How to transplant my model to Derecho

[jinmuluo]

Is this the first time you've run single-point? If so, you'd need to create a surface dataset and domain file for the gridcell you want to simulate. Some instructions are provided here:

1.6.3. Running Single Point Configurations — ctsm release-clm5.0 documentation

No, I ran single-site simulation multiple times, but it never requested me to define these two namelistes.

 

[jinmuluo]

Is this the first time you've run single-point? If so, you'd need to create a surface dataset and domain file for the gridcell you want to simulate. Some instructions are provided here:

1.6.3. Running Single Point Configurations — ctsm release-clm5.0 documentation

Do you mean the one of the result files when we created the single-site meteorology?
./subset_data point --lat 42.06620 --lon 273.65425 --site isu_point --create-surface --create-datm --datm-syr 2010 --datm-eyr 2014 --create-user-mods --outdir ${SUBDATA}

like this one?

/glade/work/jinmuluo/MESONET/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_isu_point_clarion_c230824.nc

 

[oleson]

Can you point me to a single-point case you've run successfully previously? I suspect you were using newer code for that which doesn't require a domain file, it uses a mesh file instead.

 

[jinmuluo]

Can you point me to a single-point case you've run successfully previously? I suspect you were using newer code for that which doesn't require a domain file, it uses a mesh file instead.

Hi

Here is an example I ran on Cheyenne with CTSM

/glade/work/jinmuluo/MESOCOSM_Clarion_123kgN

 

[oleson]

Right, the code you are using now is older and your single point cases require a domain file. Actually, in the newer code, I don't think you even need a mesh file for a single-point simulation.

 

[jinmuluo]

Right, the code you are using now is older and your single point cases require a domain file. Actually, in the newer code, I don't think you even need a mesh file for a single-point simulation.

So what I need to do is just point LND_DOMAIN_PATH and LND_DOMAIN_FILE to the file below.

/glade/work/jinmuluo/MESONET/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_isu_point_clarion_c230824.nc

 

[oleson]

No, you would point "fsurdat" in your user_nl_clm to that file. You need a domain file. I think if you add --create-domain to your subset_data command above, it will create a domain file for you.

 

[jinmuluo]

No, you would point "fsurdat" in your user_nl_clm to that file. You need a domain file. I think if you add --create-domain to your subset_data command above, it will create a domain file for you.

Hi Keith,

After I merged my code (ctsm5.1.dev108) with release-cesm2.2.03, the newly merged code requested more definitions of one variable. I compared the old code and merged code, I didn't delete anything about 'fan_nh3_to_atm'. Do you know if this question was caused by the different cime versions?

Best,

ERROR: Variable 'fan_nh3_to_atm' from file '/glade/work/jinmuluo/cases/DerechoTest/Buildconf/clmconf/drv_flds_in' is not in the namelist definition.

old code (works well on cheyenn, CTSM): /glade/u/home/jinmuluo/CLM-FANv3
Newly merged code: /glade/u/home/jinmuluo/CLM-FANv3tag01

 

[oleson]

I wouldn't think so. I'd difference the files containing instances of 'fan_nh3_to_atm' between the two versions of your code to see if there is anything missing.
Do you get that error when you run ./preview_namelists in your case directory?

 

[jinmuluo]

I wouldn't think so. I'd difference the files containing instances of 'fan_nh3_to_atm' between the two versions of your code to see if there is anything missing.
Do you get that error when you run ./preview_namelists in your case directory?

Yes, I got the same error when I ./preview_namelists in my case directory.
When I resolved the code conflicts between the two versions, all changes weren't made on the main code.

 

[jinmuluo]

I wouldn't think so. I'd difference the files containing instances of 'fan_nh3_to_atm' between the two versions of your code to see if there is anything missing.
Do you get that error when you run ./preview_namelists in your case directory?

Hi Keith,

Is there any ctsm release close to tag ctsm5.1.dev108 that can be run on Derecho right now?

Thanks

 

[jinmuluo]

Hi Keith,

After I merged my code (ctsm5.1.dev108) with release-cesm2.2.03, the newly merged code requested more definitions of one variable. I compared the old code and merged code, I didn't delete anything about 'fan_nh3_to_atm'. Do you know if this question was caused by the different cime versions?

Best,

ERROR: Variable 'fan_nh3_to_atm' from file '/glade/work/jinmuluo/cases/DerechoTest/Buildconf/clmconf/drv_flds_in' is not in the namelist definition.

old code (works well on cheyenn, CTSM): /glade/u/home/jinmuluo/CLM-FANv3
Newly merged code: /glade/u/home/jinmuluo/CLM-FANv3tag01

Hi Keith,

After I merged my code (ctsm5.1.dev108) with release-cesm2.2.03, the newly merged code requested more definitions of one variable. I compared the old code and merged code, I didn't delete anything about 'fan_nh3_to_atm'. Do you know if this question was caused by the different cime versions?

