Scheduled Downtime
On Tuesday 24 October 2023 @ 5pm MT the forums will be in read only mode in preparation for the downtime. On Wednesday 25 October 2023 @ 5am MT, this website will be down for maintenance and expected to return online later in the morning.
Normal Operations
The forums are back online with normal operations. If you notice any issues or errors related to the forums, please reach out to help@ucar.edu

Porting issue, trying to run the latest CLM version

K

krivers

K. Andrew Rivers
New Member
Hi,

I want to run the latest version of CLM in a stand-alone mode(https://github.com/ESCOMP/CTSM); however, the same config_machines.xml file that I created to port CESM2.15 does not work.

1. I have successfully ported CESM 2.15 to the CEDAR Compute Canada machine. To ran the model, I created these 3 files: config_batch.xml config_compilers.xml config_machines.xml following the instructions on CESM - Alliance Doc.
2. Then, I wanted to run CLM (latest version). To do this, I
2.1 cloned the repository: git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)
2.2 Updated the components: ./bin/git-fleximod update
2.3 Try to run a simple test case, such as :

/create_newcase --case ~/scratch/neon/ABBY_sp_test \ --res CLM_USRDAT \ --compset 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV \ --output-root ~/$SCRATCH/NEON_cases/ --run-unsupported

This test work great in ported CESM 2.15; however, in this stand-alone version:


Compset longname is 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV
Compset specification file is /project/6093124/bcy917/clm_works/clm_20042025/CTSM/cime_config/config_compsets.xml
Automatically adding SESP to compset
Compset forcing is 1972-2004
ATM component is Data driven ATM single point tower site data set
LND component is clm5.0:Satellite phenology:
ICE component is Stub ice component
OCN component is Stub ocn component
ROF component is Stub river component
GLC component is Stub glacier (land ice) component
WAV component is Stub wave component
ESP component is Stub external system processing (ESP) component
Pes specification file is /project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 2000-01-01
ERROR: Command: '/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/xmllint --xinclude --noout --schema /project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_machines_version3.xsd /home/bcy917/.cime/config_machines.xml' failed with error '/home/$USER/.cime/config_machines.xml:6: element NODENAME_REGEX: Schemas validity error : Element 'NODENAME_REGEX': This element is not expected. Expected is one of ( NODE_FAIL_REGEX, MPIRUN_RETRY_REGEX, MPIRUN_RETRY_COUNT, OS ).
/home/bcy917/.cime/config_machines.xml fails to validate' from dir '/project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/scripts'
I changed my real project and username for security with $PROJECT and $USER.

My overall goal is run models using this compset: 1850_DATM%CRUv7_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV_SESP

What version of the code are you using?
[$USER@cedar5 CTSM]$ ./bin/git-fleximod status
fates at tag sci.1.82.3_api.39.0.0
tools/landusedata at tag v0.1.1
cism at tag cismwrap_2_2_005
source_cism at tag cism_main_2.01.013
rtm at tag rtm1_0_86
mosart at tag mosart1.1.08
mizuRoute at tag cesm-coupling.n03_v2.2.0
ccs_config at tag ccs_config_cesm1.0.20
cime at tag cime6.1.59
e CIME/non_py/cprnc has no fxtag defined in .gitmodules, module at 0b326fd
cmeps at tag cmeps1.0.33
cdeps at tag cdeps1.0.70
fox at tag 4.1.2.1
genf90 at hash 4816965
share at tag share1.1.8
parallelio at tag pio2_6_3
mpi-serial at tag MPIserial_2.5.1
e doc-builder not checked out, aligned at tag v1.0.8 (optional)
testfails = 0, local mods = 0, needs updates 1

[$USER@cedar5 CTSM]$ git describe
ctsm5.3.040
[$USER@cedar5 CTSM]$ git log -1
commit c2a8c6c0dc75a7dee3f9546a6b5d335bf1cd84a1 (HEAD -> master, tag: ctsm5.3.040, origin/master, origin/HEAD)
Merge: f85d6a8d1 b4d07e0bd
Author: Sam Rabin <samrabin@ucar.edu>
Date: Tue Apr 15 11:05:39 2025 -0600

Merge pull request #2982 from samsrabin/ctsm_pylib_3.13.2

ctsm5.3.040: Update ctsm_pylib to 3.13.2


I was able to validate my installation:

xmllint --noout --schema /home/$USER/projects/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
config_batch.xml validates

xmllint --noout --schema /home/$USER/projects/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml/home/$USER/.cime/config_machines.xml validates



If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.
- Attached


Describe your problem or question:
 

Attachments

  • config_machines.xml.txt
    3.7 KB · Views: 2
  • config_compilers.xml.txt
    573 bytes · Views: 2
  • config_batch.xml.txt
    1.8 KB · Views: 2
Y

Yuan Sun

Yuan Sun
Active Member
krivers said:
Hi,

I want to run the latest version of CLM in a stand-alone mode(https://github.com/ESCOMP/CTSM); however, the same config_machines.xml file that I created to port CESM2.15 does not work.

