esm-tools · pgierz · May 23, 2023 · Aug 19, 2022 · Feb 21, 2023 · Mar 13, 2023
diff --git a/.github/ISSUE_TEMPLATE/support_request.md b/.github/ISSUE_TEMPLATE/support_request.md
@@ -21,7 +21,7 @@ If applicable, add screenshots to help explain your problem.
 
 **System (please complete the following information):**
  - Supercomputer: [which machine you are on]
- - Version [Please run `esm_versions check`]
+ - Version [Please run `esm_tools --version`]
 
 
 **Additional context**

diff --git a/README.rst b/README.rst
@@ -29,8 +29,9 @@ glogin.hlrn.de / blogin.hlrn.de::
 
 juwels.fz-juelich.de::
 
+    $ module load Stages/2022
     $ module load git
-    $ module load Python-3.6.8
+    $ module load Python/3.9.6
 
 aleph::
 

diff --git a/configs/components/fesom/fesom-2.0.yaml b/configs/components/fesom/fesom-2.0.yaml
@@ -149,7 +149,7 @@ choose_resolution:
                 nx: 1306775
         jane:
                 nx: 33348172
-        SO3: 
+        SO3:
                 nx: 11087062
 
 mesh_dir: "${pool_dir}/${resolution}/"
@@ -167,13 +167,17 @@ restart_in_in_work:
         par_ice_restart: fesom.${parent_date!syear}.ice.restart/*.nc
         fesom_raw_restart_info: fesom_raw_restart/*.info
         fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
 restart_in_sources:
         oce_restart: fesom.${parent_date!syear}.oce.restart.nc
         ice_restart: fesom.${parent_date!syear}.ice.restart.nc
         par_oce_restart: fesom.${parent_date!syear}.oce.restart/*.nc
         par_ice_restart: fesom.${parent_date!syear}.ice.restart/*.nc
         fesom_raw_restart_info: fesom_raw_restart/*.info
         fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
 
 restart_out_files:
         oce_restart: oce_restart
@@ -182,6 +186,8 @@ restart_out_files:
         par_ice_restart: par_ice_restart
         fesom_raw_restart_info: fesom_raw_restart_info
         fesom_raw_restart: fesom_raw_restart
+        fesom_bin_restart_info: fesom_bin_restart_info
+        fesom_bin_restart: fesom_bin_restart
 
 restart_out_in_work:
         oce_restart: fesom.${end_date!syear}.oce.restart.nc
@@ -190,6 +196,8 @@ restart_out_in_work:
         par_ice_restart: fesom.${end_date!syear}.ice.restart/*.nc
         fesom_raw_restart_info: fesom_raw_restart/*.info
         fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
 
 restart_out_sources:
         oce_restart: fesom.${end_date!syear}.oce.restart.nc
@@ -198,6 +206,8 @@ restart_out_sources:
         par_ice_restart: fesom.${end_date!syear}.ice.restart/*.nc
         fesom_raw_restart_info: fesom_raw_restart/*.info
         fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
 
 
 outdata_sources:
@@ -226,6 +236,14 @@ file_movements:
                 all_directions: move
         fesom_raw_restart_info_out:
                 all_directions: move
+        fesom_bin_restart_in:
+                all_directions: move
+        fesom_bin_restart_out:
+                all_directions: move
+        fesom_bin_restart_info_in:
+                all_directions: move
+        fesom_bin_restart_info_out:
+                all_directions: move
 
 # Is it a branchoff experiment?
 branchoff: "$(( ${lresume} and ${general.run_number}==1 ))"
@@ -241,6 +259,8 @@ choose_branchoff:
                 add_restart_in_files:
                         fesom_raw_restart_info: fesom_raw_restart_info
                         fesom_raw_restart: fesom_raw_restart
+                        fesom_bin_restart_info: fesom_bin_restart_info
+                        fesom_bin_restart: fesom_bin_restart
 
