Merge geomar branch with neat new features by seb-wahl · Pull Request #1443 · esm-tools/esm_tools

seb-wahl · 2026-02-16T14:10:20Z

This PR finally brings GEOMAR's contributions to ESM-Tools back into release. It will allow the release branch of ESM-Tools to correctly handle

the latest settings from FOCIOIFS-5.0 (OIFS48r1 with NEMO5, without (working) and with (WIP) nest, used in WHIRLS project)
the latest settings used in FOCI-MOZ (FOCI with interactive stratospheric chemistry in ECHAM6, used in SOLVe project)
the latest settings used in the RESCUE project (modified ECHAM6 and JSBACH (12 tiles))
A draft version of ICON-FESOM that compiles and runs under piControl conditions (tuning ongoing)

compiles and starts, but misses (as expected) information in existing JSBACH restart files. Cold start not yet implemented

links all currently known files correctly running not yet tested as info from Shradda is still missing

draft version of ECHAM76-LMU that start up correctly but still fails due to land sea mask mismatch

fixed restart setup in a hacky way (see foci.yaml) added a new runscript for FOCIOIFS

…geomar_dev exludes the conflicting oasis.py

This should be the only difference between geomar_dev and release that matters

…on glogin

allow different streams for restart and output for ECHAM and JSBACH

with FOCI-MOPS with the 12 tile edition

merge geomar dev into geomar branch

separate echam6 namlist templates for foci and foci_lmu

before merging this branch into geomar_dev differences where too large for an efficient direct merge

…ration

…nd for file naming

example runscript (foci-default) on how to use input from lustre-rzg on Emmy p3

This reverts commit a92860b.

made the new namelists default for an oasismct4_mops based setup

adds dask stuff, moves post run commands to computer section

configs/components/echam/echam.yaml

configs/components/jsbach/jsbach.yaml

mandresm

First round of minor requests and questions :)

mandresm · 2026-02-18T13:37:11Z

configs/components/oasis3mct/oasis3mct.env.yaml

+                                        CFLAGS: '"-fPIC"'
+                                        CCFLAGS: '"-fPIC"'
+                                        FFLAGS: '"-fPIC"'
+                                        FCFLAGS: '"-fPIC"'


Suggested change

CFLAGS: '"-fPIC"'

CCFLAGS: '"-fPIC"'

FFLAGS: '"-fPIC"'

FCFLAGS: '"-fPIC"'

This can be deleted as it's already defined as a default

mandresm · 2026-02-18T13:44:13Z

configs/components/oifs/oifs.yaml

+            input:
+                all_directions: copy


Suggested change

input:

all_directions: copy

Consider removing this as it is already defined in the defaults as copy

configs/components/oifs/oifs.yaml

mandresm · 2026-02-19T07:30:05Z

configs/components/echam/echam.yaml

    streams:
            - echam
            - accw
            - co2
            - g3bid
            - g3bim
            - g3bday
            - g3b1hi
            - glday
            - aclcim
            - sp6h
            - glim
            - spim
            - ism

+    restartstreams:
+            - echam
+            - accw
+            - co2
+            - g3bid
+            - g3bim
+            - g3bday
+            - g3b1hi
+            - glday
+            - aclcim
+            - sp6h
+            - glim
+            - spim
+            - ism
+


Hi @christian-stepanek, @chrisdane, @PengyangSong and @ackerlar,

In this PR we are merging efforts from GEOMAR team into release. This is important because it will make the whole thing more maintainable for them as well as for us (and because they have put quite some work to add ICON-FESOM ;) ). Before the PR is merged we will check that no model behavior is affected (as we usually do).

However, here is a change in how things are done in ECHAM until now, and I want to get your approval and keep you in the loop. In the past the list of streams, referenced above, was used both to compute the name of the output files and the restart files. However, it might be the case that some times some streams have restarts but do not have outputs, or the other way around. What @seb-wahl did here (and in the rest of the file) was to duplicate the the list of streams into a new list restartstreams and use the second one for all the operations that affect restart files. That does NOT lead to any change in behavior as the 2 lists are identical by default. However, this allows you to add new streams from your runscript to either streams or restartstreams so you can now you could have control of output and restarts independently if you need to.

