adds cron scripts for nightly tests by grnydawn · Pull Request #482 · E3SM-Project/polaris

grnydawn · 2026-03-05T16:46:16Z

This PR adds cron scripts to Polaris for running nightly Omega and Polaris tests, and initiates discussion regarding this feature.

xylar

@grnydawn, this looks reasonable to me. It's a lot to review, so all I did for now is a fairly quick skim. But I'm happy to be involved in updating and maintaining this infrastructure. I'm sure I'll get to know it better in that way.

xylar · 2026-03-09T14:38:44Z

One more thing. Polaris has its own linting tools. See https://docs.e3sm.org/polaris/main/developers_guide/quick_start.html#code-style-for-polaris.

I'd prefer that we lint the files added here. This would involve creating a polaris development environment and making a small edit to each file (e.g. adding white space) and then letting the linter do its thing.

If need be, we could leave these files out of the lint checking, but I would prefer not to.

Would you like me to take care of the linting?

xylar · 2026-03-10T11:42:03Z

@grnydawn, here is a commit you could cherry-pick if you want to fix most (maybe all?) of the linting issues:
xylar@65a55ab
If you make me a collaborator on your fork, I can push this to your branch.

cbegeman · 2026-03-11T18:12:41Z

cron-scripts/README.md

+
+## Overview
+
+This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:


Suggested change

This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:

This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two types of OMEGA tests:

cbegeman · 2026-03-11T18:12:58Z

cron-scripts/README.md

+
+This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:
+
+- **Omega** - Next-generation ocean model


Suggested change

- **Omega** - Next-generation ocean model

- **Omega CTests**

cbegeman · 2026-03-11T18:13:42Z

cron-scripts/README.md

+This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:
+
+- **Omega** - Next-generation ocean model
+- **Polaris** - MPAS-Ocean model with Omega integration


Suggested change

- **Polaris** - MPAS-Ocean model with Omega integration

- **Polaris** - Omega tests on MPAS meshes```

cbegeman · 2026-03-11T19:30:09Z

cron-scripts/machines/config_chrysalis.sh

+
+source /etc/bashrc
+
+export CRONJOB_BASEDIR=/lcrc/globalscratch/ac.kimy/cronjobs


Suggested change

export CRONJOB_BASEDIR=/lcrc/globalscratch/ac.kimy/cronjobs

export CRONJOB_BASEDIR=/lcrc/globalscratch/${USER}/cronjobs

implemented.

cbegeman · 2026-03-11T19:31:08Z

cron-scripts/machines/config_frontier.sh

+export https_proxy=http://proxy.ccs.ornl.gov:3128/
+export no_proxy='localhost,127.0.0.0/8,*.ccs.ornl.gov'
+
+export CRONJOB_BASEDIR=/lustre/orion/cli115/scratch/grnydawn/cronjobs


Suggested change

export CRONJOB_BASEDIR=/lustre/orion/cli115/scratch/grnydawn/cronjobs

export CRONJOB_BASEDIR=/lustre/orion/cli115/scratch/${USER}/cronjobs

implemented.

cbegeman · 2026-03-11T19:33:05Z

cron-scripts/machines/config_pm-cpu.sh

+
+module load cray-python cmake
+
+export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-cpu


Suggested change

export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-cpu

export CRONJOB_BASEDIR=/pscratch/sd/${USER:0:1}/${USER}/omega/cronjobs_pm-cpu

implemented.

cbegeman · 2026-03-11T19:33:20Z

cron-scripts/machines/config_pm-gpu.sh

+
+module load cray-python cmake
+
+export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-gpu


Suggested change

export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-gpu

export CRONJOB_BASEDIR=/pscratch/sd/${USER:0:1}/${USER}/omega/cronjobs_pm-gpu

implemented.

cbegeman · 2026-03-11T19:41:32Z

cron-scripts/tasks/omega_cdash/job_frontier_omega_cdash.sbatch

+#!/bin/bash -l
+#SBATCH  --nodes=1
+#SBATCH  -q debug
+#SBATCH  --account=cli115


Should we get account from a place that's common with that used to generate polaris job scripts, currentlypolaris/machines/*.cfg option parallel/account?

