icesst tool

[Asiya]

We are running an AMIP type simulation using mid-Holocene SST and sea ice lower boundary conditions in CAM6 (/glade/work/marcusl/CESM_model_versions/cesm2.2.0.geotrace). We want to create an SST/sea ice file for this time period using the following datasets:

SST data: /glade/collections/cdg/data/CMIP6/PMIP/NCAR/CESM2/midHolocene/r1i1p1f1/Amon/ts/gn/latest/ts_Amon_CESM2_midHolocene_r1i1p1f1_gn_050101-055012.nc

Sea ice data: /glade/u/home/marcusl/timeseries-cmip6/b.e21.B1850.f09_g17.PMIP4-midHolo.001/atm/proc/tseries/month_1/b.e21.B1850.f09_g17.PMIP4-midHolo.001.cam.h0.ICEFRAC.050101-055012.nc

I understand that I need to use the seaice tool in CAM to create the SST file for the mid-Holocene. However, I am encountering errors with the Makefiles in the bcgen and regrid components of the icesst tool (/glade/u/home/asiyab/cesm2.2.0.geotrace/components/cam/tools/icesst).

I read here (AMIP HadISST boundary conditions issue) that I may need to edit the Makefiles and preprocess my input datasets to use the icesst tool effectively. However, I am unsure about what specific edits to make in the Makefiles. I would greatly appreciate any guidance or directions on how to proceed. Thank you!

Error:

error--
(base) asiyab@derecho1:~/cesm2.2.0.geotrace/components/cam/tools/icesst/bcgen> make -f Makefile
ifort -c -I/usr/local/include -O prec.f90
ifort -c -I/usr/local/include -O solver.f90
ifort -c -I/usr/local/include -O calcclim.f90
ifort -c -I/usr/local/include -O calcfull.f90
ifort -c -I/usr/local/include -O driver.f90
ifort -c -I/usr/local/include -O types.f90
ifort -c -I/usr/local/include -O bcgen.f90
ifort -c -I/usr/local/include -O output_dateinfo.f90
ifort -c -I/usr/local/include -O setup_outfile.f90
ifort -c -I/usr/local/include -O wrap_nf.f90
ifort -o bcgen calcclim.o calcfull.o driver.o bcgen.o output_dateinfo.o prec.o setup_outfile.o solver.o wrap_nf.o types.o -L/usr/local/lib -lnetcdf
ld: driver.o: in function `MAIN__':
driver.f90:(.text+0x1d76): undefined reference to `nf_get_att_text_'
ld: setup_outfile.o: in function `setup_outfile_':
setup_outfile.f90:(.text+0x92f): undefined reference to `nf_enddef_'
ld: wrap_nf.o: in function `wrap_nf_create_':
wrap_nf.f90:(.text+0x14): undefined reference to `nf_create_'
ld: wrap_nf.f90:(.text+0xad): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_open_':
wrap_nf.f90:(.text+0x124): undefined reference to `nf_open_'
ld: wrap_nf.f90:(.text+0x1bd): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_put_att_text_':
wrap_nf.f90:(.text+0x276): undefined reference to `nf_put_att_text_'
ld: wrap_nf.f90:(.text+0x374): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_def_dim_':
wrap_nf.f90:(.text+0x3fc): undefined reference to `nf_def_dim_'
ld: wrap_nf.f90:(.text+0x4c5): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_inq_dimid_':
wrap_nf.f90:(.text+0x537): undefined reference to `nf_inq_dimid_'
ld: wrap_nf.f90:(.text+0x5e5): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_inq_dimlen_':
wrap_nf.f90:(.text+0x653): undefined reference to `nf_inq_dimlen_'
ld: wrap_nf.f90:(.text+0x702): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_inq_varid_':
wrap_nf.f90:(.text+0x777): undefined reference to `nf_inq_varid_'
ld: wrap_nf.f90:(.text+0x825): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_def_var_':
wrap_nf.f90:(.text+0x8b0): undefined reference to `nf_def_var_'
ld: wrap_nf.f90:(.text+0x994): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_get_vara_int_':
wrap_nf.f90:(.text+0x9fe): undefined reference to `nf_get_vara_int_'
ld: wrap_nf.f90:(.text+0xa8e): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_get_var_int_':
wrap_nf.f90:(.text+0xaee): undefined reference to `nf_get_var_int_'
ld: wrap_nf.f90:(.text+0xb7e): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_get_vara_double_':
wrap_nf.f90:(.text+0xbde): undefined reference to `nf_get_vara_double_'
ld: wrap_nf.f90:(.text+0xc6e): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_get_var_double_':
wrap_nf.f90:(.text+0xcce): undefined reference to `nf_get_var_double_'
ld: wrap_nf.f90:(.text+0xd5e): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_close_':
wrap_nf.f90:(.text+0xdbf): undefined reference to `nf_close_'
ld: wrap_nf.f90:(.text+0xe50): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_put_var_int_':
wrap_nf.f90:(.text+0xeba): undefined reference to `nf_put_var_int_'
ld: wrap_nf.f90:(.text+0xee5): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_put_vara_int_':
wrap_nf.f90:(.text+0xf4a): undefined reference to `nf_put_vara_int_'
ld: wrap_nf.f90:(.text+0xf75): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_put_var_double_':
wrap_nf.f90:(.text+0xfda): undefined reference to `nf_put_var_double_'
ld: wrap_nf.f90:(.text+0x1005): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `wrap_nf_put_vara_double_':
wrap_nf.f90:(.text+0x106a): undefined reference to `nf_put_vara_double_'
ld: wrap_nf.f90:(.text+0x1095): undefined reference to `nf_strerror_'
ld: wrap_nf.o: in function `handle_error_':
wrap_nf.f90:(.text+0x1106): undefined reference to `nf_strerror_'
make: *** [Makefile:77: bcgen] Error 1
(base) asiyab@derecho1:~/cesm2.2.0.geotrace/components/cam/tools/icesst/bcgen>