Best,

ERROR: Variable 'fan_nh3_to_atm' from file '/glade/work/jinmuluo/cases/DerechoTest/Buildconf/clmconf/drv_flds_in' is not in the namelist definition.

old code (works well on cheyenn, CTSM): /glade/u/home/jinmuluo/CLM-FANv3
Newly merged code: /glade/u/home/jinmuluo/CLM-FANv3tag01

Hi @erik ,

When I merged my fan code with tag ctsm5.1.dev163, two specific external software in the Externals.cfg has different repo_url like below, and they are under your repository. How can I update these two repo_url? Thank you!

[cmeps]
#tag = cmeps0.13.71
hash = 1fce4310845bff83de67d4fa52be09a02ef1954c
#branch = fancpl2-up-merge
protocol = git
repo_url = GitHub - ekluzek/CMEPS: NUOPC Coupler Code
local_path = components/cmeps
required = True

[cpl7]
#tag = cpl7.0.14
protocol = git
repo_url = GitHub - ekluzek/CESM_CPL7andDataComps: cpl7 data models
local_path = components/cpl7
#branch = fancpl2-up-merge
hash = 52afc38938202889ca42925407e77d89ca288623
required = True

 

[slevis]

@jinmuluo I tried the following command, which overwrote my Externals.cfg with the one from dev163, and I saw no reference to ekluzek:
git show ctsm5.1.dev163:Externals.cfg > Externals.cfg
So I suggest executing this command to get your Externals.cfg to be consistent with dev163.

 

[jinmuluo]

@jinmuluo I tried the following command, which overwrote my Externals.cfg with the one from dev163, and I saw no reference to ekluzek:
git show ctsm5.1.dev163:Externals.cfg > Externals.cfg
So I suggest executing this command to get your Externals.cfg to be consistent with dev163.

Hi Sam,

Thank you for your replies!
Actually, if I kept my Externals.cfg same with dev163. The model will report an error when I build it.

ERROR: Variable 'fan_nh3_to_atm' from file '/glade/work/jinmuluo/cases/DerechoTest/Buildconf/clmconf/drv_flds_in' is not in the namelist definition.

I use the grep command to search the variable 'fan_nh3_to_atm' in my old code and the new merged code. I found in the old code, that both cmeps and cpl7 have 'fan_nh3_to_atm' definitions but the newly merged code doesn't. So I guess I should use some special version of cmeps and cpl7.

If I used the older cmeps and cpl7, the model reported another error with machine definitions.

best,

Jinmu

 

[oleson]

I'm having trouble sorting this out, so apologies if my suggestions aren't making sense. But I don't think there are any versions of the externals that have fan_nh3_to_atm in them, I assume that is from the fan branch itself. So I wonder if the easiest thing to do is to modify the externals manually with the code that is associated with fan_nh3_to_atm on your fan branch? @slevis ?

 

[jinmuluo]

I'm having trouble sorting this out, so apologies if my suggestions aren't making sense. But I don't think there are any versions of the externals that have fan_nh3_to_atm in them, I assume that is from the fan branch itself. So I wonder if the easiest thing to do is to modify the externals manually with the code that is associated with fan_nh3_to_atm on your fan branch? @slevis ?

Hi,

Do you mean I should modify my branch manually? So that means I should first merge my code with dev164 then add the fan_nh3_to_atm to the cmeps and cpl7. But I am not sure if can I upload cmeps and cpl7 as source code to my github.

Best,

 

[jinmuluo]

I'm having trouble sorting this out, so apologies if my suggestions aren't making sense. But I don't think there are any versions of the externals that have fan_nh3_to_atm in them, I assume that is from the fan branch itself. So I wonder if the easiest thing to do is to modify the externals manually with the code that is associated with fan_nh3_to_atm on your fan branch? @slevis ?

Thank you for your suggestion, after I manually added the definitions into cmeps and cpl7, here is an error I met when I built my case. Could you help me take a look at it, I don't have any idea how to solve it. Thank you so much.

/glade/derecho/scratch/jinmuluo/DerechoTest/bld/cesm.bldlog.240118-042623

 

[oleson]

I don't recognize that error. However, I created the same case as yours using your code and it built successfully. I'm not sure what to say other than maybe clean the build completely (./case.build --clean-all) and try to build again. My case is here: /glade/work/oleson/FAN_runs/DerechoTest

 

[jinmuluo]

I don't recognize that error. However, I created the same case as yours using your code and it built successfully. I'm not sure what to say other than maybe clean the build completely (./case.build --clean-all) and try to build again. My case is here: /glade/work/oleson/FAN_runs/DerechoTest
Hi,

Thank you, I still met the same error even after I recreated my case.

 

[jinmuluo]

I don't recognize that error. However, I created the same case as yours using your code and it built successfully. I'm not sure what to say other than maybe clean the build completely (./case.build --clean-all) and try to build again. My case is here: /glade/work/oleson/FAN_runs/DerechoTest

I tried a global simulation, I can build the case and submit it. But I still have the error for the single site case,, don't know why.