Emulandice2 patch

docker/Dockerfile

@@ -44,14 +44,24 @@ RUN /factsVe/bin/pip install --no-cache-dir \
         dask==2025.2.0
 
 
-# installs R for ubuntu 20.04 Focal
-RUN apt-get update &&\
+# # installs R for ubuntu 20.04 Focal
+# RUN apt-get update &&\
+#     apt-get install -y --no-install-recommends r-base \
+#         cmake \
+#         libopenblas-dev \
+#         gfortran
+
+# Add CRAN repository and install R 4.5
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends software-properties-common wget && \
+    wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc && \
+    echo "deb https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" >> /etc/apt/sources.list && \
+    apt-get update && \
     apt-get install -y --no-install-recommends r-base \
         cmake \
         libopenblas-dev \
         gfortran
 
-
 ARG NB_USER=jovyan
 ARG NB_UID=1001
 ENV USER=${NB_USER}

modules/emulandice2/AIS/pipeline.global.2150.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - AIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_AIS_project_2150_240214_data.tgz"

modules/emulandice2/AIS/pipeline.global.2300.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - AIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_AIS_project_2300_240214_data.tgz"

modules/emulandice2/AIS/pipeline.global.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - AIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_AIS_project_data.tgz"

modules/emulandice2/AIS/pipeline.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - AIS
@@ -23,7 +23,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_AIS_project_data.tgz"
@@ -36,7 +37,7 @@ project:
 postprocess:
   task1:
     executable: "python3"
-    script: "emulandice_postprocess.py"
+    script_noupload: "emulandice_postprocess.py"
     arguments:
       - --ncfiles
       - "%PIPELINE_ID%_ALL_globalsl.nc"
@@ -52,6 +53,7 @@ postprocess:
       - '%MODULE_PATH%/../shared/AssignFP.py'
       - '%MODULE_PATH%/../shared/ReadFingerprint.py'
       - '%MODULE_PATH%/../shared/grd_fingerprintmap.yml'
+      - '%MODULE_PATH%/../shared/emulandice_postprocess.py'
     upload_and_extract_input_data:
       - 'grd_fingerprints_data.tgz'
     copy_shared_data:

modules/emulandice2/GrIS/pipeline.global.2100.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_GrIS_project_2100_240214_data.tgz"

modules/emulandice2/GrIS/pipeline.global.2300.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_GrIS_project_2300_240214_data.tgz"

modules/emulandice2/GrIS/pipeline.global.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GIS
@@ -25,7 +25,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_GrIS_project_data.tgz"

modules/emulandice2/GrIS/pipeline.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GIS
@@ -23,7 +23,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_GrIS_project_data.tgz"
@@ -36,7 +37,7 @@ project:
 postprocess:
   task1:
     executable: "python3"
-    script: "emulandice_postprocess.py"
+    script_noupload: "emulandice_postprocess.py"
     arguments:
       - --ncfiles
       - "%PIPELINE_ID%_ALL_globalsl.nc"
@@ -52,6 +53,7 @@ postprocess:
       - '%MODULE_PATH%/../shared/AssignFP.py'
       - '%MODULE_PATH%/../shared/ReadFingerprint.py'
       - '%MODULE_PATH%/../shared/grd_fingerprintmap.yml'
+      - '%MODULE_PATH%/../shared/emulandice_postprocess.py'
     upload_and_extract_input_data:
       - 'grd_fingerprints_data.tgz'
     copy_shared_data:

modules/emulandice2/emulandice_config.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
+set -e
 
-ROOTDIR=`dirname $0`
-MODE=$1
+ROOTDIR="$(dirname "$0")"
+MODE=${1:-}
 
 case $MODE in 
     "clean")

modules/emulandice2/glaciers/pipeline.global.2100.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GLA
@@ -61,7 +61,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_glaciers_project_2100_240223_data.tgz"

modules/emulandice2/glaciers/pipeline.global.2300.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GLA
@@ -61,7 +61,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_glaciers_project_2300_240223_data.tgz"

modules/emulandice2/glaciers/pipeline.global.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GLA
@@ -61,7 +61,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_glaciers_project_data.tgz"

modules/emulandice2/glaciers/pipeline.yml

@@ -3,7 +3,7 @@ project:
   task1:
     python_dependencies: "xarray dask numpy scipy"
     executable: "python3"
-    script: "emulandice_project.py"
+    script_noupload: "emulandice_project.py"
     arguments:
       - --ice_source
       - GLA
@@ -59,7 +59,8 @@ project:
     upload_input_data:
       - "%MODULE_PATH%/../shared/emulandice_environment.sh"
       - "%MODULE_PATH%/../shared/emulandice_steer.sh"
-      - "%MODULE_PATH%/../shared/emulandice_steer.R"
+      - "%MODULE_PATH%/../shared/emulandice2/main.R"
+      - "%MODULE_PATH%/../shared/emulandice_project.py"
     upload_and_extract_input_data:
       - "%MODULE_PATH%/../shared/emulandice_bundled_dependencies.tgz"
       - "emulandice2_glaciers_project_data.tgz"
@@ -71,7 +72,7 @@ project:
 postprocess:
   task1:
     executable: "python3"
-    script: "emulandice_postprocess.py"
+    script_noupload: "emulandice_postprocess.py"
     arguments:
       - --ncfiles
       - "%PIPELINE_ID%_RGI01_globalsl.nc"
@@ -105,6 +106,7 @@ postprocess:
       - '%MODULE_PATH%/../shared/AssignFP.py'
       - '%MODULE_PATH%/../shared/ReadFingerprint.py'
       - '%MODULE_PATH%/../shared/grd_fingerprintmap.yml'
+      - '%MODULE_PATH%/../shared/emulandice_postprocess.py'
     upload_and_extract_input_data:
       - 'grd_fingerprints_data.tgz'
     copy_shared_data:

modules/emulandice2/shared/emulandice_steer.sh

@@ -26,7 +26,7 @@ then
      exit 1
 fi
 
-Rscript -e "source('.Rprofile')" -e "library(emulandice2)" -e "source('emulandice_steer.R')" $ice_source $region $emu_file $climate_data_file $scenario $outdir $seed $pipeline_id
+Rscript -e "source('.Rprofile')" -e "library(emulandice2)" -e "source('main.R')" $ice_source $region $emu_file $climate_data_file $scenario $outdir $seed $pipeline_id
 
 # Arguments to add ____________
 # Read from emulator RData file: