Merge branch 'develop' into dev-fix-PecanProject#1747

CHANGELOG.md

@@ -76,9 +76,10 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
 - Fixed a bug in `model2netcdf.ed2()` where .nc file connections were being closed multiple times, printing warnings (#3078)
 - Fixed a bug causing the model2netcdf.ED2() step in jobs.sh to be incorrectly written (#3075)
 - Fixed a bug where `plant_min_temp` trait value wasn't being converted from ºC to K when writing config file for ED2 (#3110)
-* Fixed a bug in `PEcAn.ED2::read_E_files()` affecting `PEcAn.ED2::model2netcdf.ED2()` that resulted in incorrect calculations (#3126)
-* DDBH (change in DBH over time) is no longer extracted and summarized from monthly -E- files by `PEcAn.ED2::model2netcdf.ED2()`.  We are not sure it makes sense to summarize this variable across cohorts of different sizes.
-* The `yr` and `yfiles` arguments of `PEcAn.ED2::read_E_files()` are no longer used and the simulation date is extracted from the names of the .h5 files output by ED2.
+- Fixed a bug in `PEcAn.ED2::read_E_files()` affecting `PEcAn.ED2::model2netcdf.ED2()` that resulted in incorrect calculations (#3126)
+- DDBH (change in DBH over time) is no longer extracted and summarized from monthly -E- files by `PEcAn.ED2::model2netcdf.ED2()`.  We are not sure it makes sense to summarize this variable across cohorts of different sizes.
+- The `yr` and `yfiles` arguments of `PEcAn.ED2::read_E_files()` are no longer used and the simulation date is extracted from the names of the .h5 files output by ED2.
+- Update Dockerfile for sipnet/maespa/template to use pecan/models:tag to build.
 
 ### Changed
 
@@ -105,6 +106,7 @@ convert data for a single PFT fixed (#1329, #2974, #2981)
 
 - the check image (used in kubernetes) is removed, please use ncsa/checks instead.
 - Unused (and apparently long-broken) function `PEcAn.data.land::find.land` has been removed.
+- No longer building r136 sipnet docker image.
 
 ## [1.7.2] - 2021-10-04
 

docker.sh

@@ -217,7 +217,7 @@ for version in git; do
 done
 
 # build sipnet
-for version in git r136; do
+for version in git; do
     ${DEBUG} docker build \
         --tag pecan/model-sipnet-${version}:${IMAGE_VERSION} \
         --build-arg MODEL_VERSION="${version}" \

models/maespa/Dockerfile

@@ -4,16 +4,7 @@ ARG IMAGE_VERSION="latest"
 # ----------------------------------------------------------------------
 # BUILD MODEL BINARY
 # ----------------------------------------------------------------------
-FROM debian:stretch as model-binary
-
-# install dependencies
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-       build-essential \
-       curl \
-       git \
-       gfortran \
-    && rm -rf /var/lib/apt/lists/*
+FROM pecan/models:${IMAGE_VERSION} as model-binary
 
 # download, unzip and build ed2
 WORKDIR /src

models/sipnet/Dockerfile

@@ -4,19 +4,11 @@ ARG IMAGE_VERSION="latest"
 # ----------------------------------------------------------------------
 # BUILD SIPNET BINARY
 # ----------------------------------------------------------------------
-FROM debian:stretch as sipnet-binary
+FROM pecan/models:${IMAGE_VERSION} as model-binary
 
 # Some variables that can be used to set control the docker build
 ARG MODEL_VERSION=git
 
-# install dependencies
-RUN apt-get update \
-    && apt-get install -y \
-       gcc \
-       git \
-       make \
-    && rm -rf /var/lib/apt/lists/*
-
 # download, unzip and build sipnet
 WORKDIR /src
 RUN git clone https://github.com/PecanProject/sipnet.git \
@@ -56,4 +48,4 @@ RUN sed -i -e "s/@VERSION@/${MODEL_VERSION}/g" \
            -e "s#@BINARY@#/usr/local/bin/sipnet.${MODEL_VERSION}#g" /work/model.json
 
 # COPY sipnet binary
-COPY --from=sipnet-binary /src/sipnet/sipnet /usr/local/bin/sipnet.${MODEL_VERSION}
+COPY --from=model-binary /src/sipnet/sipnet /usr/local/bin/sipnet.${MODEL_VERSION}

models/template/Dockerfile

@@ -10,21 +10,17 @@ ARG IMAGE_VERSION="latest"
 # ----------------------------------------------------------------------
 # BUILD MODEL BINARY
 # ----------------------------------------------------------------------
-FROM debian:stretch as model-binary
+FROM pecan/models:${IMAGE_VERSION} as model-binary
 
 # Some variables that can be used to set control the docker build
 ARG MODEL_VERSION=git
 
 # install dependencies
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-       build-essential \
-       curl \
-       gfortran \
-       git \
-       libhdf5-dev \
-       libopenmpi-dev \
-    && rm -rf /var/lib/apt/lists/*
+#RUN apt-get update \
+#    && apt-get install -y --no-install-recommends \
+#       libhdf5-dev \
+#       libopenmpi-dev \
+#    && rm -rf /var/lib/apt/lists/*
 
 # download, unzip and build ed2
 WORKDIR /src
@@ -45,11 +41,11 @@ FROM pecan/models:${IMAGE_VERSION}
 # INSTALL MODEL SPECIFIC PIECES
 # ----------------------------------------------------------------------
 
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-       libgfortran3 \
-       libopenmpi2 \
-    && rm -rf /var/lib/apt/lists/*
+#RUN apt-get update \
+#    && apt-get install -y --no-install-recommends \
+#       libgfortran3 \
+#       libopenmpi2 \
+#    && rm -rf /var/lib/apt/lists/*
 
 # ----------------------------------------------------------------------
 # SETUP FOR SPECIFIC MODEL