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A query_Field missing from restart file.

D

dharmendraks841

Dharmendra Kumar Singh
Member
Hi all,
I need to generate the 6 hourly datasets for 2035 met_background. For that, I used the following path to extract the restart file through branching method
/glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17
I need following variables/fields U','V','T','PS','Q','QFLX','SHFLX','TAUX','TAUY','SST'
I am getting error as:
ERROR: Field missing from restart file.


Please look at the following command and please assist where I made mistakes:

My name list (user_nl_cam):

! Users should add all user specific namelist changes below in the form of
! namelist_var = new_namelist_value

fincl2 = 'U','V','T','PS','Q','QFLX','SHFLX','TAUX','TAUY','SST'
mfilt = 1,4
nhtfrq = 0,-6


The other branching and command details are as follows:

2023-11-20 01:11:36: xmlchange success <command> ./xmlchange STOP_OPTION=nmonths </command>

---------------------------------------------------

2023-11-20 01:12:09: xmlchange success <command> ./xmlchange STOP_N=2 </command>

---------------------------------------------------

2023-11-20 01:13:34: xmlchange success <command> ./xmlchange RESUBMIT=0 </command>

---------------------------------------------------

2023-11-20 01:14:47: case.setup starting

---------------------------------------------------

2023-11-20 01:14:52: case.setup success

---------------------------------------------------

2023-11-20 18:26:05: xmlchange success <command> ./xmlchange RUN_TYPE=branch </command>

---------------------------------------------------

2023-11-20 18:32:47: xmlchange success <command> ./xmlchange RUN_REFCASE=b.e21.BSSP245smbb.f09_g17.001,RUN_REFDATE=2033-01-01,GET_REFCASE=FALSE </command>

---------------------------------------------------

2023-11-20 20:28:59: case.build starting

---------------------------------------------------

2023-11-20 21:42:59: case.build starting

---------------------------------------------------

2023-11-20 22:54:14: xmlchange success <command> ./xmlchange JOB_WALLCLOCK_TIME=10:00:00 </command>

---------------------------------------------------

2023-11-20 22:55:18: xmlchange success <command> ./xmlchange --subgroup case.st_archive JOB_WALLCLOCK_TIME=01:00:00 </command>

---------------------------------------------------

2023-11-20 22:55:48: case.build starting

---------------------------------------------------

2023-11-20 23:26:02: xmlchange success <command> ./xmlchange JOB_WALLCLOCK_TIME=6:00:00 </command>

---------------------------------------------------

2023-11-20 23:26:20: xmlchange success <command> ./xmlchange --subgroup case.st_archive JOB_WALLCLOCK_TIME=01:00:00 </command>

---------------------------------------------------

2023-11-20 23:26:41: case.build starting

---------------------------------------------------

2023-11-21 10:54:28: case.build starting

---------------------------------------------------

CESM version is release-cesm2.1.4

Processing externals description file : Externals.cfg (/glade/work/dksingh/code/my_cesm_code)

Processing externals description file : Externals_CAM.cfg (/glade/work/dksingh/code/my_cesm_code/components/cam)

Processing externals description file : Externals_CISM.cfg (/glade/work/dksingh/code/my_cesm_code/components/cism)

Processing externals description file : Externals_CLM.cfg (/glade/work/dksingh/code/my_cesm_code/components/clm)

Processing externals description file : Externals_POP.cfg (/glade/work/dksingh/code/my_cesm_code/components/pop)

Checking local status of required & optional components: cam, chem_proc, carma, clubb, cosp2, cice, cime, cism, source_cism, clm, fates, ptclm, mosart, pop, cvmix, marbl, rtm, ww3,

