Merge remote-tracking branch 'upstream/main' into update_ug

.github/workflows/ci_test_docker.yml

@@ -4,6 +4,7 @@ on: [pull_request,workflow_dispatch]
 
 env:
   TEST_TAG: dtcenter/ccpp-scm:test
+  PR_NUMBER: ${{ github.event.number }}
 
 jobs:
   docker:
@@ -22,6 +23,7 @@ jobs:
           file: docker/Dockerfile
           load: true
           tags: ${{ env.TEST_TAG }}
+          build-args: PR_NUMBER=${{ github.event.number }}
       - name: Test
         run: |
           mkdir $HOME/output

contrib/get_all_static_data.sh

@@ -21,7 +21,7 @@ for file in "${data_files[@]}"; do
     mkdir -p $BASEDIR/scm/data/$file
     cd $BASEDIR/scm/data/$file
     echo "Retrieving $file"
-    wget https://github.com/NCAR/ccpp-scm/releases/download/v6.0.0/${file}.tar.gz
+    wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0-beta/${file}.tar.gz
     tar -xf ${file}.tar.gz
     rm -f ${file}.tar.gz
 done

docker/Dockerfile

@@ -1,27 +1,33 @@
 FROM debian:12
-MAINTAINER Michael Kavulich <[email protected]>
+LABEL maintainer="Michael Kavulich <[email protected]>"
 
-# Set up base OS environment
+# arguments that can be passed in
+ARG PR_NUMBER
 
+# Set up base OS environment
 RUN apt-get -y update
 
 # Get "essential" tools and libraries
 RUN apt-get -y install build-essential \
-  && apt-get -y install cmake curl git file gfortran-12 ksh m4 python3 tcsh time wget vim \
+  && apt-get -y install cmake cmake-curses-gui curl git file gfortran-12 ksh m4 python3 tcsh time wget vim emacs-nox \
   && apt-get -y install libnetcdf-pnetcdf-19 libnetcdff7 libnetcdf-dev libnetcdff-dev libxml2 \
-  && apt-get -y install python3-pip python3.11-venv
+  && apt-get -y install python3-pip python3.11-venv python3-netcdf4 \
+  && apt-get -y install openmpi-bin libopenmpi-dev
+RUN ln -s /usr/bin/python3 /usr/bin/python
 
-MAINTAINER Grant Firl <[email protected]> or Michael Kavulich <[email protected]>
+# Set up python needed packages, preferred Docker method is apt-get but
+# f90nml can't be installed for debian that way
+RUN pip install f90nml --break-system-packages
 
 #Compiler environment variables
-ENV CC  /usr/bin/gcc
-ENV FC  /usr/bin/gfortran
-ENV CXX /usr/bin/g++
-ENV F77 /usr/bin/gfortran
-ENV F90 /usr/bin/gfortran
+ENV CC=/usr/bin/gcc
+ENV FC=/usr/bin/gfortran
+ENV CXX=/usr/bin/g++
+ENV F77=/usr/bin/gfortran
+ENV F90=/usr/bin/gfortran
 
 # Other necessary environment variables
-ENV LD_LIBRARY_PATH /usr/lib/
+ENV LD_LIBRARY_PATH=/usr/lib/
 
 # Set up unpriviledged user account, set up user home space and make sure user has permissions on all stuff in /comsoftware
 RUN groupadd comusers -g 9999 \
@@ -32,57 +38,63 @@ RUN groupadd comusers -g 9999 \
  && chown -R comuser:comusers /comsoftware \
  && chmod -R 6755 /comsoftware
 
-# Link version-specific aliases (python3 will be created later with virtual environment)
-RUN ln -s ~comuser/.venv/bin/python3 /usr/local/bin/python
-RUN ln -s /usr/bin/gfortran-12 /usr/bin/gfortran
-
 # all root steps completed above, now continue below as regular userID comuser
 USER comuser
 WORKDIR /home
 
 # Build NCEP libraries we need for SCM
 
-ENV NCEPLIBS_DIR /comsoftware/nceplibs
+ENV NCEPLIBS_DIR=/comsoftware/nceplibs
 
 RUN mkdir -p $NCEPLIBS_DIR/src && cd $NCEPLIBS_DIR/src \
   && git clone -b v2.4.1 --recursive https://github.com/NOAA-EMC/NCEPLIBS-bacio \
   && mkdir NCEPLIBS-bacio/build && cd NCEPLIBS-bacio/build \
   && cmake -DCMAKE_INSTALL_PREFIX=$NCEPLIBS_DIR .. \
-  && make VERBOSE=1 \
-  && make install 
+  && make VERBOSE=1 -j \
+  && make install
 
 RUN cd $NCEPLIBS_DIR/src \
   && git clone -b v2.3.3 --recursive https://github.com/NOAA-EMC/NCEPLIBS-sp \
   && mkdir NCEPLIBS-sp/build && cd NCEPLIBS-sp/build \
   && cmake -DCMAKE_INSTALL_PREFIX=$NCEPLIBS_DIR .. \
-  && make VERBOSE=1 \
+  && make VERBOSE=1 -j \
   && make install
 
