I realized that myself and others probably misread this problem as needing to install libxml. But, it's the perl XML Lite code that needs to be installed. So Jim's suggestion at the start is the closest. But, it's a different library that is used. And if you load XML::Lite in your perl distribution, you might have version issues between that and the version we use in CTSM.
However, the library that is needed is part of cime. So the paths to find perl modules in build-namelist just has to be right to find it. In the list of paths in the error message at the top it includes this one:
/gpfs/fs0/scratch/y/yochen/xiaoshi/cesm/my_cesm_sandbox/cime/scripts/Tools/../../utils/perl5lib
That's where it expects to find a XML subdirectory with a Lite.pm perl module in it. If that path or file doesn't exist it shows an incompatibility between the cime version you have and what CTSM expects it should be.
So the problem really is getting a cime version that works with the CTSM version being used.
The expected path to where it is, has changed in cime, and hence the path in build-namelist has changed to coordinate with the cime version being used. Which means if you see this error -- you likely do NOT have a version of cime that corresponds with th, ce version that CTSM needs. So you 'll need to make sure you have a version of cime that will work with CTSM (and for a CESM or CAM checkout with the other components as well). This might just mean you need to update your submodules by running git-fleximod in the top level directory of your checkout (manage_externals for much older tags).
Simplest Solution
Your submodules might just not be updated to correspond to the tag you are using. For newer tags, you just run git-fleixmod to update them.
in the top level directory of your checkout:
Bash:
./bin/git-fleximod status
# If it shows that cime is out of date run
./bin/git-fleximod update
Mismatch of what CTSM needs and the version of cime used in your CESM or CAM checkout
If the above doesn't work -- because you are in a CESM or CAM checkout and CTSM needs a different version of cime. It'll take more work in figuring out what's compatible. Or you must have changes to CTSM that make the cime version incompatible with the cime version for that tag.
For newer tags, using git-fleximod, check the cime version that CTSM expects by looking at the cime setting of fxtag in the clm toplevel .gitmodules file. If you are in a CESM or CAM checkout it might be different than the .gitmodules file at the top level. Since, it can be difficult to get submodule versions that all work together, starting from a CESM, CAM, or CTSM tag is the best starting point. Then only change the submodules that you really need to.
For help in figuring out how to get submodules that work together. See this wiki page:
Help and Guidance for CESM Submodule Updates
Hopefully, this helps.