If you are okay with this change please give a thumbs up to this message, if you have concerns please reply :)

@chrisdane, since you work with streams quite a bit and modify them, can you answer to this?

mandresm

Reviews, comments and todos after the merge party

configs/components/oifs/oifs43.env.yaml

mandresm · 2026-02-19T08:28:55Z

configs/components/rnfmap/rnfmap.env.yaml

+       #add_export_vars:
+        # oasis
+        #OIFS_OASIS_BASE: '$(pwd)/oasis'
+        #OIFS_OASIS_INCLUDE: '"-I$OIFS_OASIS_BASE/build/lib/psmile -I$OIFS_OASIS_BASE/build/lib/psmile/scrip -I$OIFS_OASIS_BASE/build/lib/psmile/mct -I$OIFS_OASIS_BASE/build/lib/psmile/mct/mpeu"'
+        #OIFS_OASIS_LIB: '"-L$OIFS_OASIS_BASE/build/lib/psmile -L$OIFS_OASIS_BASE/build/lib/psmile/scrip -L$OIFS_OASIS_BASE/build/lib/psmile/mct -L$OIFS_OASIS_BASE/build/lib/psmile/mct/mpeu -lpsmile -lmct -lmpeu -lscrip"'
+      # NetCDF
+      #OIFS_NETCDF_INCLUDE: '-I$NETCDFROOT/include'
+      #OIFS_NETCDF_LIB: '"-L$NETCDF_DIR/lib -lnetcdf"'
+      #OIFS_NETCDFF_INCLUDE: '-I$NETCDFFROOT/include'
+      #OIFS_NETCDFF_LIB: '"-L$NETCDFFROOT/lib -lnetcdff"'
+      # compiler and compiler flags
+      #OIFS_FC: $FC
+


Suggested change

#add_export_vars:

# oasis

#OIFS_OASIS_BASE: '$(pwd)/oasis'

#OIFS_OASIS_INCLUDE: '"-I$OIFS_OASIS_BASE/build/lib/psmile -I$OIFS_OASIS_BASE/build/lib/psmile/scrip -I$OIFS_OASIS_BASE/build/lib/psmile/mct -I$OIFS_OASIS_BASE/build/lib/psmile/mct/mpeu"'

#OIFS_OASIS_LIB: '"-L$OIFS_OASIS_BASE/build/lib/psmile -L$OIFS_OASIS_BASE/build/lib/psmile/scrip -L$OIFS_OASIS_BASE/build/lib/psmile/mct -L$OIFS_OASIS_BASE/build/lib/psmile/mct/mpeu -lpsmile -lmct -lmpeu -lscrip"'

# NetCDF

#OIFS_NETCDF_INCLUDE: '-I$NETCDFROOT/include'

#OIFS_NETCDF_LIB: '"-L$NETCDF_DIR/lib -lnetcdf"'

#OIFS_NETCDFF_INCLUDE: '-I$NETCDFFROOT/include'

#OIFS_NETCDFF_LIB: '"-L$NETCDFFROOT/lib -lnetcdff"'

# compiler and compiler flags

#OIFS_FC: $FC

Remove this block

configs/machines/levante.yaml

src/esm_runscripts/coupler.py

mandresm · 2026-02-19T09:17:56Z

src/esm_runscripts/oasis.py

                glob_search_file = (
-                    f"{restart_file_path}*"
+                    f"{config['ini_restart_dir']}{restart_file}*"
                    f"{config['ini_restart_date'].year}"


@mandresm test these changes with restarting from the pool

src/esm_runscripts/slurm.py

src/esm_runscripts/yac_old.py

… into geomar

seb-wahl and others added 30 commits December 10, 2024 12:17

first draft of FOCI-MOPS with ECHAM6 from LMU Munich

408eb64

compiles and starts, but misses (as expected) information in existing JSBACH restart files. Cold start not yet implemented

added a first draft of runscript for LMU edition

d30a261

links all currently known files correctly running not yet tested as info from Shradda is still missing

made number of tiles a variable

024c4d7

added missing info in xios.yaml

1945cd8

draft version of ECHAM76-LMU that start up correctly but still fails due to land sea mask mismatch

added namelists templates (or links)

ef7f705

added missing ;

102d1a2

fixed dynveg file placeholder

b75f091

fix echam lmu compilation when submodule has already been cloned

e6f624b

latest version of LMU runscript, still crashes

1f455e2

FOCI-MOPS LMU runs including updated output for jsbach and echam

a2dbbf4

fixed restart setup in a hacky way (see foci.yaml) added a new runscript for FOCIOIFS

