'Abort with message NetCDF: Variable not found' in single point simulations with own atmospheric Eddy Covariance data

[UlisesMarconato]

Hi everyone,
I am trying to run some single point simulations with my own atmospheric forcing half-hourly data from an eddy covariance site. I used the flow.api.clm.R code to create the monthly netcdf datm stream files (YYYYY-MM.nc, from 2018-01.nc to 2021-04.nc, 40 files in total) containing all variables except FLDS, in one file. As I don't have FLDS, I did what it's said in this thread. I created, setup and built the case, but when submitted, it asked for a fsurdat file. I used the fsurdat file I got for previous runs using the subset_data script and it has stopped asking for it, so it seems to have accepted it. I used that fsurdat file in previous runs with the subseted atmospheric data with no problems.
I set:
./xmlchange PTS_LAT=-35.621
./xmlchange PTS_LON=298.6819
./xmlchange DATM_MODE=1PT
./xmlchange DIN_LOC_ROOT_CLMFORC=/glade/u/home/umarconato/Cases/forcingdata20182021
./xmlchange DATM_YR_ALIGN=2018,DATM_YR_START=2018,DATM_YR_END=2021,STOP_OPTION=nyears,STOP_N=4,RUN_STARTDATE='2018-01-01'
./xmlchange MPILIB=mpi-serial

in the user_nl_clm file:
fsurdat = '$/glade/u/home/umarconato/Cases/subset_data_regional20102014_crop/surfdata_ARG_CC_Ag_hist_78pfts_CMIP6_simyr2000_c231213.nc'
hist_fincl2 = 'NEE','NBP','NEP'
hist_mfilt = 1,48
hist_nhtfrq = 0,1

./create_newcase --case ~/Cases/LosGrobo_1pt --res CLM_USRDAT --compset I2000Clm51BgcCrop --run-unsupported

I could create, setup and build the case, but when I submit the case it does not run. In the log file I found this error message:

Abort with message NetCDF: Variable not found in file /glade/scratch/vanderwb/hpci-stack/221216-1550/58775/pio-2.5.10/src/clib/pio_nc.c at line 1164

I saw in this thread that it could be due to an urban stream file pointing to a mesh file, but I don't think I'm using any urban surface and also this directory (/glade/scratch/vanderwb/hpci-stack/221216-1550) doesn't exist anymore. I'm not sure how to proceed. The .nc files seem to be fine but I'm not sure either.
Any insights would be appreciated!
Thank you!

------
version: ctsm5.1.dev152-2-gd895c6eec
Case: /glade/u/home/umarconato/Cases/LosGrobo_1pt
Run and logs: /glade/scratch/umarconato/LosGrobo_1pt/run
forcing data: /glade/u/home/umarconato/Cases/forcingdata20182021

 

[oleson]

It looks like you have FLDS in your datm.streams.xml file, but not in your datm data. So I would remove FLDS as a variable in your datm.streams.xml file. It will then be calculated by the model.

 

[UlisesMarconato]

Hi Keith, thank you for your response! We tried removing FLDS in every datm.streams.xml file in the Case directory and in the Run directory. We also copied that into my case directory and prepended "user_" to the file ('user_data.streams.xml') as recommended in this thread. It seems not to be recognized and also appears to be overwriting this file with the unmodified version when we submit the case. Additionally, we attempted to remove the 1pt mode, but it gives an error because it is expecting three separate stream files (Solar, Precip, etc). Why is not pointing to the user_data.streams.xml file?
Could you please point us to a document or similar resource that shows how to specify custom atmospheric forcing extracted from an EC tower data?
Any insights would be appreciated!
Thank you!
Ulises

 

[oleson]

There are instructions in the original version of your user_nl_datm_streams in your case directory:

!------------------------------------------------------------------------
! This file is used to modify datm.streams.xml generated in $RUNDIR
! Entries should have the form
! <streamname>:<stream_variable>= <new stream_value> (NO Quotes!!!)
! The following are accepted values for a stream named foo
! foo:meshfile = character string
! foo:datafiles = comma separated string of full pathnames (e.g. file1,file2,file3...)
! foo:datavars = comma separated string of field pairs (e.g. foo foobar,foo2 foobar2...)
! foo:taxmode = one of [cycle, extend, limit]
! foo:tintalgo = one of [lower,upper,nearest,linear,coszen]
! foo:readmode = single (only suported mode right now)
! foo:mapalgo = one of [bilinear,redist,nn,consf,consd,none]
! foo:dtlimit = real (1.5 is default)
! foo:year_first = integer
! foo:year_last = integer
! foo:year_align = integer
! foo:vectors = null or the names of the vector fields in the model (i.e. Sa_u:Sa_v)
! foo:lev_dimname: = one of [null,name of level dimenion name]
! foo:offset = integer
! As an example:
! foo:year_first = 1950
! would change the stream year_first stream_entry to 1950 for the foo stream block
! NOTE: multi-line inputs are enabled by adding a \ at the end of the line
! As an emaple:
! foo:datafiles=foo1,foo2, \
! foo3
! Will yield the following new entry for datafiles in stream foo
! <datafiles>
! <file>foo1</file>
! <file>foo2</file>
! <file>foo3</file>
! </datafiles>
!------------------------------------------------------------------------