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JMMP-Group / SEVERN-SWOT

Severn estuary 500m ocean model
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Tools/DOMAINcfg/src files don't download #15

Closed jpolton closed 3 years ago

jpolton commented 3 years ago

For some reason the src code for DOMAINcfg doesn't download but the src code for other tools does... lines 10-16 in https://github.com/JMMP-Group/SEVERN-SWOT/blob/master/SCRIPTS/make_tools.sh

jpolton commented 3 years ago

@mpayopayo I think that you've fixed this. Can you update the SCRIPTS & or Wiki and close this item if you are happy with it.

mpayopayo commented 3 years ago

yes will update it.

mpayopayo commented 3 years ago

@jpolton Michela @micdom is having the same issue and hence also problem to #1

jpolton commented 3 years ago

OK this is clearly a problem. @mpayopayo @micdom Can you describe here what you do (so I can efficiently attempt to replicate the problem)

mpayopayo commented 3 years ago

@jpolton I followed step by step the wiki and scripts. - I'll check again

If that was sorted, and I had all of the files, shouldn't those files also be cloned when cloning locally the full repository to make the tidal boundaries with git clone https://github.com/JMMP-Group/SEVERN-SWOT.git ? I've checked what I have locally, and

Shouldn't I have when cloning the other .F90 in src and the namelist_ref and xmlin\DOMAINcfg```?

micdom commented 3 years ago

same as @mpayopayo, I followed step by step the wiki and scripts in this order: make_paths.sh make_directories.sh make_xios.sh make_nemo.sh make_tools.sh make_coordinates_from_parent_Severn.sh make_bathymetry_from_gebco.sh all perfectly fine up to here make_domain_cfg.sh fails because the domain_cfg_000*.nc have not been created.

I've also checked and in /BUILD_EXE/NEMO/4.0.6/tools/DOMAINcfg/src the only file is domzgr.f90.melange and domzgr.f90 in /BUILD_EXE/NEMO/4.0.6/tools/DOMAINcfg/ I have no namelist_ref or *xml

mpayopayo commented 3 years ago

checked quickly make_tools.sh from https://github.com/NOC-MSM/NEMO-RELOC/blob/master/SCRIPTS/make_tools.sh L33-L38:

  cd $NEMO/tools
  ./maketools -m X86_ARCHER2-Cray -n NESTING
  ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO
  ./maketools -m X86_ARCHER2-Cray -n WEIGHTS
  ./maketools -m X86_ARCHER2-Cray -n DOMAINcfg

make_tools.sh in https://github.com/JMMP-Group/SEVERN-SWOT/blob/master/SCRIPTS/make_tools.sh has L33 to L39:

  cd $NEMO/tools
  ./maketools -m X86_ARCHER2-Cray -n NESTING
  ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO
  ./maketools -m X86_ARCHER2-Cray -n WEIGHTS
  ./maketools -m X86_ARCHER2-Cray -n DOMAINcfg
  ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO

Could the problem be that extra L39 ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO? because the svn is the same in both

Other option can be different modules that Chris Wilson suggested on MSM meeting

micdom commented 3 years ago

I have just re-run the make_tools.sh and I have noticed now that the command ./maketools -m X86_ARCHER2-Cray -n DOMAINcfg actually fails.

I don't understand why the code doesn't get downloaded in /BUILD_EXE/NEMO/4.0.6/tools/DOMAINcfg/src.

mpayopayo commented 3 years ago

@micdom, yes, I was having that https://github.com/JMMP-Group/SEVERN-SWOT/issues/1 I think s because it doesn't have the .f90 files

jpolton commented 3 years ago

@mpayopayo @micdom together I think we have isolated the problem, which I have been able to resolve. The src/ files in DOMAINcfg didn't "svn checkout" because the directory already existed within the "git clone". Somehow the domzgr.f90.melange file got put into $NEMO/4.0.6/tools/DOMAINcfg/src/ in the repo. So when it came to check it out it was already there. domzgr.f90.melange should only have been in BUILD_CFG/DOMAIN/ ready for copying into ''$NEMO/4.0.6/tools/DOMAINcfg/src/'' after the checkout.

To fix the problem:

cd /work/n01/n01/$USER/SEVERN-SWOT
git pull # to get the repo updates
rm -rf $NEMO/4.0.6 # to purge all the messed up bits
cd SCRIPTS
. ./make_nemo.sh
. ./make_tools.sh

The nice thing about 'git' is that you can look through the history and detect that rogue user @jpolton introduced the spurious file...

micdom commented 3 years ago

@jpolton @mpayopayo it works, problem solved. minor issues: do we need repeating twice ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO in make_tools.sh? also, there is a need for a waiting command after the sbatch command in make_domain_cfg.sh, otherwise the rebuild starts (and it fails) before the end of the domain creating job.

jpolton commented 3 years ago

@jpolton @mpayopayo it works, problem solved. minor issues: do we need repeating twice ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO in make_tools.sh? also, there is a need for a waiting command after the sbatch command in make_domain_cfg.sh, otherwise the rebuild starts (and it fails) before the end of the domain creating job.

@micdom 1) We do not need twice ./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO. Have a go at editing the file to fix that (if you are unfamiliar with git the easiest way to start is through the web browser).

2) You are right again that we do need a wait function. Alternatively I was thinking about maybe adding the rebuild command to the batch script. My naive attempt to do that failed. I think because of the rebuilding command works on a single thread whereas the create_domain.slurm script does not. If you have any good ideas how to do this then please have a go and share.

jpolton commented 3 years ago

@micdom @mpayopayo My guess is that we can close this issue now. Reopen it if you disagree. We can create new tickets for new issues.