1. I have successfully ported CESM 2.15 to the CEDAR Compute Canada machine. To ran the model, I created these 3 files: config_batch.xml config_compilers.xml config_machines.xml following the instructions on CESM - Alliance Doc.
2. Then, I wanted to run CLM (latest version). To do this, I
2.1 cloned the repository: git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)
2.2 Updated the components: ./bin/git-fleximod update
2.3 Try to run a simple test case, such as :

/create_newcase --case ~/scratch/neon/ABBY_sp_test \ --res CLM_USRDAT \ --compset 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV \ --output-root ~/$SCRATCH/NEON_cases/ --run-unsupported

This test work great in ported CESM 2.15; however, in this stand-alone version:


Compset longname is 2000_DATM%1PT_CLM50%SP_SICE_SOCN_SROF_SGLC_SWAV
Compset specification file is /project/6093124/bcy917/clm_works/clm_20042025/CTSM/cime_config/config_compsets.xml
Automatically adding SESP to compset
Compset forcing is 1972-2004
ATM component is Data driven ATM single point tower site data set
LND component is clm5.0:Satellite phenology:
ICE component is Stub ice component
OCN component is Stub ocn component
ROF component is Stub river component
GLC component is Stub glacier (land ice) component
WAV component is Stub wave component
ESP component is Stub external system processing (ESP) component
Pes specification file is /project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 2000-01-01
ERROR: Command: '/cvmfs/soft.computecanada.ca/gentoo/2023/x86-64-v3/usr/bin/xmllint --xinclude --noout --schema /project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_machines_version3.xsd /home/bcy917/.cime/config_machines.xml' failed with error '/home/$USER/.cime/config_machines.xml:6: element NODENAME_REGEX: Schemas validity error : Element 'NODENAME_REGEX': This element is not expected. Expected is one of ( NODE_FAIL_REGEX, MPIRUN_RETRY_REGEX, MPIRUN_RETRY_COUNT, OS ).
/home/bcy917/.cime/config_machines.xml fails to validate' from dir '/project/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/scripts'
I changed my real project and username for security with $PROJECT and $USER.

My overall goal is run models using this compset: 1850_DATM%CRUv7_CLM60%BGC_SICE_SOCN_SROF_SGLC_SWAV_SESP

What version of the code are you using?
[$USER@cedar5 CTSM]$ ./bin/git-fleximod status
fates at tag sci.1.82.3_api.39.0.0
tools/landusedata at tag v0.1.1
cism at tag cismwrap_2_2_005
source_cism at tag cism_main_2.01.013
rtm at tag rtm1_0_86
mosart at tag mosart1.1.08
mizuRoute at tag cesm-coupling.n03_v2.2.0
ccs_config at tag ccs_config_cesm1.0.20
cime at tag cime6.1.59
e CIME/non_py/cprnc has no fxtag defined in .gitmodules, module at 0b326fd
cmeps at tag cmeps1.0.33
cdeps at tag cdeps1.0.70
fox at tag 4.1.2.1
genf90 at hash 4816965
share at tag share1.1.8
parallelio at tag pio2_6_3
mpi-serial at tag MPIserial_2.5.1
e doc-builder not checked out, aligned at tag v1.0.8 (optional)
testfails = 0, local mods = 0, needs updates 1

[$USER@cedar5 CTSM]$ git describe
ctsm5.3.040
[$USER@cedar5 CTSM]$ git log -1
commit c2a8c6c0dc75a7dee3f9546a6b5d335bf1cd84a1 (HEAD -> master, tag: ctsm5.3.040, origin/master, origin/HEAD)
Merge: f85d6a8d1 b4d07e0bd
Author: Sam Rabin <samrabin@ucar.edu>
Date: Tue Apr 15 11:05:39 2025 -0600

Merge pull request #2982 from samsrabin/ctsm_pylib_3.13.2

ctsm5.3.040: Update ctsm_pylib to 3.13.2


I was able to validate my installation:

xmllint --noout --schema /home/$USER/projects/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_batch.xsd ~/.cime/config_batch.xml
config_batch.xml validates

xmllint --noout --schema /home/$USER/projects/$PROJECT/$USER/clm_works/clm_20042025/CTSM/cime/CIME/data/config/xml_schemas/config_machines.xsd ~/.cime/config_machines.xml/home/$USER/.cime/config_machines.xml validates



If this is a port to a new machine: Please attach any files you added or changed for the machine port (e.g., config_compilers.xml, config_machines.xml, and config_batch.xml) and tell us the compiler version you are using on this machine.
Please attach any log files showing error messages or other useful information.
- Attached


Describe your problem or question:
Click to expand...
CTSM5.3 and CESM2.3.X used ccs_config/machines/cmake_macros/ instead of config_compilers.xml. Please refer to CESM2.3.beta08 porting issue
 
You must log in or register to reply here.
Top