$Header$ -*-text-*-

netCDF Operators NCO version 5.2.9 scratch an itch

http://nco.sf.net (Homepage, Mailing lists, Help)
http://github.com/nco/nco (Source Code, Issues, Releases)

What's new?
Version 5.2.9 significantly improves the unpacking of ELM/CLM/CTSM
history and restart datasets. ncclimo and ncremap benefit from a
few updates and fixes. This release many be skipped if these changes
do not interest you.

Work on 5.3.0 is underway and includes yet more capability in
unpacking ELM/CLM history/restart files.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. ncks leveled-up the way it unpacks ELM/CLM history/restart files. 
This is by far the biggest feature in this release.
New features include support for PFTs in history files, support
for topounits in ELM (PCT_LANDUNIT, PCT_NAT_PFT, TS_TOPO), a
workaround for invalid topounits coordinates, and outputting a pft 
coordinate variable with vegetation names.

ncks --s1d history_h2.nc out.nc # History files usually h2, h3...
ncks --s1d --hrz=history.nc restart.nc out.nc # Restart files

http://nco.sf.net/nco.html#s1d
http://nco.sf.net/nco.html#unpack_sparse

B. ncremap now automagically horizontall regids the latest EAMxx and
SCREAM files without needing manual invocation of long, hairy
options. In particular, users can invoke

ncremap -P eamxx --map=map.nc eamxx.nc out.nc

instead of this:

ncremap -P eamxx
--prm_opt=time,lwband,swband,ilev,lev,plev,cosp_tau,cosp_cth,cosp_prs,dim2,ncol
--map=map.nc eamxx.nc out.nc

http://nco.sf.net/nco.html#eamxx

BUG FIXES:
   
A. ncremap fixes a regression with the vertical interpolation of ECMWF
datasets in IFS format. The regression, introduced 1-2 years ago,
causes the interpolation to abort. To vertically interpolate a hybrid
coordinate dataset in IFS format, one must now specify that the
surface pressure variable is named lnsp: 

ncremap --ps_nm=lnsp --vrt_grd=vrt_grd.nc in.nc out.nc

Thanks to Erik Koene for reporting this issue. There is no
workaround. The solution is to upgrade, or to use an older NCO
version, e.g., 4.9.0.
http://nco.sf.net/nco.html#vrt_hyb_ifs

B. ncclimo fixes an illegal Bash string->numeric conversion error.
This error could occur when invoking non-default start and end
months. There is no workaround. The solution is to upgrade. 

Full release statement at http://nco.sf.net/ANNOUNCE
    
KNOWN PROBLEMS DUE TO NCO:

This section of ANNOUNCE reports and reminds users of the
existence and severity of known, not yet fixed, problems. 
These problems occur with NCO 5.2.7 built/tested under
MacOS 15.0 with netCDF 4.9.4-development on HDF5 1.14.3
and with Linux FC40 with netCDF 4.9.2 on HDF5 1.14.3.

A. NOT YET FIXED (NCO problem)
   Correctly read arrays of NC_STRING with embedded delimiters in ncatted arguments

   Demonstration:
   ncatted -D 5 -O -a new_string_att,att_var,c,sng,"list","of","str,ings" ~/nco/data/in_4.nc ~/foo.nc
   ncks -m -C -v att_var ~/foo.nc

   20130724: Verified problem still exists
   TODO nco1102
   Cause: NCO parsing of ncatted arguments is not sophisticated
   enough to handle arrays of NC_STRINGS with embedded delimiters.

B. NOT YET FIXED (NCO problem?)
   ncra/ncrcat (not ncks) hyperslabbing can fail on variables with multiple record dimensions

   Demonstration:
   ncrcat -O -d time,0 ~/nco/data/mrd.nc ~/foo.nc

   20140826: Verified problem still exists
   20140619: Problem reported by rmla
   Cause: Unsure. Maybe ncra.c loop structure not amenable to MRD?
   Workaround: Convert to fixed dimensions then hyperslab

KNOWN PROBLEMS DUE TO BASE LIBRARIES/PROTOCOLS:

A. NOT YET FIXED (netCDF4 or HDF5 problem?)
   Specifying strided hyperslab on large netCDF4 datasets leads
   to slowdown or failure with recent netCDF versions.

   Demonstration with NCO <= 4.4.5:
   time ncks -O -d time,0,,12 ~/ET_2000-01_2001-12.nc ~/foo.nc
   Demonstration with NCL:
   time ncl < ~/nco/data/ncl.ncl   
   20140718: Problem reported by Parker Norton
   20140826: Verified problem still exists
   20140930: Finish NCO workaround for problem
   20190201: Possibly this problem was fixed in netCDF 4.6.2 by https://github.com/Unidata/netcdf-c/pull/1001
   Cause: Slow algorithm in nc_var_gets()?
   Workaround #1: Use NCO 4.4.6 or later (avoids nc_var_gets())
   Workaround #2: Convert file to netCDF3 first, then use stride
   Workaround #3: Compile NCO with netCDF >= 4.6.2

B. NOT YET FIXED (netCDF4 library bug)
   Simultaneously renaming multiple dimensions in netCDF4 file can corrupt output

   Demonstration:
   ncrename -O -d lev,z -d lat,y -d lon,x ~/nco/data/in_grp.nc ~/foo.nc # Completes but produces unreadable file foo.nc
   ncks -v one ~/foo.nc

   20150922: Confirmed problem reported by Isabelle Dast, reported to Unidata
   20150924: Unidata confirmed problem
   20160212: Verified problem still exists in netCDF library
   20160512: Ditto
   20161028: Verified problem still exists with netCDF 4.4.1
   20170323: Verified problem still exists with netCDF 4.4.2-development
   20170323: https://github.com/Unidata/netcdf-c/issues/381
   20171102: Verified problem still exists with netCDF 4.5.1-development
   20171107: https://github.com/Unidata/netcdf-c/issues/597
   20190202: Progress has recently been made in netCDF 4.6.3-development
   More details: http://nco.sf.net/nco.html#ncrename_crd

C. NOT YET FIXED (would require DAP protocol change?)
   Unable to retrieve contents of variables including period '.' in name
   Periods are legal characters in netCDF variable names.
   Metadata are returned successfully, data are not.
   DAP non-transparency: Works locally, fails through DAP server.

   Demonstration:
   ncks -O -C -D 3 -v var_nm.dot -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc # Fails to find variable

   20130724: Verified problem still exists. 
   Stopped testing because inclusion of var_nm.dot broke all test scripts.
   NB: Hard to fix since DAP interprets '.' as structure delimiter in HTTP query string.

   Bug tracking: https://www.unidata.ucar.edu/jira/browse/NCF-47

D. NOT YET FIXED (would require DAP protocol change)
   Correctly read scalar characters over DAP.
   DAP non-transparency: Works locally, fails through DAP server.
   Problem, IMHO, is with DAP definition/protocol

   Demonstration:
   ncks -O -D 1 -H -C -m --md5_dgs -v md5_a -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc

   20120801: Verified problem still exists
   Bug report not filed
   Cause: DAP translates scalar characters into 64-element (this
   dimension is user-configurable, but still...), NUL-terminated
   strings so MD5 agreement fails 

"Sticky" reminders:

A. Reminder that NCO works on most HDF4 and HDF5 datasets, e.g., 
   HDF4: AMSR MERRA MODIS ...
   HDF5: GLAS ICESat Mabel SBUV ...
   HDF-EOS5: AURA HIRDLS OMI ...

B. Pre-built executables for many OS's at:
   http://nco.sf.net#bnr