./case.build error when using f05_g17

[Ceil]

I try to run "--res f05_g17 --compset FHIST_BGC", but I got errors when I ran ./case.build as below,
ERROR: Need to provide valid mapping file between atm and ice in xml variable atm2ice_smapname

I checked to find that the below similar file is needed,
atm2ice_smapname = /inputdata/cpl/gridmaps/fv0.9x1.25/map_fv0.9x1.25_TO_gx1v7_blin.151008.nc
I want to make this file to f05_g17.

From 3. Model grids — CIME master documentation, it seems that I should use ./gen_cesm_maps.sh. But I am very confused what these files (--fileocn, --fileatm, --filelnd, --filertm) are, can I download them from https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/, or should I make them by myself?

 

[mlevy]

I'm a little confused -- the map you are asking about is available in inputdata (and I would expect CESM to download it for you)... what is the error you are getting? The full message might hint at a solution.

In the meantime you can get the missing file directly from https://svn-ccsm-inputdata.cgd.ucar...9x1.25/map_fv0.9x1.25_TO_gx1v7_blin.151008.nc I expect the manual download will be an iterative process, where every time you pull down a file and try to build you get an error about a different missing file but eventually you'll have a complete set.

 

[Ceil]

I'm a little confused -- the map you are asking about is available in inputdata (and I would expect CESM to download it for you)... what is the error you are getting? The full message might hint at a solution.

In the meantime you can get the missing file directly from https://svn-ccsm-inputdata.cgd.ucar...9x1.25/map_fv0.9x1.25_TO_gx1v7_blin.151008.nc I expect the manual download will be an iterative process, where every time you pull down a file and try to build you get an error about a different missing file but eventually you'll have a complete set.

Hi Mlevy,

Many thanks for your reply!
I do not want map_fv0.9x1.25_TO_gx1v7_blin.151008.nc. Because this is for --res f09_g17. I want the similar file for --res f05_g17, and I could not find this on online inputdata.

 

[mlevy]

Sorry, I completely misread your post! To use gen_cesm_maps.sh you need to have the ESMF tools installed and you need the SCRIP grid files for the two grids (f05 and g17). Do you have access to the NCAR supercomputers? It would be easiest to point you to all of this stuff on the the glade filesystem, otherwise I can try to track it down in inputdata. (I have a meeting in a few minutes, so I might be a little slow to reply)

 

[Ceil]

Sorry, I completely misread your post! To use gen_cesm_maps.sh you need to have the ESMF tools installed and you need the SCRIP grid files for the two grids (f05 and g17). Do you have access to the NCAR supercomputers? It would be easiest to point you to all of this stuff on the the glade filesystem, otherwise I can try to track it down in inputdata. (I have a meeting in a few minutes, so I might be a little slow to reply)

ESMF is already installed in the supercomputer I am using, so I just need to module load it. But I am confused where I can find the SCRIP grid files for the two grids (f05 and g17).
I have no access to the NCAR supercomputer.
It does not matter. When you are free, please help me. Many thanks!

 

[mlevy]

The SCRIP grid files are also in inputdata, but they are buried in the inputdata/share/scripgrids/ directory. You want to use fv0.47x0.63_141008.nc and gx1v7_151008.nc

 

[mlevy]

Alternatively, I realized the mapping files you wanted are already in inputdata on the NCAR machine, so I added them to the SVN repository in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/cpl/gridmaps/fv0.47x0.63/ -- map_0.47x0.63_TO_gx1v7_aave.180517.nc, map_0.47x0.63_TO_gx1v7_blin.180517.nc, and map_0.47x0.63_TO_gx1v7_patc.180517.nc

If you need the ocean -> atm maps, they are in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/cpl/gridmaps/gx1v7/ -- map_gx1v7_TO_fv0.47x0.63_aave.180517.nc and map_gx1v7_TO_fv0.47x0.63_blin.180517.nc

 

[Ceil]

f

Alternatively, I realized the mapping files you wanted are already in inputdata on the NCAR machine, so I added them to the SVN repository in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/cpl/gridmaps/fv0.47x0.63/ -- map_0.47x0.63_TO_gx1v7_aave.180517.nc, map_0.47x0.63_TO_gx1v7_blin.180517.nc, and map_0.47x0.63_TO_gx1v7_patc.180517.nc

If you need the ocean -> atm maps, they are in https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/cpl/gridmaps/gx1v7/ -- map_gx1v7_TO_fv0.47x0.63_aave.180517.nc and map_gx1v7_TO_fv0.47x0.63_blin.180517.nc