@cbegeman , I think it would be better to get the account from a common place. Do any of the polaris/machines/*.cfg files have a parallel/account entry? I couldn’t find any account information in those files. While I do see a group entry in the cfg files, some values of group do not match the actual account name—for example, e3sm_g on PM-GPU.

It looks like they don't but they could/should, e.g.,

polaris/polaris/job/__init__.py

Line 76 in 1981a58

if config.has_option('parallel', 'account'):

cbegeman · 2026-03-11T19:47:08Z

cron-scripts/tasks/omega_cdash/job_chrysalis_omega_cdash.sbatch

+if [[ "$CRONJOB_MACHINE" == "chrysalis" ]]; then
+    module load python cmake
+    PARMETIS_TPL="/lcrc/soft/climate/polaris/chrysalis/spack/dev_polaris_0_10_0_COMPILER_openmpi/var/spack/environments/dev_polaris_0_10_0_COMPILER_openmpi/.spack-env/view"
+
+elif [[ "$CRONJOB_MACHINE" == "frontier" ]]; then
+    module load cray-python cmake git-lfs
+	PARMETIS_TPL="/ccs/proj/cli115/software/polaris/frontier/spack/dev_polaris_0_10_0_COMPILER_mpich/var/spack/environments/dev_polaris_0_10_0_COMPILER_mpich/.spack-env/view"
+
+elif [[ "$CRONJOB_MACHINE" == "unknown" ]]; then
+  echo "CRONJOB_MACHINE is not set."
+  exit -1
+
+else
+  echo "It seems that the cron job is not configured with CRONJOB_MACHINE."
+  exit -1
+
+fi


Since we already have some logic here for different machines, it would be good to pull out the pieces that are common to each job*.sbatch file to a single file for ease of maintenance

implemented.

cbegeman · 2026-03-11T19:57:18Z

cron-scripts/tasks/polaris_cdash/launch_polaris_ctest.sh

+POLARIS_CDASH_BASEDIR=${CRONJOB_BASEDIR}/tasks/polaris_cdash
+POLARIS_CDASH_TESTDIR="${POLARIS_CDASH_BASEDIR}/tests"
+OMEGA_HOME="${POLARIS_CDASH_BASEDIR}/polaris/e3sm_submodules/Omega"
+MINIFORGE3_HOME="${POLARIS_CDASH_BASEDIR}/miniforge3"


Can we make this a command-line argument to launch_all.sh so we can use an existing miniforge install?

@xylar Does this need to be changed to pixi?

Is it preferable to test the latest Polaris with a nightly Cronjob? Originally, I thought of using the Polaris code base that contains the cron-scripts sub-directory, but I realized that the repo might not be up to date. I probably still need to clone or update it to ensure I am using the latest version.

Sorry, I'm not understanding your question. When we merge this PR, the polaris code base would include the cron-scripts directory. So maybe the answer is yes, clone/update polaris nightly to use the latest main

Sorry for the confusion. To run the nightly tests, crontab should execute the launch_all.sh script every day. Since all files under the cron-scripts folder, including launch_all.sh, are part of the Polaris repository, we may need to update the Polaris repository to the latest version before running launch_all.sh.

Ah, I see. I guess that's the downside of having cron-scripts in polaris.

cbegeman · 2026-03-11T20:12:32Z

In order to use launch_all.sh, I needed cd ${source_path} here

polaris/configure_polaris_envs.py

Line 150 in c59cd32

print('Creating the polaris conda environment\n')

, otherwise the error is:

FileNotFoundError: [Errno 2] No such file or directory: '/pscratch/sd/c/cbegeman/polaris-repos/cron-scripts/cron-scripts/deploy/unsupported.txt'

because it's trying to run the command from wherever I executed launch_all.sh

cbegeman · 2026-03-11T21:41:48Z

I get the following error when I attempt to launch_all.sh -m pm-cpu

--------------------------------------------------------------------------------
Building Omega (dev) with gnu in /pscratch/sd/c/cbegeman/omega/cronjobs_pm-cpu/tasks/polaris_cdash/tests/gnu/omega_build
--------------------------------------------------------------------------------
...
-- Caching compiler settings in /pscratch/sd/c/cbegeman/omega/cronjobs_pm-cpu/tasks/polaris_cdash/tests/gnu/omega_build/SCORPIO_CMakeCache.txt...
...
CMake Error at /pscratch/sd/c/cbegeman/omega/cronjobs_pm-cpu/tasks/polaris_cdash/polaris/e3sm_submodules/Omega/externals/scorpio/cmake/SPIOTypeUtils.cmake:223 (message):
  Could not find a type for representing PIO Offsets
Call Stack (most recent call first):
  /pscratch/sd/c/cbegeman/omega/cronjobs_pm-cpu/tasks/polaris_cdash/polaris/e3sm_submodules/Omega/externals/scorpio/src/clib/CMakeLists.txt:287 (get_pio_offset_type)