 
 

diff --git a/configs/components/fesom/fesom-2.1.yaml b/configs/components/fesom/fesom-2.1.yaml
@@ -132,31 +132,65 @@ choose_resolution:
 restart_in_files:
         oce_restart: oce_restart
         ice_restart: ice_restart
+        par_oce_restart: par_oce_restart
+        par_ice_restart: par_ice_restart
+
 restart_in_in_work:
         oce_restart: fesom.${parent_date!syear}.oce.restart.nc
         ice_restart: fesom.${parent_date!syear}.ice.restart.nc
+        par_oce_restart: fesom.${parent_date!syear}.oce.restart/*.nc
+        par_ice_restart: fesom.${parent_date!syear}.ice.restart/*.nc
+        fesom_raw_restart_info: fesom_raw_restart/*.info
+        fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
         wiso_restart: fesom.${parent_date!syear}.wiso.restart.nc
         icb_restart: iceberg.restart #.${parent_date!syear!month}
         icb_restart_ISM: iceberg.restart.ISM
 restart_in_sources:
         oce_restart: fesom.${parent_date!syear}.oce.restart.nc
         ice_restart: fesom.${parent_date!syear}.ice.restart.nc
+        par_oce_restart: fesom.${parent_date!syear}.oce.restart/*.nc
+        par_ice_restart: fesom.${parent_date!syear}.ice.restart/*.nc
+        fesom_raw_restart_info: fesom_raw_restart/*.info
+        fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
         wiso_restart: fesom.${parent_date!syear}.wiso.restart.nc
         icb_restart: iceberg.restart #.${parent_date!syear!month}
         icb_restart_ISM: iceberg.restart.ISM
 
 restart_out_files:
         oce_restart: oce_restart
         ice_restart: ice_restart
+        par_oce_restart: par_oce_restart
+        par_ice_restart: par_ice_restart
+        fesom_raw_restart_info: fesom_raw_restart_info
+        fesom_raw_restart: fesom_raw_restart
+        fesom_bin_restart_info: fesom_bin_restart_info
+        fesom_bin_restart: fesom_bin_restart
+
 restart_out_in_work:
         oce_restart: fesom.${end_date!syear}.oce.restart.nc
         ice_restart: fesom.${end_date!syear}.ice.restart.nc
+        par_oce_restart: fesom.${end_date!syear}.oce.restart/*.nc
+        par_ice_restart: fesom.${end_date!syear}.ice.restart/*.nc
+        fesom_raw_restart_info: fesom_raw_restart/*.info
+        fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
         wiso_restart: fesom.${end_date!syear}.wiso.restart.nc
         icb_restart: iceberg.restart #.${parent_date!syear}
         icb_restart_ISM: iceberg.restart.ISM
 restart_out_sources:
         oce_restart: fesom.${end_date!syear}.oce.restart.nc
         ice_restart: fesom.${end_date!syear}.ice.restart.nc
+        par_oce_restart: fesom.${end_date!syear}.oce.restart/*.nc
+        par_ice_restart: fesom.${end_date!syear}.ice.restart/*.nc
+        fesom_raw_restart_info: fesom_raw_restart/*.info
+        fesom_raw_restart: fesom_raw_restart/np${nproc}/*.dump
+        fesom_bin_restart_info: fesom_bin_restart/*.info
+        fesom_bin_restart: fesom_bin_restart/np${nproc}/*
         wiso_restart: fesom.${end_date!syear}.wiso.restart.nc
         icb_restart: iceberg.restart #.${parent_date!syear}
         icb_restart_ISM: iceberg.restart.ISM
@@ -247,6 +281,23 @@ log_sources:
         clock: fesom.clock
         mesh_diag: fesom.mesh.diag.nc
 
+file_movements:
+        fesom_raw_restart_in:
+                all_directions: move
+        fesom_raw_restart_out:
+                all_directions: move
+        fesom_raw_restart_info_in:
+                all_directions: move
+        fesom_raw_restart_info_out:
+                all_directions: move
+        fesom_bin_restart_in:
+                all_directions: move
+        fesom_bin_restart_out:
+                all_directions: move
+        fesom_bin_restart_info_in:
+                all_directions: move
+        fesom_bin_restart_info_out:
+                all_directions: move
 
 # Is it a branchoff experiment?
 branchoff: "$(( ${lresume} and ${general.run_number}==1 ))"
@@ -259,6 +310,12 @@ choose_branchoff:
         false:
                 daynew: "${initial_date!sdoy}"
                 yearnew: "${initial_date!syear}"
+                add_restart_in_files:
+                        fesom_raw_restart_info: fesom_raw_restart_info
+                        fesom_raw_restart: fesom_raw_restart
+                        fesom_bin_restart_info: fesom_bin_restart_info
+                        fesom_bin_restart: fesom_bin_restart
+
 
 
 namelist_changes:

diff --git a/configs/components/oifs/oifs.env.yaml b/configs/components/oifs/oifs.env.yaml
@@ -341,18 +341,13 @@ compiletime_environment_changes:
         OIFS_CCDEFS: '"LINUX LITTLE INTEGER_IS_INT _ABI64 BLAS _OPENMP"'
 
     albedo:
-#      add_module_actions:
-#        - "load libaec/1.0.5-intel-2021.5.0"
       add_export_vars:
 
