ai2cm · spencerkclark · Apr 12, 2023 · Apr 28, 2023 · Apr 28, 2023 · spencerkclark
diff --git a/.circleci/config.yml b/.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"}}

diff --git a/FV3/gfsphysics/physics/samfdeepcnv.f b/FV3/gfsphysics/physics/samfdeepcnv.f
@@ -1547,22 +1547,22 @@ subroutine samfdeepcnv(im,ix,km,delt,itc,ntc,ntk,ntr,delp,
       enddo
       enddo
       do i = 1, im
-        betamn = betas
-        if(islimsk(i) == 1) betamn = betal
-        if(ntk > 0) then
-          betamx = betamn + dbeta
-          if(tkemean(i) > tkemx) then
-            beta = betamn
-          else if(tkemean(i) < tkemn) then
-            beta = betamx
+        if(cnvflg(i)) then
+          betamn = betas
+          if(islimsk(i) == 1) betamn = betal
+          if(ntk > 0) then
+            betamx = betamn + dbeta
+            if(tkemean(i) > tkemx) then
+              beta = betamn
+            else if(tkemean(i) < tkemn) then
+              beta = betamx
+            else
+              tem = (betamx - betamn) * (tkemean(i) - tkemn)
+              beta = betamx - tem  / dtke
+            endif
           else
-            tem = (betamx - betamn) * (tkemean(i) - tkemn)
-            beta = betamx - tem  / dtke
+            beta = betamn
           endif
-        else
-          beta = betamn
-        endif
-        if(cnvflg(i)) then
           dz  = (sumx(i)+zi(i,1))/float(kbcon(i))
           tem = 1./float(kbcon(i))
           xlamd(i) = (1.-beta**tem)/dz

diff --git a/Makefile b/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)
 

diff --git a/docker/Dockerfile b/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

diff --git a/tests/pytest/reference/circleci/baroclinic-debug/md5.txt b/tests/pytest/reference/circleci/baroclinic-debug/md5.txt
@@ -0,0 +1,37 @@
+131fab4e3cd1feae7cb6bdaff881e725  atmos_4xdaily_fine_inst.tile1.nc
+fe45eab4a5c25ec93a5a348ee08881a0  atmos_4xdaily_fine_inst.tile2.nc
+fad54c07bf8692b0bb1296a189306dff  atmos_4xdaily_fine_inst.tile3.nc
+bdf349ecd9d8065fb7bc27d69b438c00  atmos_4xdaily_fine_inst.tile4.nc
+1094331a6b0aa718e6509521ae268159  atmos_4xdaily_fine_inst.tile5.nc
+d4b2fe8b386577cb3d2eeb9d7cd727e2  atmos_4xdaily_fine_inst.tile6.nc
+82157501c5b777a6e51603f36d381a8c  RESTART/fv_core.res.nc
+3776fd756dace0f597ec422043c7f118  RESTART/fv_core.res.tile1.nc
+f9fdbac96cf7a0fb09c6fef4e2529cff  RESTART/fv_core.res.tile2.nc
+9d34f5adfd62b4e47e35d85bd5a2af24  RESTART/fv_core.res.tile3.nc
+a6feac056ec48e4ca8289d4180d8d396  RESTART/fv_core.res.tile4.nc
+6654dcf19e08d45aff075cdf09148cf5  RESTART/fv_core.res.tile5.nc
+7fe463915eec05ad8d003ea8304a3269  RESTART/fv_core.res.tile6.nc
+fbeeab6ab11e26787de05bafb7853ab1  RESTART/fv_srf_wnd.res.tile1.nc
+91e20c755b0f9545e73db907b1282706  RESTART/fv_srf_wnd.res.tile2.nc
+b01f7387d64a8e49c94199892361e6de  RESTART/fv_srf_wnd.res.tile3.nc
+61affb199928a3b9e7b0ca351709083d  RESTART/fv_srf_wnd.res.tile4.nc
+f62cee640bc26fa4d5e9bf70b1104304  RESTART/fv_srf_wnd.res.tile5.nc
+a08a35fd458971b5a4f2f81b3eba529f  RESTART/fv_srf_wnd.res.tile6.nc
+173da4ef4a258e778c47dd31271a3b8e  RESTART/fv_tracer.res.tile1.nc
+ee308d968032d9f83bac94957f68ea9f  RESTART/fv_tracer.res.tile2.nc
+c53da594d7e006ad0ef132410cd1f19b  RESTART/fv_tracer.res.tile3.nc
+0079487895fb0a593b52d8e760aa0614  RESTART/fv_tracer.res.tile4.nc
+63f49f4d21ced8ba0fc50337271414d3  RESTART/fv_tracer.res.tile5.nc
+3792fbcadc42564cd134495cf1e87381  RESTART/fv_tracer.res.tile6.nc
+009eee5d146a8dd492bfc6052ccad11e  RESTART/phy_data.tile1.nc
+ed094092b41c9853bf85d84d43d1f7fd  RESTART/phy_data.tile2.nc
+e7122fe73228aca73a13c89a3d53f149  RESTART/phy_data.tile3.nc
+ecc9f494e54293e09d50981300be7c26  RESTART/phy_data.tile4.nc
+f6ac59fc70a90e246c28db7ee9da4c6d  RESTART/phy_data.tile5.nc
+8b15f645ac7f3fd52bcee6180edd1522  RESTART/phy_data.tile6.nc
+e05299c68f47918b78d8df63aa939e22  RESTART/sfc_data.tile1.nc
+5315048f47ab00fddf8834258fd2f080  RESTART/sfc_data.tile2.nc
+05daf9a231493c752d251c676478744b  RESTART/sfc_data.tile3.nc
+1193578f82de05926290fbbf11099912  RESTART/sfc_data.tile4.nc
+9c1e823605a277322c4231a5cedec333  RESTART/sfc_data.tile5.nc
+7065033ee348c8f9d0f877b0712fbac7  RESTART/sfc_data.tile6.nc
diff --git a/tests/pytest/reference/circleci/baroclinic/md5.txt b/tests/pytest/reference/circleci/baroclinic/md5.txt