Update miniconda3/4.12.0 module and regional_workflow environment on Cheyenne, Hera, Jet, Orion #431

natalie-perlin · 2022-10-25T21:47:26Z

DESCRIPTION OF CHANGES:

Update SRW modulefiles and use miniconda3/4.12.0 conda/python updated modules that have identical installations in EPIC-managed common space on the following HPC systems: Cheyenne, Hera, Orion, Jet. The installations are similar to that on Gaea, which has been already merged PR-352, PR-353. A regional_workflow virtual environment is installed under miniconda3 module and contains all the python packages needed to run the SRW and prepare basic plots.

Miniconda3/4.12.0 locations on the RDHPCs, with the regional_workflow environment created containing all the packages for running, plotting, and met verification.

Cheyenne:
module use /glade/work/epicufsrt/contrib/miniconda3/modulefiles
module load miniconda3/4.12.0
Hera:
module use /scratch1/NCEPDEV/nems/role.epic/miniconda3/modulefiles
module load miniconda3/4.12.0
Orion:
module use /work/noaa/epic-ps/role-epic-ps/miniconda3/modulefiles
module load miniconda3/4.12.0
Jet:
module use /mnt/lfs4/HFIP/hfv3gfs/role.epic/miniconda3/modulefiles
module load miniconda3/4.12.0

Earlier similar installation on Gaea; the repo changes have been already merged:
module use /lustre/f2/dev/role.epic/contrib/modulefiles
module load miniconda3/4.12.0

Type of change

New feature (non-breaking change which adds functionality)
This change requires a documentation update - Maybe to a minimal extent

TESTS CONDUCTED:

It is a part of a larger PR-419. The tests have been made as reported in PR-419, and additional successful tests have been run on Cheyenne.

DEPENDENCIES:

DOCUMENTATION:

ISSUE:

This PR is referenced in SRW-Issue-427

CHECKLIST

My code follows the style guidelines in the Contributor's Guide
I have performed a self-review of my own code using the Code Reviewer's Guide
I have commented my code, particularly in hard-to-understand areas
My changes may need updates to the documentation, to be determined.
My changes do not require updates to the documentation (explain).
My changes generate no new warnings. - Some new warnings in run-time log files appeared, such as BASH_SOURCE[1]: unbound variable . This was observed following recent PR merges.

LABELS (optional):

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remove loading of system python3

remove loading system python module

Load updated miniconda3 and ask to activate regional_workflow enviroment

Load an updated miniconda3 and ask to activate regional_workflow environment

Update miniconda3 module location and ask to activate regional_workflow

Update miniconda3/4.12.0 module location and ask to activate regional_workflow environment

Run an additional cycle of "conda deactivate" and "conda activate regional_workflow". It ensures that _python3_ binary path from the *regional_workflow* environment becomes prepended to the search $PATH, and is found first, before the _python3_ from miniconda3/4.12.0 from the *base* environment.

"conda activate regional_workfow"

…orkflow.lua use new miniconda3/4.12.0 with regional_workflow environment

all the requested packages for the python3 are found in regional_workflow environment

load updated miniconda3/4.12.0 with regional_workflow environment

Load an updated miniconda3/4.12.0 with the regional_workflow environment

danielabdi-noaa · 2022-10-25T22:39:33Z

modulefiles/wflow_cheyenne.lua

   LmodMsgRaw([===[Please do the following to activate conda:
-       > conda activate /glade/p/ral/jntp/UFS_SRW_app/conda/regional_workflow
+       > conda activate regional_workflow


Good to see Cheyenne is similar to other systems in this regard now! I think you would need to do the same in ush/load_modules_wflow.sh lines 63-69

-if [[ "${machine}" == 'cheyenne' ]]; then - conda activate /glade/p/ral/jntp/UFS_SRW_app/conda/regional_workflow -else - if [ ! -z $(command -v conda) ]; then - conda activate regional_workflow - fi +if [ ! -z $(command -v conda) ]; then + conda activate regional_workflow fi

danielabdi-noaa · 2022-10-25T22:42:19Z

ush/load_modules_run_task.sh

  conda activate ${SRW_ENV}
-  if [ $machine = "gaea" ]; then
+#  if [ $machine = "gaea" ]; then
     conda deactivate
     conda activate ${SRW_ENV}
-  fi
+#  fi


It looks like now you had to do the deactivate->activate process for all systems now -- we were hoping for the opposite with your PR! I guess it must be the transition from TCL to Lua of miniconda3 file epic installations that is causing this. Did you have to do this with your previous PR?

@natalie-perlin Looking at PR #419, I didn't see this modification. Is this required due to only using the new miniconda3 modules? @mark-a-potts has opened PR #428 to remove this logic, along with the conda deactivate and conda activate ${SRW_ENV}. It would be best to remove this, rather than make all machines require it. Would you be able to run tests of removing this logic and making similar changes that @mark-a-potts made for the Gaea local modulefiles in PR #428?

