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LMWG questions

J

jinmuluo

Jinmu Luo
Member
What version of the code are you using?
ctsm5.3.027-1-gf0199d7f0


Have you made any changes to files in the source tree?
I have developed a leaching module for this tag, and all checks and initial simulations have been passed, no error meet.


Describe your problem or question:

Hi @slevis

I want to clone a case to spin up and test the hist run of my leaching method, but I fail to clone your case

./create_clone --clone ~slevis/cases_LMWG_dev/ctsm53019_f09_BNF_AD/ --case $WORK/cases/ctsm53027_LEACHING_AD

ERROR: Missing cloneroot directory /glade/u/home/slevis/cases_LMWG_dev/ctsm53019_f09_BNF_AD

I have several other questions
(1) Should I use the parameter set 1-deg I-case spin-up and historical to test new CLM6 paramfile (ctsm53026_f09_BNF_[AD, SASU, pSASU, hist]) · Issue #91 · NCAR/LMWG_dev
(2) I have never cloned someone's case before, so I just want to check that ./create_clone only replicates the case setup, not the source code.
(3) Will told me that if I can't use SASU method, I should spin up my AD longer, so how long I should run this ad case?

Thank you!
 
slevis

slevis

Moderator
Staff member
@jinmuluo you may need read permission, so I did
chmod a+r -R ctsm53026_BNF_*
on my most recent cases. Now try
./create_clone --clone ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD/ --case $WORK/cases/ctsm53027_LEACHING_AD
1) The clone will pick up the same paramfile that i'm using. I think it's the same as in issue #91. You may as well use that since you're running a very recent version of the model.
2) Correct: it does NOT replicate my source code.
3) For AD without SASU we recommend at least 600 years. You can use tools/contrib/SpinupStability_BGC_v10.ncl to assess equilibrium status. To use it, I modify some lines in the script as necessary. Then I "module load ncl" and run ncl SpinupStability_BGC_v10.ncl.
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
@jinmuluo you may need read permission, so I did
chmod a+r -R ctsm53026_BNF_*
on my most recent cases. Now try
./create_clone --clone ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD/ --case $WORK/cases/ctsm53027_LEACHING_AD
1) The clone will pick up the same paramfile that i'm using. I think it's the same as in issue #91. You may as well use that since you're running a very recent version of the model.
2) Correct: it does NOT replicate my source code.
3) For AD without SASU we recommend at least 600 years. You can use tools/contrib/SpinupStability_BGC_v10.ncl to assess equilibrium status. To use it, I modify some lines in the script as necessary. Then I "module load ncl" and run ncl SpinupStability_BGC_v10.ncl.
Click to expand...
Sorry, the case clone command fails again. Did I miss anything important?


./create_clone --clone ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD/ --case $WORK/cases/ctsm53027_LEACHING_AD

ERROR: Missing cloneroot directory /glade/u/home/slevis/cases_LMWG_dev/ctsm53026_BNF_AD
 
slevis

slevis

Moderator
Staff member
I'm trying another change in permissions. I hope this takes care of it...
chmod a+x -R ctsm53026_BNF_*
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
I'm trying another change in permissions. I hope this takes care of it...
chmod a+x -R ctsm53026_BNF_*
Click to expand...
Sorry, I still can't clone the case, as the same error shows up again. I think I can't even access your account under the permission denied, maybe because I am outside of NCAR.
 
slevis

slevis

Moderator
Staff member
Strange, so you are not even able to see the contents of my directory when you type:
ls -l ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD

That was a question, but you won't be able to answer because I will update permissions one more level up from there, maybe that's the problem. Please try once more. We should be able to get this to work, even if it takes a few more iterations :-)
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
Strange, so you are not even able to see the contents of my directory when you type:
ls -l ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD

That was a question, but you won't be able to answer because I will update permissions one more level up from there, maybe that's the problem. Please try once more. We should be able to get this to work, even if it takes a few more iterations :-)
Click to expand...
Yes, I am not permitted to see anything under your account,

jinmuluo@derecho6:~> ls -l ~slevis/cases_LMWG_dev/ctsm53026_BNF_AD

ls: cannot access '/glade/u/home/slevis/cases_LMWG_dev/ctsm53026_BNF_AD': Permission denied

jinmuluo@derecho6:~> cd ~slevis

-bash: cd: /glade/u/home/slevis: Permission denied
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
@jinmuluo please try one more time. I tried this command:
setfacl -R -m u:jinmuluo:rX $HOME
Click to expand...
Hi Sam,

I have successfully cloned the case, /glade/work/jinmuluo/cases/ctsm53027_LEACHING_AD, and I guess this case is pointing to my source code ( /glade/u/home/jinmuluo/CTSM ). I only changed the REST_N=15 and kept other things untouched. If possible, could you please help me take a look at this case? Thanks!