I have already put atm2ice_smapname file at inputdata/cpl/gridmaps/fv0.47x0.63/map_0.47x0.63_TO_gx1v7_blin.180517.nc
but after I ran ./case.build, I still got ERROR: Need to provide valid mapping file between atm and ice in xml variable atm2ice_smapname

I checked Buildconf/cpl.input_data_list, and there is no atm2ice_smapname written in the file.
vi Buildconf/cpl.input_data_list
rof2ocn_liq_rmapname = /cluster/work/users/inputdata/cpl/gridmaps/r05/map_r05_to_gx1v7_nn_open_ocean_nnsm_e1000r300_marginal_sea_170413.nc
glc2ocn_liq_rmapname = /cluster/work/users/inputdata/cpl/gridmaps/gland4km/map_gland4km_to_gx1v7_nn_open_ocean_nnsm_e1000r300_marginal_sea_171105.nc
rof2ocn_ice_rmapname = /cluster/work/users/inputdata/cpl/gridmaps/r05/map_r05_to_gx1v7_nnsm_e1000r300_170413.nc
glc2lnd_smapname = /cluster/work/users/inputdata/cpl/gridmaps/gland4km/map_gland4km_TO_fv0.47x0.63_aave.171105.nc
rof2ocn_fmapname = /cluster/work/users/inputdata/cpl/gridmaps/r05/map_r05_TO_gx1v7_aave.161012.nc
lnd2rof_fmapname = /cluster/work/users/inputdata/lnd/clm2/mappingdata/maps/0.47x0.63/map_0.47x0.63_nomask_to_0.5x0.5_nomask_aave_da_c120306.nc
glc2lnd_fmapname = /cluster/work/users/inputdata/cpl/gridmaps/gland4km/map_gland4km_TO_fv0.47x0.63_aave.171105.nc
lnd2glc_fmapname = /cluster/work/users/inputdata/cpl/gridmaps/fv0.47x0.63/map_fv0.47x0.63_TO_gland4km_aave.171105.nc
glc2ocn_ice_rmapname = /cluster/work/users/inputdata/cpl/gridmaps/gland4km/map_gland4km_to_gx1v7_nnsm_e1000r300_171105.nc
rof2lnd_fmapname = /cluster/work/users/inputdata/lnd/clm2/mappingdata/maps/0.47x0.63/map_0.5x0.5_nomask_to_0.47x0.63_nomask_aave_da_c120306.nc
lnd2glc_smapname = /cluster/work/users/inputdata/cpl/gridmaps/fv0.47x0.63/map_fv0.47x0.63_TO_gland4km_blin.171105.nc

I guess that atm2ice_smapname should be written in the cpl.input_data_list. But I do not know where I can write. Because it does not make sense to directly write in the Buildconf/cpl.input_data_list.

 

[Ceil]

The SCRIP grid files are also in inputdata, but they are buried in the inputdata/share/scripgrids/ directory. You want to use fv0.47x0.63_141008.nc and gx1v7_151008.nc

I try to use the two files to generate map_*nc files by myself, because I later need to do another experiments which require user-defined resolution.
But I got errors "Can not determine machine name from hostname 'login-2.betzy.sigma2.no'" after I ran the commands below,
module load ESMF/8.0.1-intel-2020a
export MPIEXEC=/cluster/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpirun
export ESMFBIN_PATH=/cluster/software/ESMF/8.0.1-intel-2020a/bin
cd cesm2.1.3/my_cesm_sandbox/cime/tools/mapping/gen_mapping_files
./gen_cesm_maps.sh --fileatm fv0.47x0.63_141008.nc --fileocn gx1v7_151008.nc --nameatm fv0.47x0.63 --nameocn gx1v7

From 3. Model grids — CIME master documentation, I learn that I should edit gen_ESMF_mapping_file/create_ESMF_map.sh. But I am confused how to edit the create_ESMF_map.sh.

 

[mlevy]

I have already put atm2ice_smapname file at inputdata/cpl/gridmaps/fv0.47x0.63/map_0.47x0.63_TO_gx1v7_blin.180517.nc
but after I ran ./case.build, I still got ERROR: Need to provide valid mapping file between atm and ice in xml variable atm2ice_smapname

What version of CESM are you running, and what steps did you take to set atm2ice_smapname?