Merge remote-tracking branch 'origin/feature/add-foci-mops-lmu' into …

03a6565

…geomar_dev exludes the conflicting oasis.py

manually add the modifications in oasis.py again

0b20a63

This should be the only difference between geomar_dev and release that matters

fixed merge error in foci.yaml

d3dd469

renamed nest restart labels to fix Sayantanis restart issues

957fcdc

added Joakims additions to slurm.py which are required to use mpirun …

88bd5cb

…on glogin

added hotfix for oasis_time_stamp support needed by focioifs

2556665

added postprocessing for RESCUE (temporary, should go somewhere else)

a5cd423

allow different streams for restart and output for ECHAM and JSBACH

fix paths in echam_monitoring

7ae29ad

fixed all bugs that occurred before the first longer run

8c11b6b

with FOCI-MOPS with the 12 tile edition

added working FOCILMU piCtl setup

802e5a8

updated pp echam RESCUE, now netCDF

0431584

increased compression to zip_3

ebf5633

Merge pull request #1350 from esm-tools/geomar_dev

2eb0efa

merge geomar dev into geomar branch

separate echam6 namelist templates for foci and foci_lmu

3c66177

updated settings for NEMO4 standalone done a loooong time ago

79edfd9

Merge pull request #1351 from esm-tools/geomar_dev

9f2de6f

separate echam6 namlist templates for foci and foci_lmu

manually resolve conflicts between release and geomar_dev

4d7c6b3

before merging this branch into geomar_dev differences where too large for an efficient direct merge

manual merge of selected yaml from release to avoid conflicts

9b454b7

Merge branch 'release_geomar_dev_intermediate' into geomar_dev

0d93f0f

fixed indentation bug in jsbach.yaml, remove deprecated env var decla…

ea78915

…ration

seb-wahl added 13 commits February 4, 2026 12:32

added daily restart template for tests, workaround with pre_run_comma…

da8e94a

…nd for file naming

updated settings for system_intel_libs on levante

2fce012

added runscripts for hist and perpetual year (the latter to be tested)

c87c8a6

Merge remote-tracking branch 'origin/feature/echam6-moz' into geomar_dev

0ad6b4d

Merge branch 'feature/focioifs-5.0' into geomar_dev

5d8db58

Merge remote-tracking branch 'origin/release' into geomar_dev

23f31f8

generalized all_machines.yaml for Emmy p2 and p3

31efa04

example runscript (foci-default) on how to use input from lustre-rzg on Emmy p3

generalize base_dir in example

acd2bc7

Merge branch 'geomar_dev' into feature/rescue

ad33bda

Revert "Added tracer co2 output for echam"

ae09101

This reverts commit a92860b.

Merge branch 'geomar_dev' into geomar

9477d5c

added namelist templates with tracer

03bfb76

made the new namelists default for an oasismct4_mops based setup

Merge branch 'geomar_dev' into geomar

5110ae4

seb-wahl mentioned this pull request Feb 16, 2026

merge geomar dev into latest release #1352

Closed

Merge remote-tracking branch 'origin/release' into geomar_dev

2b5c26b

adds dask stuff, moves post run commands to computer section

mandresm reviewed Feb 18, 2026

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configs/components/echam/echam.yaml Show resolved Hide resolved

mandresm reviewed Feb 18, 2026

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configs/components/jsbach/jsbach.yaml Show resolved Hide resolved

mandresm requested changes Feb 18, 2026

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fix get_rel_paths_compare_files

0ff4755

mandresm reviewed Feb 19, 2026

View reviewed changes

seb-wahl added 4 commits February 19, 2026 08:32

updated post_run_commands in several runscripts

10be687

fixed duplicate grid for focioifs

4d9375d

removed an HEAD statement left from the manual merge

41a992f

Merge branch 'geomar_dev' into geomar

7e5a1ef

mandresm requested changes Feb 19, 2026

View reviewed changes

mandresm and others added 5 commits February 19, 2026 18:12

Apply suggestions from code review

0f7dbdf

remove unnecessary yac_old.py file

2501639

Merge remote-tracking branch 'origin/fix/get_rel_paths_compare_files'…

ea5851f

… into geomar

fix another bug on get_rel_paths_compare_files for esm_tests

0300f0d

fix some issues in esm_tests

b05399c

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seb-wahl commented Feb 16, 2026 •

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