Bump base Ubuntu image

This bumps the base Ubuntu image used to one with a version of 20.04. The
pinned SHA makes things consistent with the base image we use when building the
prognostic run in fv3net.

Note that due to NOAA-EMC/fv3atm#33, the tests with the TKE-EDMF scheme active
fail in debug mode.  We currently mark them as expected failures.  To
demonstrate that answers do not change when we fix this bug, we run the
coarse-graining tests in repro mode here and checkpoing the checksums.  In a
followup commit, we will fix the bug, unmark the relevant debug mode tests, but
retain the repro mode tests to demonstrate that the tests still all pass
without modifying those checksums.  Finally in one last commit we will remove
those temporary repro mode tests as well as their checksums, as they will no
longer be needed.

Because the serialize_image fails to build with the new compilers, we also
elect to remove the infrastructure and tests associated with it.

.circleci/config.yml

@@ -152,7 +152,7 @@ jobs:
           command: |
             git submodule init
             git submodule update
-      - run: DOCKER_BUILDKIT=1 BUILDKIT_PROGRESS=plain BUILD_FROM_INTERMEDIATE=y make build build_debug build_serialize
+      - run: DOCKER_BUILDKIT=1 BUILDKIT_PROGRESS=plain BUILD_FROM_INTERMEDIATE=y make build build_debug
       - restore_cache:
           keys:
             - v1.4-{{ checksum "requirements.txt"}}

Makefile

@@ -13,8 +13,11 @@ OTHER_MOUNTS ?=
 
 # base images w/ or w/o CUDA
 ifeq ($(CUDA),n)
-	BASE_IMAGE ?=ubuntu:18.04
-	DEP_TAG_NAME ?=gnu7-mpich314-nocuda
+	# Note this BASE_IMAGE version is the same as the one used in the
+	# fv3net prognostic_run image.  It corresponds to an image with Ubuntu
+	# version 20.04.
+	BASE_IMAGE ?=ubuntu@sha256:9101220a875cee98b016668342c489ff0674f247f6ca20dfc91b91c0f28581ae
+	DEP_TAG_NAME ?=gnu9-mpich314-nocuda
 else
 	BASE_IMAGE ?=nvidia/cuda:10.2-devel-ubuntu18.04
 	DEP_TAG_NAME ?=gnu7-mpich314-cuda102
@@ -24,21 +27,19 @@ BUILD_ARGS += --build-arg BASE_IMAGE=$(BASE_IMAGE)
 # image names (use XXX_IMAGE=<name> make <target> to override)
 COMPILED_TAG_NAME ?=$(DEP_TAG_NAME)
 COMPILED_IMAGE ?= $(GCR_URL)/$(COMPILE_TARGET):$(COMPILED_TAG_NAME)
-SERIALIZE_IMAGE ?= $(GCR_URL)/$(COMPILE_TARGET):$(COMPILED_TAG_NAME)-serialize
 EMULATION_IMAGE ?= $(GCR_URL)/$(COMPILE_TARGET):$(COMPILED_TAG_NAME)-emulation
 ENVIRONMENT_IMAGE ?= $(GCR_URL)/$(ENVIRONMENT_TARGET):$(ENVIRONMENT_TAG_NAME)
 MPI_IMAGE ?= $(GCR_URL)/mpi-build:$(DEP_TAG_NAME)
 FMS_IMAGE ?= $(GCR_URL)/fms-build:$(DEP_TAG_NAME)
 ESMF_IMAGE ?= $(GCR_URL)/esmf-build:$(DEP_TAG_NAME)
-SERIALBOX_IMAGE ?= $(GCR_URL)/serialbox-build:$(DEP_TAG_NAME)
 
 # used to shorten build times in CircleCI
 ifeq ($(BUILD_FROM_INTERMEDIATE),y)
-	BUILD_ARGS += --build-arg FMS_IMAGE=$(FMS_IMAGE) --build-arg ESMF_IMAGE=$(ESMF_IMAGE) --build-arg SERIALBOX_IMAGE=$(SERIALBOX_IMAGE) --build-arg MPI_IMAGE=$(MPI_IMAGE)
+	BUILD_ARGS += --build-arg FMS_IMAGE=$(FMS_IMAGE) --build-arg ESMF_IMAGE=$(ESMF_IMAGE) --build-arg MPI_IMAGE=$(MPI_IMAGE)
 endif
 
-.PHONY: help build build_environment build_compiled build_serialize build_debug
-.PHONY: build_deps push_deps pull_deps enter enter_serialize test update_circleci_reference clean
+.PHONY: help build build_environment build_compiled build_debug
+.PHONY: build_deps push_deps pull_deps enter test update_circleci_reference clean
 
 help:
 	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z0-9_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
@@ -60,41 +61,29 @@ build_compiled: ## build production container image
 build_debug: ## build container image for debugging
 	COMPILED_TAG_NAME=$(COMPILED_TAG_NAME)-debug COMPILE_OPTION="REPRO=\\\nDEBUG=Y" $(MAKE) build
 