-#        SZIPROOT: "/sw/spack-levante/libaec-1.0.5-gij7yv"
-        HDF5_ROOT: $HDF5ROOT #TODO remove!
-        ECCODESROOT: "/albedo/home/mandresm/.spack/sw/eccodes/2.25.0-hwsa4h3/"
-        #ECCODESROOT: "/albedo/soft/sw/spack-sw/eccodes/2.25.0-e3frvr6/"
+        HDF5_ROOT: $HDF5ROOT
 
-        HDF5_C_INCLUDE_DIRECTORIES: $HDF5_ROOT/include #TODO remove!
-        NETCDF_Fortran_INCLUDE_DIRECTORIES: $NETCDFFROOT/include #TODO remove!
-        NETCDF_C_INCLUDE_DIRECTORIES: $NETCDFROOT/include #TODO remove!
+        HDF5_C_INCLUDE_DIRECTORIES: $HDF5_ROOT/include
+        NETCDF_Fortran_INCLUDE_DIRECTORIES: $NETCDFFROOT/include
+        NETCDF_C_INCLUDE_DIRECTORIES: $NETCDFROOT/include
         OASIS3MCT_FC_LIB: '"-L$NETCDFFROOT/lib -lnetcdff"'
         # TODO: figure out whether those two are still needed
         ESM_NETCDF_C_DIR: "$NETCDFROOT"

diff --git a/configs/components/oifs/oifs.yaml b/configs/components/oifs/oifs.yaml
@@ -339,6 +339,14 @@ choose_resolution:
                 res_number: 639
                 res_number_tl: "639_4"
                 truncation: "TCO"
+        TCO1279:
+                nx: 6599680
+                ny: 1
+                time_step: 300
+                oasis_grid_name: 128
+                res_number: 1279
+                res_number_tl: "1279_4"
+                truncation: "TCO"
         TL511:
                 nx: 348528
                 ny: 1

diff --git a/configs/machines/albedo.yaml b/configs/machines/albedo.yaml
@@ -95,9 +95,10 @@ choose_compiler_suite:
 
         add_export_vars:
             # I/O libraries
-            HDF5ROOT: "/albedo/home/mandresm/.spack/sw/hdf5/1.12.2-7bogsh7/"
-            NETCDFROOT: "/albedo/home/mandresm/.spack/sw/netcdf-c/4.8.1-2u6p2ge/"
-            NETCDFFROOT: "/albedo/home/mandresm/.spack/sw/netcdf-fortran/4.5.4-2gawmpc/"
+            HDF5ROOT: "/albedo/soft/sw/spack-sw/hdf5/1.12.2-rgostku/"
+            NETCDFROOT: "/albedo/soft/sw/spack-sw/netcdf-c/4.8.1-i5n4n63/"
+            NETCDFFROOT: "/albedo/soft/sw/spack-sw/netcdf-fortran/4.5.4-yb7woqz/"
+            ECCODESROOT: "/albedo/soft/sw/spack-sw/eccodes/2.25.0-vhmiess/"
 
     intel-oneapi:
         compiler_module: intel-oneapi-compilers/2022.1.0
@@ -142,7 +143,7 @@ module_actions:
     - "load cdo/2.0.5"
     - "load nco/5.0.1"
     - "load git/2.35.2"
-    #- "load perl/5.35.0-gcc12.1.0"
+    - "load perl/5.35.0-gcc12.1.0"
     - "load python/3.10.4"
     # Show what is there in the log:
     - "list"
@@ -163,9 +164,7 @@ export_vars:
     FESOM_PLATFORM_STRATEGY: albedo
 
     # PERL library
-    # TODO: change that to lib systems
-    #PERL5LIB: "/albedo/soft/sw/spack-sw/perl/5.35.0-asf6m5t/lib/5.35.0/"
-    PERL5LIB: "/albedo/home/mandresm/my_libs/perl-5.32.0/lib"
+    PERL5LIB: "/albedo/soft/sw/spack-sw/perl-uri/1.72-epj7s32/lib/perl5:/albedo/soft/sw/spack-sw/perl/5.35.0-asf6m5t/lib"
 