./cime

clean sandbox, on cime5.6.44

./components/cam

clean sandbox, on cam_cesm2_1_rel_r58

./components/cam/chem_proc

clean sandbox, on tools/proc_atm/chem_proc/release_tags/chem_proc5_0_03_rel

./components/cam/src/physics/carma/base

clean sandbox, on carma/release_tags/carma3_49_rel

./components/cam/src/physics/clubb

clean sandbox, on vendor_clubb_r8099_n03

./components/cam/src/physics/cosp2/src

clean sandbox, on CFMIP/COSPv2.0/tags/v2.1.4cesm/src

./components/cice

clean sandbox, on cice5_cesm2_1_1_20190321

./components/cism

clean sandbox, on cism-release-cesm2.1.2_02

./components/cism/source_cism

clean sandbox, on release-cism2.1.03

./components/clm

clean sandbox, on release-clm5.0.35

./components/clm/src/fates

clean sandbox, on sci.1.30.0_api.8.0.0

./components/clm/tools/PTCLM

clean sandbox, on PTCLM2_20200902

./components/mosart

clean sandbox, on release-cesm2.0.04

./components/pop

clean sandbox, on pop2_cesm2_1_rel_n14

./components/pop/externals/CVMix

clean sandbox, on v0.93-beta

./components/pop/externals/MARBL

clean sandbox, on cesm2.1-n00

./components/rtm

clean sandbox, on release-cesm2.0.04

./components/ww3

clean sandbox, on ww3_181001

2023-11-21 11:13:42: case.build success

---------------------------------------------------

2023-11-21 12:30:17: case.submit starting

---------------------------------------------------

2023-11-21 12:30:38: case.submit success case.run:4232080.chadmin1.ib0.cheyenne.ucar.edu, case.st_archive:4232081.chadmin1.ib0.cheyenne.ucar.edu

---------------------------------------------------

2023-11-21 12:31:31: case.run starting

---------------------------------------------------

2023-11-21 12:31:42: model execution starting

---------------------------------------------------

2023-11-21 12:33:27: model execution success

---------------------------------------------------

2023-11-21 12:33:27: case.run error

ERROR: RUN FAIL: Command 'mpiexec_mpt -p "%g:" -np 720 omplace -tm open64 /glade/scratch/dksingh/bssp245smbb_2035/bld/cesm.exe >> cesm.log.$LID 2>&1 ' failed

See log file for details: /glade/scratch/dksingh/bssp245smbb_2035/run/cesm.log.4232080.chadmin1.ib0.cheyenne.ucar.edu.231121-123131
 
P

peverley

Courtney Peverley
Moderator
Staff member
Hi,

I'm not an expert in branch runs, but here's what I'm thinking:

Since you're setting $GET_REFCASE to false, the code is looking for the restart files in your run directory. Would it be easier to use $GET_REFCASE=True and then point directly to the refcase directory with $RUN_REFDIR='/glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17' ?

I find the documentation here helpful:

$CESM/cime/doc/source/users_guide/running-a-case.rst
Click to expand...

Hope that helps. If not, let me know.

Courtney
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
peverley said:
Hi,

I'm not an expert in branch runs, but here's what I'm thinking:

Since you're setting $GET_REFCASE to false, the code is looking for the restart files in your run directory. Would it be easier to use $GET_REFCASE=True and then point directly to the refcase directory with $RUN_REFDIR='/glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17' ?

I find the documentation here helpful:



Hope that helps. If not, let me know.

Courtney
Click to expand...
Showing the following error while building the case:

ERROR: Reference case directory /glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17 does not contain any rpointer files

(base) dksingh@cheyenne5:/glade/work/dksingh/cases/bssp245smbb_2035> qcmd -A UIUC0044 -- ./case.build


Submitting command to PBS using account UIUC0044:


./case.build





Requested custom PBS options:


-A UIUC0044





Waiting for job 4354379.chadmin1.ib0.cheyenne.ucar.edu to start ...