 

[Asiya]

Hi Again,

Update:
By adding -lnetcdff to the Makefiles, I was also able to get the build to work!

Following the instructions in the README file for the icesst tool (~/cesm2.2.0.geotrace/components/cam/tools/icesst), I tried to regrid my input files using the following command:

./regrid -i /glade/work/asiyab/grids_maps/MAPS/sstice.ice.nc -s /glade/work/asiyab/grids_maps/MAPS/sstice.ts.nc -g /glade/p/cesmdata/inputdata/atm/cam/sst/sst_HadOIBl_bc_1x1_1850_2017_c180507.nc -o ~/VR_codes/sstice0.nc

However, I am receiving the following error:

NetCDF: Variable not found

abort:

Does anyone here know what this error might be about? The SEAICE and SST variables are present in these files.

 

[hannay]

regrid was written to work with specific files and the script expect some variables with some names:

The expected format is:
/glade/campaign/cgd/cas/asphilli/cam_input_data/MODEL.ICE.HAD187001-198110.OI198111-202206.nc
/glade/campaign/cgd/cas/asphilli/cam_input_data/MODEL.SST.HAD187001-198110.OI198111-202206.nc

I just tried:

cd /glade/work/hannay/cesm_tags/cesm3_0_beta02/components/cam/tools/icesst/regrid
./regrid -i /glade/campaign/cgd/cas/asphilli/cam_input_data/MODEL.ICE.HAD187001-198110.OI198111-202206.nc \
-s /glade/campaign/cgd/cas/asphilli/cam_input_data/MODEL.SST.HAD187001-198110.OI198111-202206.nc \
-g /glade/u/home/hannay/sst/sstice_fv_0.9x1.25.nc \
-o /glade/derecho/scratch/hannay/sst/sstice_0.9x1.25.nc

and it worked.

Then I tried, and I get teh same error as you:

cd /glade/work/hannay/cesm_tags/cesm3_0_beta02/components/cam/tools/icesst/regrid
./regrid -i /glade/work/asiyab/grids_maps/MAPS/sstice.ice.nc -s /glade/work/asiyab/grids_maps/MAPS/sstice.ts.nc \
-g /glade/u/home/hannay/sst/sstice_fv_0.9x1.25.nc \
-o /glade/derecho/scratch/hannay/sst/sstice_0.9x1.25.nc

I briefly looked at your fiels and they don't have the variables date, datesec. I believe it might be teh issue.

 

[Asiya]

Thank you, Cecile! I found a thread (ncl scripts to create SST/ICE data files to drive an F compset using B compset history files) where you shared an NCL script to create the regridded data with datesec and date in an appropriate format for processing with the bcgen tool. I edited script file to use my input files, and it worked (so far, looking good). So thank you again for putting those files there!