-- Configuring incomplete, errors occurred!

grnydawn · 2026-03-26T14:32:44Z

@cbegeman Thanks for the review. All the suggestions make sense to me. Since the error you noted above appears to be related to Phil’s recent PR (E3SM-Project/Omega#362), I’ll review the Phil's PR and let it be merged into Omega first, then update the branch for this PR.

grnydawn · 2026-04-01T14:07:15Z

@cbegeman , I have run the omega_nightly test suite on Chrysalis and PM-CPU using the latest Polaris, and all tests passed. The test results from PM-GPU include only two test tasks, which I believe is a separate issue related to slow Slurm jobs on PM-GPU. Interestingly, all tests passed on Chrysalis and PM-CPU both with and without Phil’s recent PR (E3SM-Project/Omega#362). I’m wondering if you are still seeing the issue you reported above.

grnydawn · 2026-04-01T14:21:17Z

@cbegeman , @xylar , I was trying to implement Carolyn’s suggestion, but I realized that she has pushed several commits to this PR. I’m wondering what the best way is to proceed with incorporating those changes using Git. I tried to pull the commits, but it didn’t work.

xylar · 2026-04-01T14:36:53Z

I was trying to implement Carolyn’s suggestion, but I realized that she has pushed several commits to this PR. I’m wondering what the best way is to proceed with incorporating those changes using Git. I tried to pull the commits, but it didn’t work.

It sounds like you have both local changes and those on the remote branch. In such circumstances, you should fetch the remote branch:

git fetch --all -p

and then rebase your local branch onto the remote one, e.g.:

git rebase --interactive grnydawn/ykim/cron-scripts

You may then end up with merge conflicts you need to resolve in the usual way.

xylar added the cron Related to cron jobs (nightly testing) label Mar 5, 2026

xylar self-assigned this Mar 5, 2026

xylar requested review from cbegeman and xylar March 5, 2026 16:58

xylar approved these changes Mar 9, 2026

View reviewed changes

cbegeman reviewed Mar 11, 2026

View reviewed changes

grnydawn and others added 6 commits March 16, 2026 09:02

adds cron scripts for nightly tests

760ff9a

fix a bug of using old omega_pr instead of omega_nightly suite name

e0b6827

Lint code

bebd6c1

factor omega cdash logic into shared driver

b6c1ba0

Use shared omega cdash driver

0666164

Use USER env variable for paths

c12641d

xylar force-pushed the ykim/cron-scripts branch from 65a55ab to c12641d Compare March 16, 2026 17:03

grnydawn and others added 3 commits April 7, 2026 14:16

Merge branch 'E3SM-Project:main' into ykim/cron-scripts

9d683ae

updates README

d4e4c1e

updtes tasks for being launched as a part of polaris

86fee0e


		## Overview

		This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:


		This repository orchestrates the compilation, testing, and result submission to [CDash](https://my.cdash.org) for two major OMEGA ocean model components:

		- Omega - Next-generation ocean model

	- Polaris - MPAS-Ocean model with Omega integration
	- Polaris - Omega tests on MPAS meshes```


		source /etc/bashrc

		export CRONJOB_BASEDIR=/lcrc/globalscratch/ac.kimy/cronjobs

	export CRONJOB_BASEDIR=/lustre/orion/cli115/scratch/grnydawn/cronjobs
	export CRONJOB_BASEDIR=/lustre/orion/cli115/scratch/${USER}/cronjobs


		module load cray-python cmake

		export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-cpu

	export CRONJOB_BASEDIR=/pscratch/sd/y/youngsun/omega/cronjobs_pm-cpu
	export CRONJOB_BASEDIR=/pscratch/sd/${USER:0:1}/${USER}/omega/cronjobs_pm-cpu

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