-build_serialize: ## build container image for serialization
-	BUILD_ARGS="$(BUILD_ARGS) --build-arg serialize=true" \
-	COMPILED_IMAGE=$(SERIALIZE_IMAGE) \
-	$(MAKE) build_compiled
-
-build_deps: ## build container images of dependnecies (FMS, ESMF, SerialBox)
+build_deps: ## build container images of dependnecies (FMS, ESMF)
 	docker build -f $(DOCKERFILE) -t $(MPI_IMAGE) $(BUILD_ARGS) --target fv3gfs-mpi .
 	docker build -f $(DOCKERFILE) -t $(FMS_IMAGE) $(BUILD_ARGS) --target fv3gfs-fms .
 	docker build -f $(DOCKERFILE) -t $(ESMF_IMAGE) $(BUILD_ARGS) --target fv3gfs-esmf .
-	docker build -f $(DOCKERFILE) -t $(SERIALBOX_IMAGE) $(BUILD_ARGS) --target fv3gfs-environment-serialbox .
 
 push_image_%:
 	docker tag $(GCR_URL)/$*:$(DEP_TAG_NAME) $(GCR_URL)/$*:$(DEP_TAG_NAME)-$(COMMIT_SHA)
 	docker push $(GCR_URL)/$*:$(DEP_TAG_NAME)
 	docker push $(GCR_URL)/$*:$(DEP_TAG_NAME)-$(COMMIT_SHA)
 
 ## push container images of dependencies to GCP 
-push_deps: push_image_mpi-build push_image_fms-build push_image_esmf-build push_image_serialbox-build
+push_deps: push_image_mpi-build push_image_fms-build push_image_esmf-build
 
 pull_deps: ## pull container images of dependencies from GCP (for faster builds)
 	docker pull $(MPI_IMAGE)
 	docker pull $(FMS_IMAGE)
 	docker pull $(ESMF_IMAGE)
-	docker pull $(SERIALBOX_IMAGE)
 
 enter: ## run and enter production container for development
 	docker run --rm \
 		-v $(shell pwd)/FV3:/FV3 $(OTHER_MOUNTS) \
 		-w /FV3 -it $(COMPILED_IMAGE) bash
 
-enter_serialize: ## run and enter serialization container for development
-	docker run --rm \
-		-v $(shell pwd)/FV3:/FV3/original $(OTHER_MOUNTS) \
-		-w /FV3 -it $(SERIALIZE_IMAGE) bash
-
 test: ## run tests (set COMPILED_TAG_NAME to override default)
 	pytest tests/pytest --capture=no --verbose --refdir $(shell pwd)/tests/pytest/reference/circleci --image_version $(COMPILED_TAG_NAME)
 

docker/Dockerfile

@@ -1,10 +1,7 @@
-ARG serialize=false
-ARG fv3_build_env_tag=standard
 ARG BASE_IMAGE
 ARG MPI_IMAGE=fv3gfs-mpi
 ARG FMS_IMAGE=fv3gfs-fms
 ARG ESMF_IMAGE=fv3gfs-esmf
-ARG SERIALBOX_IMAGE=fv3gfs-environment-serialbox
 
 FROM $BASE_IMAGE AS fv3gfs-mpi
 
@@ -25,7 +22,8 @@ RUN wget -q http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz && \
 FROM $MPI_IMAGE AS mpi_image
 
 FROM $BASE_IMAGE AS fv3gfs-environment
-RUN apt-get update && apt-get install -y \
+RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get -y install tzdata && \
+    apt-get install -y \
     wget \
     gcc \
     libtool-bin \
@@ -55,53 +53,6 @@ RUN git config --global http.sslverify false && \
     git checkout 3da51e139d5cd731c9fc27f39d88cb4e1328212b && \
     echo "y" | ./make_ncep_libs.sh -s linux -c gnu -d /opt/NCEPlibs -o 1
 
-##
-## Setup environment for Serialbox
-##---------------------------------------------------------------------------------
-FROM fv3gfs-environment as fv3gfs-environment-serialbox
-# set TZ
-ENV DEBIAN_FRONTEND=noninteractive TZ=US/Pacific
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-
-# install dependencies for serialbox
-RUN apt-get update && apt-get install -y \
-    libssl-dev \
-    clang \
-    clang-format \
-    clang-tidy \
-    python3-numpy \
-    python3-nose \
-    python3-sphinx
-
-# RUN wget -q https://github.com/Kitware/CMake/releases/download/v3.18.3/cmake-3.18.3-Linux-x86_64.sh && \
-#     chmod +x ./cmake-3.18.3-Linux-x86_64.sh && \
-#     cmake-3.18.3-Linux-x86_64.sh
-
-RUN wget https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3.tar.gz && \
-    tar xzf cmake-3.17.3.tar.gz && \
-    cd cmake-3.17.3 && \
-    ./bootstrap && make -j4 && make install
-
-# Install headers from the Boost library
-RUN wget -q https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.gz && \
-    tar xzf boost_1_74_0.tar.gz && \
-    cd boost_1_74_0 && \
-    cp -r boost /usr/include/ && cd /    
-
-# install serialbox from source
-COPY serialbox serialbox
-RUN cd serialbox && \
-    mkdir build && \
-    cd build && \
-    cmake -DSERIALBOX_USE_NETCDF=ON -DSERIALBOX_ENABLE_FORTRAN=ON \
-      -DSERIALBOX_TESTING=ON  ../ && \
-    make -j16 && \
-    make test && \
-    make install
-
-# setup link for backwards comatibility
-RUN ln -s /serialbox /serialbox2
-
 ## Build FMS
 ##---------------------------------------------------------------------------------
 FROM fv3gfs-environment AS fv3gfs-fms
@@ -140,9 +91,9 @@ RUN git clone -b ESMF_8_0_0 --depth 1 https://git.code.sf.net/p/esmf/esmf $ESMF_
     make install && \
     make installcheck
 