     # I/O libraries
     HDF5ROOT: ""
@@ -201,7 +200,7 @@ warning:
             environment variables, pool problems, incorrect or not optimal compiler
             flags... Feel free to try it a report and issue in https://github.com/esm-tools/esm_tools/issues
             labelling it with the ``albedo`` tag, if things don't work as expected. By
-            running ``esm_tools --test-state`` you'll get information of what you can
+            running ``esm_tools test-state`` you'll get information of what you can
             expect to work and what not. Bare in mind that the ESM-Tools configurations
             specific to Albedo will be changing fast on the following weeks, until
             Albedo is fully supported. We recommend against using it for production

diff --git a/configs/templates/component_template.yaml b/configs/templates/component_template.yaml
@@ -0,0 +1,99 @@
+# NAME OF YOUR MODEL OR COMPONENT HERE
+#
+# For more information about the extended YAML syntax, please consult:
+# https://esm-tools.readthedocs.io/en/latest/yaml.html#esm-tools-extended-yaml-syntax
+#
+# For more information about the ESM-Tools feature variables available, please consult:
+# https://esm-tools.readthedocs.io/en/latest/esm_variables.html#esm-tools-variables
+
+model: name of your component
+version: default version
+
+metadata:
+        Institute: where it was developed
+        Description:
+                A brief description here
+        Authors: Authors
+        Publications:
+                - "Main publication for this component here <link_to_the_publication>"
+        License:
+                License details here
+
+git-repository: if your code is hosted in git place here the address
+branch: default branch
+comp_command: command used to compile your component
+install_bins: subpath within ``model_dir`` where the comp command produces the binaries
+clean_command: ${defaults.clean_command}
+executable: medusa_recom_paleo
+
+choose_version:
+    # Here you can place all the variables you would want to control via the version
+    # variable above (for example, you could also add ``git-repository``,
+    # ``comp_command``, ``destination``, ...) 
+    a_version_of_your_choice:
+        branch: name of the branch/tag associated to that version if you use git
+    another_version_of_your_choice:
+        branch: name of the branch/tag associated to that version if you use git
+
+# ``model_dir`` let's ESM-Tools know where is the source code of your component (must
+# be an absolute path). Normally, changed via the runscript. We recommend you leave it
+# as below, changing only the ``name_of_your_model`` part to whatever you defined as 
+# the ``model`` var. This will automatically select the source code for esm_master if
+# the command is operating with a coupled setup
+model_dir: "${general.esm_master.dir}/name_of_your_model-${version}"
+
+# This section takes care of dealing with environment changes you might want to do, to
+# deviated from the defaults define for the specific machine
+# (``configs/machine/<the_machine_used>.yaml``). For more information consult:
+# https://esm-tools.readthedocs.io/en/latest/esm_environment.html#esm-environment
+environment_changes:
+    a_variable_in_the_computer_yaml: here you can over
+    add_module_actions:
+        - module command without ``module`` word (e.g. ``load hdf5``)
+        - module command without ``module`` word (e.g. ``load netcdf``)
+    add_export_vars:
+        VARIABLE_TO_EXPORT: '"value of the variable you want to export"'
+        VARIABLE_TO_EXPORT: '"value of the variable you want to export"'
+
+# Some recommended defaults
+lresume: false
+
+# Some commonly used variables in other ESM-Tools components (but optional)
+input_dir: ${pool_dir}/path/within/the/pool/dir/to/the/input/of/your/component
+namelist_dir: /absolute/path/to/the/namelist/folder
+
+# If your components has namelist the following syntax allows you to control the values
+# of their values. For more information consult:
+# https://esm-tools.readthedocs.io/en/latest/yaml.html#changing-namelists
+namelist_changes:
+    namelist_name:
+        section_in_the_namelist:
+            variable_in_the_namelist: its new value here
+
+namelists:
+    - name of the namelist
+
+# File dictionaries to control the copying/moving/linking of all files associated to
+# the simulation. This syntax will change for something better soon. For more details
+# about this syntax consult:
+# https://esm-tools.readthedocs.io/en/latest/yaml.html#file-dictionaries
+input_files:
+    file_name: file_tag
+input_source:
+    file_tag: /absolute/path/to/the/file
+input_in_work:
+    file_tag: /relative/path/to/the/file/in/the/work/directory
+
+config_files:
+    namelist_name: namelist_tag # Or any other configuration file
+config_sources:
+    namelist_tag: ${namelist_dir}/<namelist_name> # Use ${namelist_dir} here if you
+        # defined it above
+
+create_config:
+    name_of_the_config_you_want_to_create:
+        - "<--append-- line 1"
+        - "<--append-- line 2"
+
+bin_sources:
+    bin_tag: ${model_dir}/bin/${executable} # This would be the normal way to do it