LMWG questions

[jinmuluo]

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]

@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.

 

[jinmuluo]

@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.

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]

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

 

[jinmuluo]

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

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]

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 :-)

 

[jinmuluo]

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 :-)

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