@danielabdi-noaa - this fix was temporary that we found would work on all systems. It is likely related to additional loads of miniconda3 in *.local.lua files if/when they are used. This module loading changes the binaries search $PATH once again. The use of *local.lua files may still need revisiting, checking the options now (@mark-a-potts does testing as well)

need to have miniconda3 loaded in build module

need to have miniconda3 loaded in the build module

need to have miniconda3 loaded in build module

need to have miniconda3 loaded in the build modulefile

need to have miniconda3 loaded in build modulefile

conda activate command same across the platforms

miniconda3 is now loaded in build_<system>_<compiler>, not in *.local files

natalie-perlin · 2022-10-31T23:13:31Z

The changes addressed in PR-444.

natalie-perlin · 2022-11-01T13:05:35Z

PR-444 (#444) merged into develop

natalie-perlin added 22 commits October 25, 2022 16:03

Update build_cheyenne_gnu.lua

790f87d

remove loading of system python3

Update build_cheyenne_intel.lua

eb1ceca

remove loading system python module

Update wflow_cheyenne.lua

2ccdc92

Load updated miniconda3 and ask to activate regional_workflow enviroment

Update wflow_hera.lua

5c7282c

Load an updated miniconda3 and ask to activate regional_workflow environment

Update wflow_jet.lua

01ed3ba

Update miniconda3 module location and ask to activate regional_workflow

Update wflow_orion.lua

3e535f1

Update miniconda3/4.12.0 module location and ask to activate regional_workflow environment

Update wflow_cheyenne.lua

ac4a2dd

"conda activate regional_workfow"

Update and rename conda_regional_workflow.lua to miniconda_regional_w…

9e47ee6

…orkflow.lua use new miniconda3/4.12.0 with regional_workflow environment

Update make_grid.local.lua

8b1aa08

Update get_extrn_ics.local.lua

d94c44c

Update get_extrn_lbcs.local.lua

67fe20e

Update make_ics.local.lua

5e62ff5

Update make_lbcs.local.lua

ada2e20

Update and rename make_orog.hardcoded.lua to make_orog.local.lua

7394e9f

Update run_fcst.local.lua

846e01b

Update run_vx.local.lua

4c94608

Create make_sfc_climo.local.lua

0e1b216

Update miniconda_regional_workflow.lua

4615ab9

Update get_obs.local.lua

05eb788

all the requested packages for the python3 are found in regional_workflow environment

Update miniconda_regional_workflow.lua

776de68

load updated miniconda3/4.12.0 with regional_workflow environment

Update miniconda_regional_workflow.lua

835d841

Load an updated miniconda3/4.12.0 with the regional_workflow environment

natalie-perlin requested review from mkavulich, gsketefian, JeffBeck-NOAA, RatkoVasic-NOAA, BenjaminBlake-NOAA, ywangwof, chan-hoo and panll as code owners October 25, 2022 21:47

natalie-perlin requested review from jkbk2004, willmayfield, dmwright526, gspetro-NOAA, EdwardSnyder-NOAA and MichaelLueken as code owners October 25, 2022 21:47

danielabdi-noaa reviewed Oct 25, 2022

View reviewed changes

MichaelLueken added enhancement New feature or request release This PR/issue is related to a release branch labels Oct 26, 2022

danielabdi-noaa mentioned this pull request Oct 26, 2022

fix for conda on gaea #428

Closed

21 tasks

ulmononian mentioned this pull request Oct 26, 2022

Update noaacloud module files #433

Closed

30 tasks

natalie-perlin added 13 commits October 27, 2022 06:49

Update build_cheyenne_gnu.lua

feb66bb

need to have miniconda3 loaded in build module

Update build_cheyenne_intel.lua

4d56e78

need to have miniconda3 loaded in the build module

Update build_gaea_intel.lua

9febdcb

need to have miniconda3 loaded in build module

Update build_hera_intel.lua

542f6b7

need to have miniconda3 loaded in build module

Update build_jet_intel.lua

d15f89f

need to have miniconda3 loaded in the build modulefile

Update build_orion_intel.lua

7545fb9

need to have miniconda3 loaded in build modulefile

Merge branch 'ufs-community:develop' into develop_miniconda3_update

07288d6

Update load_modules_wflow.sh

74b8420

conda activate command same across the platforms

Update miniconda_regional_workflow.lua

a974451

miniconda3 is now loaded in build_<system>_<compiler>, not in *.local files

Update miniconda_regional_workflow.lua

65c3704

miniconda3 is now loaded in build_<system>_<compiler>, not in *.local files

Update miniconda_regional_workflow.lua

4ea989a

miniconda3 is now loaded in build_<system>_<compiler>, not in *.local files

Update miniconda_regional_workflow.lua

1a3f26b

miniconda3 is now loaded in build_<system>_<compiler>, not in *.local files

Update miniconda_regional_workflow.lua

13ac404

panll approved these changes Oct 28, 2022

View reviewed changes

natalie-perlin closed this Nov 1, 2022

natalie-perlin mentioned this pull request Nov 9, 2022

Issues with new EPIC modulefiles #458

Closed

natalie-perlin deleted the develop_miniconda3_update branch October 13, 2023 03:59

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Update miniconda3/4.12.0 module and regional_workflow environment on Cheyenne, Hera, Jet, Orion #431

Update miniconda3/4.12.0 module and regional_workflow environment on Cheyenne, Hera, Jet, Orion #431

natalie-perlin commented Oct 25, 2022 •

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MichaelLueken Oct 26, 2022

natalie-perlin Oct 26, 2022

natalie-perlin commented Oct 31, 2022

natalie-perlin commented Nov 1, 2022

Update miniconda3/4.12.0 module and regional_workflow environment on Cheyenne, Hera, Jet, Orion #431

Update miniconda3/4.12.0 module and regional_workflow environment on Cheyenne, Hera, Jet, Orion #431

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natalie-perlin commented Oct 25, 2022 • edited Loading

DESCRIPTION OF CHANGES:

Type of change

TESTS CONDUCTED:

DEPENDENCIES:

DOCUMENTATION:

ISSUE:

CHECKLIST

LABELS (optional):

CONTRIBUTORS (optional):

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