create_clone Permission Denied

[katiemurenbeeld@u_boisestate_edu]

Hi All,

Background:
machine = Cheyenne
ctsm = ctsm1.0.dev102
manage_externals =
./cime
clean sandbox, on branch_tags/cime5.8.24_a01
./cime/src/drivers/nuopc/
clean sandbox, on 386e1631a6a1e1900700c3a04d693df8692c9420
./cime/src/drivers/nuopc/nems/lib/ParallelIO
clean sandbox, on pio2_4_4
./cime/src/drivers/nuopc/nems/lib/genf90
clean sandbox, on genf90_140121
./components/cism
clean sandbox, on cism2_1_68
./components/cism/source_cism
clean sandbox, on 9f57475aadf2d807b97b9c20f53e6ddc6daf0dfb
./components/mosart
clean sandbox, on mosart1_0_36
./components/rtm
clean sandbox, on rtm1_0_71
./src/fates
clean sandbox, on sci.1.30.0_api.8.0.0
./tools/PTCLM
clean sandbox, on PTCLM2_20200121

I am trying to clone two cases from a colleague of mine. This case is a spin up that I would like to rerun and use the restart files for future runs. I've had trouble completing a spin up myself for the CONUS NLDAS resolution and compset, and this case to clone is a successfully completed spin up. I used the following command:

/glade/work/katiem/git/ctsm_sits/cime/scripts> ./create_clone --case /glade/work/katiem/SITS_cases/cnash_spinup_p1c1_001 --clone /glade/work/cnash/cases_ctsm/spinup_p1c1_001 --cime-output-root /glade/scratch/katiem/

However, I am receiving this error:
ERROR: Command: '/glade/work/katiem/miniconda3/bin/xmllint --format --output /glade/work/cnash/cases_ctsm/spinup_p1c1_001/env_workflow.xml -' failed with error 'I/O error : Permission denied
I/O error : Permission denied' from dir '/glade/work/katiem/git/ctsm_sits/cime/scripts'

I did find this issue on github Add --cime-output-root option to create_clone and mention it's use if can't write to it · Issue #1020 · ESMCI/cime so I thought that by adding the --cime-output-root I would be able to clone.

The case I am trying to clone was created ~10 months ago and so was created using different versions of cime, etc.

Any help is greatly appreciated!

Cheers,
Katie

PS: For the older case I want to clone
machine = cheyenne
ctsm = ctsm1.0.dev068-1-g6ba8f156
manage_externals =
./cime
clean sandbox, on branch_tags/cime5.8.3_chint17-05
./components/cism
clean sandbox, on cism2_1_68
./components/cism/source_cism
clean sandbox, on 9f57475aadf2d807b97b9c20f53e6ddc6daf0dfb
./components/mosart
clean sandbox, on mosart1_0_33
./components/rtm
clean sandbox, on rtm1_0_68
./src/fates
clean sandbox, on fates_s1.8.1_a3.0.0_rev2
./tools/PTCLM
clean sandbox, on PTCLM2_180611

 

[dbailey]

So, is the error generated on the create_clone step? Or is it happening when you are doing the xmllint? You have the following on your xmllint statement:

/glade/work/katiem/miniconda3/bin/xmllint --format --output /glade/work/cnash/cases_ctsm/spinup_p1c1_001/env_workflow.xml

You don't have permission to write to cnash case directory.