filter plugin path with nccopy

[allibco]

have a question about getting netcdf to find my filter plugin.
I am trying to use a self-installed hdf5 plugin with hdf5 and netcdf
installed on the NCAR system (casper).

For example, for zfp, I installed H5Z-ZFP-1.1.1( with the HDF5_ROOT set to a system-installed
hdf5 (1.12.2). I then sent HDF5_PLUGIN_PATH to the location of the
zfp plugin that I installed myself.

echo $HDF5_PLUGIN_PATH
/glade/work/abaker/compress-libs/zfp_plugin/plugin

But when I use the nccopy command with the zfp filter it can't find
it:

nccopy -F TS,32013,3,0,1202590843,1065646817 TS.nc TS_zfp_a1e-2.nc
NetCDF: Filter error: undefined filter encountered
Location: file nccopy.c; fcn copy_var_specials line 1175

And when I check nc-config for the plugin dir:

nc-config --plugindir
/glade/u/apps/casper/23.10/spack/opt/spack/netcdf/4.9.2/packages/netcdf-c/4.9.2/gcc/12.2.0/obej/plugins

But I can't copy my plugin to the system directory, so how can I
specify nccopy to use the $HDF5_PLUGIN_PATH?

Thanks!

[WardF]

I'm guessing that you are using netCDF 4.9.2. I'm reviewing a PR, #3034 and I wonder if you might be able to either test using the his branch, or possibly even with netCDF-C 4.9.3-rc1. @DennisHeimbigner, does any other solution for v4.9.2 leap out at you?

[DennisHeimbigner]

Lets start with some information. Can you do this command and send be the output as text?

ncdump -h TS.nc

Second, you should have files called something like H5Zzfp.c and (maybe) H5Zzfp.h.
Can you send me those files? You can mail them directly to me at dennis.heimbiger@gmail.com

[allibco]

netcdf TS {
dimensions:
time = UNLIMITED ; // (60 currently)
lat = 192 ;
lon = 288 ;
chars = 8 ;
ilev = 31 ;
lev = 30 ;
slat = 191 ;
slon = 288 ;
nbnd = 2 ;
variables:
double P0 ;
P0:long_name = "reference pressure" ;
P0:units = "Pa" ;
float TS(time, lat, lon) ;
TS:units = "K" ;
TS:long_name = "Surface temperature (radiative)" ;
TS:cell_methods = "time: mean" ;
double ch4vmr(time) ;
ch4vmr:long_name = "ch4 volume mixing ratio" ;
double co2vmr(time) ;
co2vmr:long_name = "co2 volume mixing ratio" ;
int date(time) ;
date:long_name = "current date (YYYYMMDD)" ;
char date_written(time, chars) ;
int datesec(time) ;
datesec:long_name = "current seconds of current date" ;
double f11vmr(time) ;
f11vmr:long_name = "f11 volume mixing ratio" ;
double f12vmr(time) ;
f12vmr:long_name = "f12 volume mixing ratio" ;
double gw(lat) ;
gw:long_name = "gauss weights" ;
double hyai(ilev) ;
hyai:long_name = "hybrid A coefficient at layer interfaces" ;
double hyam(lev) ;
hyam:long_name = "hybrid A coefficient at layer midpoints" ;
double hybi(ilev) ;
hybi:long_name = "hybrid B coefficient at layer interfaces" ;
double hybm(lev) ;
hybm:long_name = "hybrid B coefficient at layer midpoints" ;
double ilev(ilev) ;
ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
ilev:units = "level" ;
ilev:positive = "down" ;
ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
double lat(lat) ;
lat:long_name = "latitude" ;
lat:units = "degrees_north" ;
double lev(lev) ;
lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
lev:units = "level" ;
lev:positive = "down" ;
lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
double lon(lon) ;
lon:long_name = "longitude" ;
lon:units = "degrees_east" ;
int mdt ;
mdt:long_name = "timestep" ;
mdt:units = "s" ;
double n2ovmr(time) ;
n2ovmr:long_name = "n2o volume mixing ratio" ;
int nbdate ;
nbdate:long_name = "base date (YYYYMMDD)" ;
int nbsec ;
nbsec:long_name = "seconds of base date" ;
int ndbase ;
ndbase:long_name = "base day" ;
int ndcur(time) ;
ndcur:long_name = "current day (from base day)" ;
int nlon(lat) ;
nlon:long_name = "number of longitudes" ;
int nsbase ;
nsbase:long_name = "seconds of base day" ;
int nscur(time) ;
nscur:long_name = "current seconds of current day" ;
int nsteph(time) ;
nsteph:long_name = "current timestep" ;
int ntrk ;
ntrk:long_name = "spectral truncation parameter K" ;
int ntrm ;
ntrm:long_name = "spectral truncation parameter M" ;
int ntrn ;
ntrn:long_name = "spectral truncation parameter N" ;
double slat(slat) ;
slat:long_name = "staggered latitude" ;
slat:units = "degrees_north" ;
double slon(slon) ;
slon:long_name = "staggered longitude" ;
slon:units = "degrees_east" ;
double sol_tsi(time) ;
sol_tsi:long_name = "total solar irradiance" ;
sol_tsi:units = "W/m2" ;
double time(time) ;
time:long_name = "time" ;
time:units = "days since 2006-01-01 00:00:00" ;
time:calendar = "noleap" ;
time:bounds = "time_bnds" ;
double time_bnds(time, nbnd) ;
time_bnds:long_name = "time interval endpoints" ;
char time_written(time, chars) ;
double w_stag(slat) ;
w_stag:long_name = "staggered latitude weights" ;
int wnummax(lat) ;
wnummax:long_name = "cutoff Fourier wavenumber" ;