Building case in directory /glade/work/dksingh/cases/bssp245smbb_2035


sharedlib_only is False


model_only is False


Setting resource.RLIMIT_STACK to -1 from (-1, -1)


Generating component namelists as part of build


- Prestaging REFCASE (/glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17) to /glade/scratch/dksingh/bssp245smbb_2035/run


ERROR: Reference case directory /glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17 does not contain any rpointer files
 
P

peverley

Courtney Peverley
Moderator
Staff member
Ah, looking at the CIME documentation I referenced in my previous answer, it says:

If ``$RUN_REFDIR`` is an absolute pathname, then it is expected that initial/restart files needed to start up a model run are in ``$RUN_REFDIR``.
Click to expand...

So you'll want to set $RUN_REFDIR to the full path to wherever it is you found those history/restart files you extracted previously. So presumably this will be the first part of your path (but then I don't know where to go from there):

/glade/campaign/cesm/development/cvcwg/cvwg/b.e21.BSSP245smbb.f09_g17/b.e21.BSSP245smbb.f09_g17.001
Click to expand...

Sorry for the confusion. Hope that helps/works!

Courtney
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
yes, but for the r-pointer, I think, I have to extract the "rest" file in my directory then it can be built, I am trying as follows:(let's see what happens)

(base) dksingh@cheyenne5:/glade/work/dksingh/cases/bssp245smbb_2035> ./xmlchange RUN_REFDIR=/glade/scratch/dksingh/b.e21.BSSP245smbb.f09_g17.001/rest/2033-01-01-00000


(base) dksingh@cheyenne5:/glade/work/dksingh/cases/bssp245smbb_2035> ./xmlquery RUN_REFDIR


RUN_REFDIR: /glade/scratch/dksingh/b.e21.BSSP245smbb.f09_g17.001/rest/2033-01-01-00000
Based on my understanding, we cannot use the CESM path directly, as the rest file (2033-01-01-00000), containing the r-pointers, must be extracted first. I anticipate a successful execution of ./case.build, although uncertainties remain regarding the subsequent model run and the generation of the 6-hour 2035 dataset for the required variables to drive the F compset.
I am making the best effort on my own as now I am attending AGU 23 in SF, and unfortunately, I have not found anyone to discuss these fundamental issues. I appreciate your assistance and extend my gratitude to all the members of the CESM forum who contribute to valuable discussions and support.

Kind regards
Dharmendra
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
The case was successfully built But the model run failed again with the same previous error:
ERROR: Field missing from restart file
 
P

peverley

Courtney Peverley
Moderator
Staff member
Ah, ok. So I think you should revert to your original set-up (RUN_REFCASE=b.e21.BSSP245smbb.f09_g17.001,RUN_REFDATE=2033-01-01,GET_REFCASE=FALSE). Apologies for the run-around.

Looking at the log files again, it looks like (at least some of) the missing field errors are coming from the land side of things. The lnd log file has this error message:

ERROR: Field missing from restart file: rc13_canair
Missing fields are not allowed in branch or continue (restart) runs.
Click to expand...

To skirt this error, you can set use_c13 = .false. in your user_nl_clm file. If you really need to use c13, you'll probably have to find a different data set for branching.

Let me know if this works and if/when you get a different error!

Courtney
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
peverley said:
Ah, ok. So I think you should revert to your original set-up (RUN_REFCASE=b.e21.BSSP245smbb.f09_g17.001,RUN_REFDATE=2033-01-01,GET_REFCASE=FALSE). Apologies for the run-around.

Looking at the log files again, it looks like (at least some of) the missing field errors are coming from the land side of things. The lnd log file has this error message:



To skirt this error, you can set use_c13 = .false. in your user_nl_clm file. If you really need to use c13, you'll probably have to find a different data set for branching.

Let me know if this works and if/when you get a different error!

Courtney
Click to expand...
Thanks
I will try again
I need to run CAM6 for driving F compset
And need 2035 met background using B compset that we are doing at this forum
I don't need any variables related to CLM
I need those variables given above in my previous post fro running CAM6 model
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
Hi,
I am getting an error while building the case after putting the value of use_c13 = .false. in the following place in user_nl_clm:


! Settings from cmip6_carbon_isotopes

use_c13 = .false.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.


err=ERROR : CLM build-namelist::CLMBuildNamelist::setup_logic_c_isotope() : use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set




Submitting command to PBS using account UIUC0044:


./case.build





Requested custom PBS options:


-A UIUC0044





Waiting for job 4367369.chadmin1.ib0.cheyenne.ucar.edu to start ...