-## Copy FV3GFS sources for non-serialize image
+## Copy FV3GFS sources
 ##---------------------------------------------------------------------------------
-FROM $BASE_IMAGE AS fv3gfs-src-serialize-false
+FROM $BASE_IMAGE AS fv3gfs-src
 
 ARG compile_option
 ARG configure_file=configure.fv3.gnu_docker
@@ -168,55 +119,28 @@ RUN cp /FV3/conf/$configure_file \
 
 COPY FV3/atmos_cubed_sphere /FV3/atmos_cubed_sphere
 
-## Convert FV3GFS sources for serialize image
-##---------------------------------------------------------------------------------
-FROM $SERIALBOX_IMAGE AS fv3gfs-src-serialize-true
-
-ARG compile_option
-ARG configure_file=configure.fv3.gnu_docker_serialize
-
-ENV SERIALBOX_OUTDIR=/FV3
-ENV FV3_BASE=/FV3/original
-
-COPY --from=fv3gfs-src-serialize-false /FV3 $FV3_BASE
-COPY --from=fv3gfs-src-serialize-false /stochastic_physics $(FV3_BASE)/../stochastic_physics 
-
-# copy appropriate configuration file to configure.fv3
-RUN cp $FV3_BASE/conf/$configure_file \
-        $FV3_BASE/conf/configure.fv3 && \
-    if [ ! -z $compile_option ]; then sed -i "33i $compile_option" \
-        $FV3_BASE/conf/configure.fv3; fi && \
-    cd $FV3_BASE && \
-    make serialize_preprocess
-
-
 ## Convert FV3GFS sources for emulation image
 ##---------------------------------------------------------------------------------
 
-FROM fv3gfs-src-serialize-$serialize AS fv3gfs-sources
+FROM fv3gfs-src AS fv3gfs-sources
 
 FROM $FMS_IMAGE AS fms_image
 FROM $ESMF_IMAGE AS esmf_image
-FROM $SERIALBOX_IMAGE AS serialbox_image
 
 FROM fv3gfs-environment AS fv3gfs-environment-standard
 
 ## Build FV3 executable in its own image
 ##---------------------------------------------------------------------------------
-FROM fv3gfs-environment-${fv3_build_env_tag} AS fv3gfs-build
+FROM fv3gfs-environment-standard AS fv3gfs-build
 
 ENV ESMFMKFILE=/usr/local/esmf/lib/esmf.mk
 
-ENV SERIALBOX_DIR=/serialbox \
-    SERIALBOX_OUTDIR=/FV3 \
-    FMS_DIR=/FMS \
+ENV FMS_DIR=/FMS \
     ESMF_DIR=/usr/local/esmf
 
 ENV ESMF_INC="-I/usr/local/esmf/include" \
-    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ESMF_DIR}/lib:${FMS_DIR}/libFMS/.libs/:${SERIALBOX_DIR}/lib \
-    PPSER_PY=$(SERIALBOX_DIR)/python/pp_ser/pp_ser.py
+    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ESMF_DIR}/lib:${FMS_DIR}/libFMS/.libs
 
-COPY --from=serialbox_image /serialbox/install $SERIALBOX_DIR
 COPY --from=fms_image /FMS $FMS_DIR
 COPY --from=esmf_image /usr/local/esmf $ESMF_DIR
 
@@ -235,9 +159,7 @@ FROM fv3gfs-build AS fv3gfs-compiled
 
 RUN apt-get update && apt-get install -y \
     python3 \
-    python3-pip && \
-    ln -s /bin/python3 /bin/python && \
-    ln -s /bin/pip3 /bin/pip
+    python3-pip
 # install python packages needed to convert to netcdf data
 RUN pip3 install --upgrade setuptools pip && \
     pip3 install --no-cache-dir pyyaml xarray==0.16.2 f90nml==1.1.0 netCDF4

tests/pytest/reference/circleci/baroclinic-debug/md5.txt

@@ -0,0 +1,37 @@
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+d4b2fe8b386577cb3d2eeb9d7cd727e2  atmos_4xdaily_fine_inst.tile6.nc
+82157501c5b777a6e51603f36d381a8c  RESTART/fv_core.res.nc
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tests/pytest/reference/circleci/default-debug/md5.txt

@@ -0,0 +1,55 @@
+c018112e0d1e1df1233ba9fab96e979f  atmos_8xdaily.tile1.nc
+133739ee6ea94fd326bfe86b7c418915  atmos_8xdaily.tile2.nc
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