// global attributes:
:Conventions = "CF-1.0" ;
:source = "CAM" ;
:case = "b.e11.BRCP85C5CNBDRD.f09_g16.031" ;
:title = "UNSET" ;
:logname = "mickelso" ;
:host = "ys1023" ;
:Version = "$Name$" ;
:revision_Id = "$Id$" ;
:initial_file = "b.e11.B20TRC5CNBDRD.f09_g16.031.cam.i.2006-01-01-00000.nc" ;
:topography_file = "/glade/p/cesmdata/cseg/inputdata/atm/cam/topo/USGS-gtopo30_0.9x1.25_remap_c051027.
nc" ;
:history = "Mon May 10 15:27:00 2021: ncks -d time,0,59,1 b.e11.BRCP85C5CNBDRD.f09_g16.031.cam.h0.TS.2
00601-208012.nc b.e11.BRCP85C5CNBDRD.f09_g16.031.cam.h0.TS.200601-2007012.nc" ;
:NCO = "netCDF Operators version 4.9.5 (Homepage = http://nco.sf.net, Code = http://github.com/nco/nco
)" ;
}

[allibco]

I'll email the other files. Thanks for your help.

[DennisHeimbigner]

Look into your HDF5_PLUGIN_PATH directory (i.e. /glade/work/abaker/compress-libs/zfp_plugin/plugin).
Look for all files matching the pattern 'zfp.so'
Please tell me what it shows.

[allibco]

abaker@casper-login2:~> cd $HDF5_PLUGIN_PATH
abaker@casper-login2:/glade/work/abaker/compress-libs/zfp_plugin/plugin> ls
libh5z-sperr.so* libh5zzfp.so*

[DennisHeimbigner]

Ok, it appears you are using the wrong value for HDF5_PLUGIN_PATH.
I suspect that you need to use "/glade/work/abaker/compress-libs/zfp_plugin/plugin/.libs".
You can verify by trying this command:

find /glade/work/abaker/compress-libs/zfp_plugin/plugin -name '*zfp*'

[allibco]

abaker@casper-login2:/glade/work/abaker/compress-libs/zfp_plugin/plugin> ls -a
./ ../ libh5z-sperr.so* libh5zzfp.so*
abaker@casper-login2:/glade/work/abaker/compress-libs/zfp_plugin/plugin> find /glade/work/abaker/compress-libs/zfp_plugin/plugin -name 'zfp'
/glade/work/abaker/compress-libs/zfp_plugin/plugin/libh5zzfp.so

[DennisHeimbigner]

The naming is wrong: there should be a file named 'lib__nch5zfp.so' in the
'/glade/work/abaker/compress-libs/zfp_plugin/plugin/' directory

Can you tell where the 'libh5zzfp.so' is coming from?
Can you show the fragment of code in some Makefile.am or CMakeLists.txt?

[allibco]

Thanks for you help. I just followed the cmake instructions on https://h5z-zfp.readthedocs.io/en/latest/installation.html, which indicates that it will install the following:

$(PREFIX)/include/{H5Zzfp.h,H5Zzfp_plugin.h,H5Zzfp_props.h,H5Zzfp_lib.h}
$(PREFIX)/plugin/libh5zzfp.{so,dylib}
$(PREFIX)/lib/libh5zzfp.a

which is what I have. The documentation also says:

"To use the installed filter as an HDF5 plugin, you would specify, for example, setenv HDF5_PLUGIN_PATH $(PREFIX)/plugin"

Here is what I did:
abaker@casper-login2:/glade/work/abaker/H5Z-ZFP-1.1.1> mkdir build
export ZFP_DIR=/glade/work/abaker/zfp-1.0.1/build
export HDF5_DIR=/glade/u/apps/casper/23.10/spack/opt/spack/hdf5/1.12.2/gcc/12.2.0/hsod

(These below are already set:
CC=gcc
FC=gfortran
)

cd build
cmake -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX=/glade/work/abaker/compress-libs/zfp_plugin ..
make
make install

The only modification I made was to add the link for the math libraries in CMakeLIsts.txt:
target_link_libraries(test_write_plugin m h5z_zfp_shared)
(https://github.com/LLNL/H5Z-ZFP/blob/master/CMakeLists.txt)

Do you want my CMakeCache.txt in my build directory? (If you have access to glade, my files are readable).

[DennisHeimbigner]

Can you send me the file "H5Zzfp_props_private.h"`; I am trying to build.

[allibco]

I sent H5Zzfp_props.h and H5Zzfp_props_private.h