Building case in directory /glade/work/dksingh/cases/bssp245smbb_2035


sharedlib_only is False


model_only is False


Setting resource.RLIMIT_STACK to -1 from (-1, -1)


Generating component namelists as part of build


GET_REFCASE is false, the user is expected to stage the refcase to the run directory.


Creating component namelists


Calling /glade/work/dksingh/code/my_cesm_code/components/cam//cime_config/buildnml


...calling cam buildcpp to set build time options


CAM namelist copy: file1 /glade/work/dksingh/cases/bssp245smbb_2035/Buildconf/camconf/atm_in file2 /glade/scratch/dksingh/bssp245smbb_2035/run/atm_in


Calling /glade/work/dksingh/code/my_cesm_code/components/clm//cime_config/buildnml


ERROR: Command /glade/work/dksingh/code/my_cesm_code/components/clm/bld/build-namelist failed rc=255


out=CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'sim_year' with val '1850'


CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'sim_year_range' with val '1850-2100'


CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'ssp_rcp' with val 'SSP2-4.5'


CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'use_case_desc' with val 'Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario'


err=ERROR : CLM build-namelist::CLMBuildNamelist::setup_logic_c_isotope() : use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
I set and encountered the following error while ./case.build


(base) dksingh@cheyenne6:/glade/work/dksingh/cases/bssp245smbb_2035> qcmd -A UIUC0044 -- ./case.build


Submitting command to PBS using account UIUC0044:


./case.build





Requested custom PBS options:


-A UIUC0044





Waiting for job 4369643.chadmin1.ib0.cheyenne.ucar.edu to start ...








Building case in directory /glade/work/dksingh/cases/bssp245smbb_2035


sharedlib_only is False


model_only is False


Setting resource.RLIMIT_STACK to -1 from (-1, -1)


Generating component namelists as part of build


GET_REFCASE is false, the user is expected to stage the refcase to the run directory.


Creating component namelists


Calling /glade/work/dksingh/code/my_cesm_code/components/cam//cime_config/buildnml


...calling cam buildcpp to set build time options


ERROR: Command /glade/work/dksingh/code/my_cesm_code/components/cam/bld/build-namelist -ntasks 576 -csmdata /glade/campaign/cesm/cesmdata/inputdata -infile /glade/work/dksingh/cases/bssp245smbb_2035/Buildconf/camconf/namelist -ignore_ic_year -use_case ssp245BB_cam6 -inputdata /glade/work/dksingh/cases/bssp245smbb_2035/Buildconf/cam.input_data_list -namelist " &atmexp co2_cycle_rad_passive=.true. /" failed rc=255


out=


err=CAM build-namelist - ERROR: Invalid namelist variable in '-infile' /glade/work/dksingh/cases/bssp245smbb_2035/Buildconf/camconf/namelist.


ERROR: in _validate_pair (package Build::NamelistDefinition): Variable name use_c13_timeseries not found in /glade/work/dksingh/code/my_cesm_code/components/cam/bld/namelist_files/namelist_definition.xml
Please correct if something is missing from the following both name list (cam and clm)
My user_nl_cam.

! namelist_var = new_namelist_value

fincl2 = 'U','V','T','PS','Q','QFLX','SHFLX','TAUX','TAUY','SST'

mfilt = 1,4


nhtfrq = 0,6



use_c13 = .false.
use_c13_timeseries = .false.

My user_nl_clm

! Settings from cmip6_carbon_isotopes

!----------------------------------------------------------------------------------


use_c13 = .false.

use_c14 = .true.

use_c13_timeseries = .false.

use_c14_bombspike = .true.
 
