prt_nbr=48 --alg_typ=fv2fv_flx ...
Limitations that MOAB anticipates removing in future releases:
Currently MOAB is only trustworthy for the fv2fv_flx algorithm.
High order and spectral element maps require more work in MOAB.
Currently mbtempest only generates map-files that regrid to rank 1
(unstructured) grids. mbtempest "unrolls" any rank 2 (e.g.,
latxlon) destination grid into its rank 1 equivalent.
Users seeking to regrid to rank 2 grids can manually alter the
MOAB-generated mapfile with something like:
ncks -O -x -v dst_grid_dims ~/map.nc ~/map_fix.nc
ncap2 -O -s
'defdim("dst_grid_dims",2);dst_grid_dims($dst_grid_dims)={256,129};'
~/map_tmp.nc ~/map_fix.nc
Replace 256,129 by the lon,lat (Fortran order!) of your grid.
The resulting map-file, map_fix.nc, will almost regrid as intended.
The regridded output will have curvilinear coordinates (e.g,
lat(lat,lon)) instead of rectangular coordinates (e.g., lat(lat)),
and the coordinate "bounds" variables (e.g., lat_bnds) will not be
correct and may cause plotting issues at poles and Greenwich.
Nevertheless, the weights are correct and of unsurpassed accuracy.
MOAB anticipates supporting rank 2 mapfiles and TR high-order and
spectral element algorithms in the future.
This initial NCO support gives the opportunity to adopt ncremap
to generate FV->FV mapfiles with 1D destination grids, an important
class of regridding problems for model coupling purposes.
We welcome suggestions for new/improved options/features.
Due to its complexity, only MOAB insalled via Conda is supported.
Thanks to Vijay Mahadevan of ANL for his help with MOAB.
http://nco.sf.net/nco.html#tr
http://nco.sf.net/nco.html#moab
C. Bit-Adjustment-Algorithms (BAAs) for lossy quantization
(e.g., BitGrooming) now only quantize the values NC_FILL_FLOAT or
NC_FILL_DOUBLE for float and double variables, respectively, when
the _FillValue attribute has been set to some other value.
Previously all BAAs always quantized NC_FILL_FLOAT or
NC_FILL_DOUBLE unless they were explicitly set as _FillValue.
Thanks to Ed Hartnett of NOAA for this suggestion.
D. Similarly, the ncremap regridder and vertical interpolation
routines now treat the values NC_FILL_FLOAT and NC_FILL_DOUBLE as
missing values for float and double variables, respectively,
unless their _FillValue has been explicitly set to some other
value. Now datasets that never explicitly set a _FillValue
will be regridded/interpolated properly.
E. Operators like ncks and ncrcat that utilize the UDUnits library
will now report more thorough diagnostics when that library cannot
be successfully opened, e.g., because the database file could not
be found. This has been helpful in diagnosing the issues that
underlie unexpected workflow failures that turn out to be due to
incorrectly configured UDUnits environments. Thanks to Tom Vo of
LLNL for helping uncover related issues.
F. ncremap now infers curvilinear grids from data files that include
coordinates named west_east and south_north.
Thanks to a StackOverflow user for suggesting this feature.
G. ncclimo now assumes the model name string in input files is 'eam'
not 'cam'. The old behavior can be recovered by explicitly
specifying ncclimo --mdl_nm=cam.
BUG FIXES:
A. ncclimo automatically turns-on splitter mode when clm_md=hfs
and files are provided by globbing the input directory.
Previously ncclimo would not enter splitter mode automatically
under these circumstances. The workaround is to force splitter
mode by specifying the --ypf=ypf option. The solution is to
upgrade.
B. A minor change to OpenMP behavior now allows Intel compilers
to build NCO from source (once again). This bug was introduced
in NCO ~4.9.9 and affects only Intel compilers. The solution is to
upgrade. Thanks to Matthew Thompson of GSFC for pointing this out.
C. ncclimo and ncremap now passes the option --mem=0 to srun
on Cori at NERSC. Previously it passed the option --mem=20000,
which could exhaust the available RAM at high-resolution.
Full release statement at http://nco.sf.net/ANNOUNCE
--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(