 RUN cd $NCEPLIBS_DIR/src \
   && git clone -b v2.11.0 --recursive https://github.com/NOAA-EMC/NCEPLIBS-w3emc \
   && mkdir NCEPLIBS-w3emc/build && cd NCEPLIBS-w3emc/build \
   && cmake -DCMAKE_INSTALL_PREFIX=$NCEPLIBS_DIR .. \
-  && make VERBOSE=1 \
+  && make VERBOSE=1 -j \
   && make install
 
-ENV bacio_ROOT /comsoftware/nceplibs
-ENV sp_ROOT /comsoftware/nceplibs
-ENV w3emc_ROOT /comsoftware/nceplibs
+ENV bacio_ROOT=/comsoftware/nceplibs
+ENV sp_ROOT=/comsoftware/nceplibs
+ENV w3emc_ROOT=/comsoftware/nceplibs
+
+# Obtain CCPP SCM source code, build code, and download static data
+RUN if [ -z "$PR_NUMBER" ]; then \
+        cd /comsoftware \
+        && git clone --recursive -b main https://github.com/NCAR/ccpp-scm; \
+    else \
+        cd /comsoftware \
+        && git clone https://github.com/NCAR/ccpp-scm \
+        && cd ccpp-scm \
+        && git fetch origin pull/${PR_NUMBER}/head:test_pr \
+        && git checkout test_pr \
+        && git submodule update --init --recursive; \
+    fi
+
+RUN mkdir /comsoftware/ccpp-scm/scm/bin \
+  && cd /comsoftware/ccpp-scm/scm/bin \
+  && cmake ../src \
+  && make -j
 
-# Obtain CCPP SCM source code and static data, build code
-RUN cd /comsoftware \
-  && git clone --recursive -b main https://github.com/NCAR/ccpp-scm \
-  && cd /comsoftware/ccpp-scm/ \
+RUN cd /comsoftware/ccpp-scm/ \
   && ./contrib/get_all_static_data.sh \
-  && ./contrib/get_thompson_tables.sh \
-  && cd /comsoftware/ccpp-scm/scm \
-  && mkdir bin \
-  && cd bin \
-  && cmake ../src \
-  && make -j4
+  && ./contrib/get_thompson_tables.sh
 
 # The analysis scripts have options for using LaTeX when making figure labels.
-# If you would like to install LaTeK, uncomment the section below. 
+# If you would like to install LaTeK, uncomment the section below.
 # Note: This will increase the image size by 1 GB.
 #USER root
 #RUN yum -y update \
@@ -96,9 +108,3 @@ ENV SCM_ROOT=/comsoftware/ccpp-scm/
 
 # For interactive use, vim mouse settings are infuriating
 RUN echo "set mouse=" > ~/.vimrc
-
-# Set up python virtual environment and install needed packages
-ENV VIRTUAL_ENV=~/.venv
-RUN python3 -m venv $VIRTUAL_ENV
-ENV PATH="$VIRTUAL_ENV/bin:$PATH"
-RUN pip3 install f90nml==1.4.4 netcdf4==1.6.5

scm/etc/case_config/COMBLE.nml

@@ -0,0 +1,9 @@
+$case_config
+case_name = 'COMBLE',
+input_type = 1
+lsm_ics = .false.,
+do_spinup = .false.,
+spinup_timesteps = 0,
+reference_profile_choice = 2,
+column_area = 1.45E8,
+/

scm/etc/case_config/LASSO_2016051812.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_2016051812',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2016,
-month = 5,
-day = 18,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_2016051812'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_2016051812_MSDA.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_2016051812_MSDA',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2016,
-month = 5,
-day = 18,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_2016051812_MSDA'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_2016051812_VARA.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_2016051812_VARA',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2016,
-month = 5,
-day = 18,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_2016051812_VARA'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180514_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180514_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 5,
-day = 14,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180514_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180522_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180522_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 5,
-day = 22,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180522_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180606_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180606_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 6,
-day = 06,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180606_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180618_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180618_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 6,
-day = 18,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180618_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180619_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180619_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 6,
-day = 19,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180619_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/

scm/etc/case_config/LASSO_20180705_s02.nml

@@ -1,16 +1,7 @@
-$case_config
-case_name = 'LASSO_20180705_s02',
-runtime = 54000,
-thermo_forcing_type = 2,
-mom_forcing_type = 3,
-relax_time = 7200.0,
-sfc_flux_spec = .true.,
-sfc_roughness_length_cm = 10.0
-sfc_type = 1,
-reference_profile_choice = 2,
-year = 2018,
-month = 7,
-day = 05,
-hour = 12,
-column_area = 2.0E9,
-$end
+&case_config
+    case_name = 'LASSO_20180705_s02'
+    column_area = 2000000000.0
+    input_type = 1
+    reference_profile_choice = 2
+    sfc_roughness_length_cm = 10.0
+/