P

peverley

Courtney Peverley
Moderator
Staff member
Oops, yes. I meant your set use_c13_timeseries = .false. in your user_nl_clm file (not the user_nl_cam file - you should remove those namelist options from there as that's where the error is coming from)
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
peverley said:
Oops, yes. I meant your set use_c13_timeseries = .false. in your user_nl_clm file (not the user_nl_cam file - you should remove those namelist options from there as that's where the error is coming from)
Click to expand...
Yes, I tried many ways:
now after this name list in user_nl_clm

Settings from cmip6_carbon_isotopes
!----------------------------------------------------------------------------------
use_c13 = .false.
use_c14 = .true.
use_c13_timeseries = .false.
use_c14_bombspike = .true.

The following Error is again found while ./case.build
Building case in directory /glade/work/dksingh/cases/bssp245smbb_2035

sharedlib_only is False

model_only is False

Setting resource.RLIMIT_STACK to -1 from (-1, -1)

Generating component namelists as part of build

GET_REFCASE is false, the user is expected to stage the refcase to the run directory.

Creating component namelists

Calling /glade/work/dksingh/code/my_cesm_code/components/cam//cime_config/buildnml

...calling cam buildcpp to set build time options

CAM namelist copy: file1 /glade/work/dksingh/cases/bssp245smbb_2035/Buildconf/camconf/atm_in file2 /glade/scratch/dksingh/bssp245smbb_2035/run/atm_in

Calling /glade/work/dksingh/code/my_cesm_code/components/clm//cime_config/buildnml

ERROR: Command /glade/work/dksingh/code/my_cesm_code/components/clm/bld/build-namelist failed rc=255

out=CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'sim_year' with val '1850'

CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'sim_year_range' with val '1850-2100'

CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'ssp_rcp' with val 'SSP2-4.5'

CLM adding use_case 1850-2100_SSP2-4.5_transient defaults for var 'use_case_desc' with val 'Simulate transient land-use, aerosol deposition, and Nitrogen deposition changes from 1850 to current day with historical data, and then to 2100 with the CMIP6 SSP2-4.5 scenario'

err=ERROR : CLM build-namelist::CLMBuildNamelist::setup_logic_c_isotope() : use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set
 
P

peverley

Courtney Peverley
Moderator
Staff member
Hi,

Since the default case had use_c13=true, it automatically set the atm_c13_filename. I'm not 100% sure it'll work, but try (in your user_nl_clm file):

atm_c13_filename=''
Click to expand...

(where '' is two single quotes). If that doesn't work, you may have to change the defaults for the compset and then create a new case.

Courtney
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
peverley said:
If that doesn't work, you may have to change the defaults for the compset and then create a new case.
Click to expand...
can you explain more about this?

should the following be as follows in user_nl_clm

atm_c13_filename='false'
use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
peverley said:
Hi,

Since the default case had use_c13=true, it automatically set the atm_c13_filename. I'm not 100% sure it'll work, but try (in your user_nl_clm file):



(where '' is two single quotes). If that doesn't work, you may have to change the defaults for the compset and then create a new case.

Courtney
Click to expand...
sorry,
you suggested file name atm_c13_filename='file name'
Which 'file name', please clarify, I may be confused.
 
D

dharmendraks841

Dharmendra Kumar Singh
Member
After setting the variables, the previous error (Field missing from restart file.) is NOT there, however, a new error is found as follows:

ERROR: Unknown error submitted to shr_abort_abort.

In user_nl_clm, I set as follows:

use_c13 = .true.
use_c14 = .true.
use_c13_timeseries = .true.
use_c14_bombspike = .true.
atm_c13_filename=''
 
P

peverley

Courtney Peverley
Moderator
Staff member
Can you try

use_c13 = .false.
use_c14 = .true.
use_c13_timeseries = .false.
use_c14_bombspike = .true.
atm_c13_filename=''
Click to expand...
And let me know what you get?
Courtney
 
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