Will gave several tips to run the spin-up, but I am not sure does these are important to my case.

Will:
You'll also need to initially set the model to do a :
ColdStart = True
continue_run = False
resubmit = lots

The code I added in CLM is not ready to run with SASU, I am wondering how to turn SASU off.


Thank you.
 
slevis

slevis

Moderator
Staff member
@jinmuluo
1) Looking at my user_nl_clm, you could remove the lines for isotopes to save computer time, unless you plan to look at c13 and/or c14 output.
2) Your env_run.xml seems correct. You can see where sasu can be set in the CLM_ACCELERATED_SPINUP setting (currently not set to sasu). Will also mentioned the CLM_FORCE_COLDSTART setting (currently set to ON).

...sorry for the delayed response. I usually look at these Forums on Mondays.
 
slevis

slevis

Moderator
Staff member
Typically after AD we run 1850 (or 1600 in your case?) for some time (say 100 yrs initially) to convince ourselves that our starting point is spun up. We use tools/contrib/SpinupStability_BGC_v10.ncl to assess equilibrium status. To use it, I modify some lines in the script as necessary. Then I "module load ncl" and run ncl SpinupStability_BGC_v10.ncl.

After that we proceed to the historical transient simulation.
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
Typically after AD we run 1850 (or 1600 in your case?) for some time (say 100 yrs initially) to convince ourselves that our starting point is spun up. We use tools/contrib/SpinupStability_BGC_v10.ncl to assess equilibrium status. To use it, I modify some lines in the script as necessary. Then I "module load ncl" and run ncl SpinupStability_BGC_v10.ncl.

After that we proceed to the historical transient simulation.
Click to expand...
Hi Sam

May I ask does this case "slevis/cases_LMWG_dev/ctsm53026_BNF_hist" works for my purpose?

thank you!
 
slevis

slevis

Moderator
Staff member
I think so. Notice in that directory that I have saved copies of env_run and user_nl_clm from various segments of the simulation.
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
I think so. Notice in that directory that I have saved copies of env_run and user_nl_clm from various segments of the simulation.
Click to expand...
Hi Sam,

By looking at the equilibrium summary below, I think I can just go with the historical run starting at 1850-2023? And is there any standard version output I can use to compare with my case?

best,


=======================================================================
(0) EQUILIBRIUM SUMMARY
(0) =======================================================================
(0) TOTECOSYSC is in equilibrium. Eq. Yr. = 162
(0) TOTSOMC is in equilibrium. Eq. Yr. = 102
(0) TOTVEGC is in equilibrium. Eq. Yr. = 62
(0) TLAI is in equilibrium. Eq. Yr. = 42
(0) GPP is in equilibrium. Eq. Yr. = 102
(0) TWS is in equilibrium. Eq. Yr. = 202
(0) H2OSNO is in equilibrium. Eq. Yr. = 182
(0) At least 97 percent of the land surface is in TOTECOSYSC equilibrium. Eq. Yr. = 302
(0) Percent of the land surface not in equilibrium ( 1.01% )
(0) Congratulations! Your simulation is in equilibrium
(0) =======================================================================
 
J

jinmuluo

Jinmu Luo
Member
slevis said:
I think so. Notice in that directory that I have saved copies of env_run and user_nl_clm from various segments of the simulation.
Click to expand...
And I have created a hybrid run which try to run from 1850 to 2010 in

/glade/work/jinmuluo/cases/ctsm53027_LEACHING_hist

does this case make sense to you? especially I specify the "RUN_REFDIR", "RUN_REFCASE", "RUN_REFDATE", and "CONTINUE_RUN"

best,

Jinmu
 
slevis

slevis

Moderator
Staff member
Sounds great. I will let you go ahead and test out your case, since you already compared it to mine. It will be excellent practice for you to troubleshoot if something doesn't work in the first few attempts. And don't worry, this happens to all of us :-)

You are using very recent code, so the only available comparison would be against my ctsm53026 case that you've been looking at.
 
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