I try to use the two files to generate map_*nc files by myself, because I later need to do another experiments which require user-defined resolution.
But I got errors "Can not determine machine name from hostname 'login-2.betzy.sigma2.no'" after I ran the commands below,
module load ESMF/8.0.1-intel-2020a
export MPIEXEC=/cluster/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpirun
export ESMFBIN_PATH=/cluster/software/ESMF/8.0.1-intel-2020a/bin
cd cesm2.1.3/my_cesm_sandbox/cime/tools/mapping/gen_mapping_files
./gen_cesm_maps.sh --fileatm fv0.47x0.63_141008.nc --fileocn gx1v7_151008.nc --nameatm fv0.47x0.63 --nameocn gx1v7

From 3. Model grids — CIME master documentation, I learn that I should edit gen_ESMF_mapping_file/create_ESMF_map.sh. But I am confused how to edit the create_ESMF_map.sh.

There are two places you need to edit that file. First, you just need to remove the exit call if MACH="UNSET"; the block of code is probably around line 225 depending on which version of the model you have?

Next, you should put those module load and export statements in the second case statement around line 340 (and remove the exit statement there as well).

 

[Ceil]

What version of CESM are you running, and what steps did you take to set atm2ice_smapname?


There are two places you need to edit that file. First, you just need to remove the exit call if MACH="UNSET"; the block of code is probably around line 225 depending on which version of the model you have?

Next, you should put those module load and export statements in the second case statement around line 340 (and remove the exit statement there as well).

I use CESM2.1.3.
I only found atm2ice_smapname in Buildconf/cpl.input_data_list through running --res f19_g17. Because there is no atm2ice_smapname when running --res f05_g17. But it does not make sense to directly write in the Buildconf/cpl.input_data_list. I have no idea where I can add atm2ice_smapname.

The method works well to generate map*nc files. Thank you very much!

 

[mlevy]

Try

$ ./xmlchange ATM2ICE_SMAPNAME=cpl/gridmaps/fv0.47x0.63/map_0.47x0.63_TO_gx1v7_blin.180517.nc

The mapping variables are set in env_run.xml and then the various CIME scripts (e.g. preview_namelists) populates the files in Buildconf/. You are correct to say

But it does not make sense to directly write in the Buildconf/cpl.input_data_list

as everything in Buildconf/ will be overwritten by the scripts in your case directory.

 

[Ceil]

Try

$ ./xmlchange ATM2ICE_SMAPNAME=cpl/gridmaps/fv0.47x0.63/map_0.47x0.63_TO_gx1v7_blin.180517.nc

The mapping variables are set in env_run.xml and then the various CIME scripts (e.g. preview_namelists) populates the files in Buildconf/. You are correct to say



as everything in Buildconf/ will be overwritten by the scripts in your case directory.

Hi Michael,
./xmlchange works well to solve the problem. But I had another problem when running ./case.build. The error is "ERROR: No default value found for ncdata". I learned that I should edit user_nl_cam and add the following initial file,
ncdata="/cluster/work/inputdata/atm/cam/inic/fv/cami-mam3_0000-01-01_0.47x0.63_L32_c{date}.nc"
I have tried to use cesm2.1.3/my_cesm_sandbox/components/cam/tools/interpic_new to generate the initial file.
But I could not create an executable named "interpic". I tried to run gnumake in the directory components/cam/tools/interpic_new, but I got errors "-bash: gnumake: command not found".
I tried to run the following commands,
../../../../cime/tools/configure --machine betzy --macros-format Makefile --mpilib mpi-serial
. ./.env_mach_specific.sh
gmake
But I got errors "gmake: *** [interpic] Error 1".

 

[Ceil]

Try

$ ./xmlchange ATM2ICE_SMAPNAME=cpl/gridmaps/fv0.47x0.63/map_0.47x0.63_TO_gx1v7_blin.180517.nc

The mapping variables are set in env_run.xml and then the various CIME scripts (e.g. preview_namelists) populates the files in Buildconf/. You are correct to say



as everything in Buildconf/ will be overwritten by the scripts in your case directory.

Hi Michael,

I still can not install interpic. I run the following commands, but I always get errors that can be seen in the attached make_log.txt
module purge
module load netCDF-Fortran/4.5.2-iimpi-2020a
cd cesm2.1.3/my_cesm_sandbox/components/cam/tools/interpic_new
vi Makefile #edit the following paths
LIB_NETCDF := /cluster/software/netCDF-Fortran/4.5.2-iimpi-2020a/lib
INC_NETCDF := /cluster/software/netCDF-Fortran/4.5.2-iimpi-2020a/include
gmake

I have tried all methods I know but I failed every time. I sincerely hope to get your help. Many thanks!