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Final updates of develop from release 1.9.3 #1790
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eba995d
Update .gitmodules and submodule pointer for spack for code review an…
climbfuji 4978c6c
Update configs/** from release/1.9.0
climbfuji 50554bc
Revert .gitmodules and update submodule pointer for spack
climbfuji f29dbd5
Update .gitmodules and submodule pointer for spack for code review an…
climbfuji 5245b1b
Revert .gitmodules and update submodule pointer for spack
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -324,6 +324,7 @@ packages: | |
| wgrib2: | ||
| require: | ||
| - '@3.6.0' | ||
| - '+ipolates +netcdf' | ||
| wrf-io: | ||
| require: '@1.2.0' | ||
| zstd: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,49 +1,131 @@ | ||
| # How to build spack-stack at NAS | ||
|
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| ## Generic | ||
| In the commands below some will be run on login nodes (with internet access) and some | ||
| on compute nodes as, at NAS, you aren't allowed more than 2 processes on a login node. | ||
|
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| ## Clone spack-stack | ||
|
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| ``` | ||
| git clone --recursive https://github.com/JCSDA/spack-stack.git -b release/1.9.0 spack-stack-1.9.3 | ||
| ``` | ||
|
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| ## Grab interactive node | ||
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| Since NAS limits you to 2 processes on a login node, you'll need to grab an interactive node. For example: | ||
| ``` | ||
| git clone --recursive https://github.com/JCSDA/spack-stack.git -b release/1.9.0 spack-stack-1.9.1 | ||
| qsub -I -V -X -l select=1:ncpus=128:mpiprocs=128:model=mil_ait -l walltime=12:00:00 -W group_list=s1873 -m b -N Interactive | ||
| ``` | ||
| will get you a Milan node for 12 hours | ||
|
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||
| ## Setup spack-stack on each node | ||
|
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||
| ## oneapi | ||
| We will start on a login node with internet access. This is mainly needed for the | ||
| `spack mirror create` command which downloads all the source code for the packages. | ||
|
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||
| ``` | ||
| cd spack-stack-1.9.1 | ||
| cd spack-stack-1.9.3 | ||
| . setup.sh | ||
| spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler oneapi | ||
| cd envs/ue-oneapi-2024.2.0 | ||
| spack env activate . | ||
| spack concretize 2>&1 | tee log.concretize | ||
| spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install | ||
| ``` | ||
|
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||
| NOTE: You might need to run the `spack install` command multiple times because sometimes | ||
| it just fails. But then you run it more and more and it will eventually succeed. | ||
| ## Create environments | ||
|
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| We create two different environments, one for oneAPI and one for GCC. The commands below | ||
| are used to create the environments. You only need to do this once. | ||
|
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| ### oneAPI | ||
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| To create the oneAPI environment, do: | ||
|
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| ``` | ||
| spack module tcl refresh -y | ||
| spack stack setup-meta-modules | ||
| spack env deactivate | ||
| spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler oneapi | ||
| cd envs/ue-oneapi-2024.2.0 | ||
| ``` | ||
|
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| ## gcc | ||
| ### GCC | ||
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| To create the GCC environment, do: | ||
|
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| ``` | ||
| cd spack-stack-1.9.1 | ||
| . setup.sh | ||
| spack stack create env --name ue-gcc-12.3.0 --template unified-dev --site nas --compiler gcc | ||
| cd envs/ue-gcc-12.3.0 | ||
| ``` | ||
|
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| ## Activate environment | ||
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| Now enter the spack environment you just created: | ||
|
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| ``` | ||
| spack env activate . | ||
| ``` | ||
|
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| NOTE: You need to make sure you do this in *any* terminal where you want to do any commmand | ||
| below with this environment. | ||
|
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| ## Concretize and create source cache | ||
|
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| ``` | ||
| spack concretize 2>&1 | tee log.concretize | ||
| spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install | ||
| ``` | ||
|
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| ## Create source cache (LOGIN NODE ONLY) | ||
|
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| Because this step downloads all the source code for all packages and all versions, it | ||
| should be done on a login node with internet access. | ||
|
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| ``` | ||
| spack mirror create -a -d /nobackup/gmao_SIteam/spack-stack/source-cache | ||
| ``` | ||
|
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| NOTE: Make sure you are in an environment when you run that `spack mirror create` command. Otherwise, | ||
| you will download *EVERY* package and *EVERY* version in spack! | ||
|
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| ## Install packages | ||
|
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| Our install process will actually have (at least) three steps. This is because of the `crtm` package | ||
| which requires internet access at build time. | ||
|
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| ### Install crtm dependencies (COMPUTE NODE) | ||
|
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| ``` | ||
| spack install -j 10 --verbose --fail-fast --show-log-on-error --no-check-signature --only dependencies crtm 2>&1 | tee log.install.crtm_dependencies | ||
| ``` | ||
|
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| ### Install crtm (LOGIN NODE) | ||
|
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| ``` | ||
| spack install -j 2 --verbose --fail-fast --show-log-on-error --no-check-signature crtm 2>&1 | tee log.install.crtm | ||
| ``` | ||
|
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| Note we are only using 2 processes here because NAS limits you to 2 processes on a login node. | ||
|
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| ### Install rest of packages (COMPUTE NODE) | ||
|
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| ``` | ||
| spack install -j 10 --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install.after_crtm | ||
| ``` | ||
|
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| NOTE: You might need to run the `spack install` command multiple times because sometimes | ||
| it just fails. But then you run it more and more and it will eventually succeed. | ||
|
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| ### Packages needing internet access to build | ||
|
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| If you encounter other packages that need internet access to build, you can install them with: | ||
|
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| ``` | ||
| spack install -j 2 --verbose --fail-fast --show-log-on-error --no-check-signature <package> |& tee log.install.<package> | ||
| ``` | ||
|
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| Then, once that package is built, you can go back to the compute node and run the `spack install` command again. | ||
|
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| ## Update module files and setup meta-modules | ||
|
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| ``` | ||
| spack module tcl refresh -y | ||
| spack stack setup-meta-modules | ||
| ``` | ||
|
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| ## Deactivate environment | ||
|
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| ``` | ||
| spack env deactivate | ||
| ``` |
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While building
wgrib2this way "works" (see: JCSDA/spack#561),wgrib2/package.pyought to be properly fixed.There was a problem hiding this comment.
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Good point, see the CI failure: https://github.com/JCSDA/spack-stack/actions/runs/18286538992/job/52062910954
@AlexanderRichert-NOAA @rickgrubin-noaa What is the permanent fix? Will that be made for spack-packages only i.e. do we bring over the temporary fix from the spack submodule release/1.9.0 branch for the time being?
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@rickgrubin-noaa I've decided to pull in your temporary fix for the reasons stated in JCSDA/spack#568. I assume this hasn't been fixed yet in the new spack-packages repo?
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This has not been fixed in the new
spack-packagesrepo.As far as I can tell (and @AlexanderRichert-NOAA certainly understand better than I), the temporary fix implemented for
v3.6.0isn't necessarily applicable for other, earlier versions. I have not looked into it further.