From adafc50da9ec8721c44894594c405942c2bd4f1d Mon Sep 17 00:00:00 2001 From: Spencer Clark Date: Thu, 7 Sep 2023 14:56:38 -0400 Subject: [PATCH] Run all tests in the `nix-shell`; eliminate docker infrastructure (#379) This PR refactors the build infrastructure in this repo to eliminate the need for the Docker component. All development and testing is now done in the `nix` shell. This should be a quality of life improvement for anyone developing the fortran model, as it no longer requires maintaining checksums in two separate build environments. In so doing it introduces the following changes: - New `make` rules are provided for compiling the model in different modes: - `build` -- build executables in `repro` (our production mode) and `debug` mode. - `build_repro` -- build only the `repro` mode executable. - `build_debug` -- build only the `debug` mode executable. - Tests are run with each of the executables available in the local `bin` directory, and are tagged with the associated compile mode. - An option, `check_layout_invariance`, is provided to trigger regression tests be run with a 1x2 domain decomposition instead of a 1x1 domain decomposition to check invariance to the domain decomposition layout; this is used for the all the coarse-graining regression tests and replaces the previous `test_run_reproduces_across_layouts` test that would run in the docker image. - `debug`-mode and `repro`-mode simulations produce different answers, which is something we noticed in #364 when upgrading compiler versions as well, and so require different reference checksums. In working on this PR, we ran the fortran model in `debug` mode in more contexts than we had previously, some of which turned up errors, which we currently work around by using `pytest.skip` (something we had implicitly already been doing before): - #365 - #381 Working on this PR also brought my attention to the fact that `pytest`'s `tmpdir` fixture does not automatically get cleaned up after each test; `pytest` versions older than 7.3.0 keep around directories from the last three runs of `pytest`, which fill up disk space quickly since running these tests requires creating 10's of run directories, each with their own initial conditions and input files (#380). For the time being I manually clean up these run directories after successful tests. Resolves #340. --- .circleci/config.yml | 248 ++- .dockerignore | 7 - FV3/conf/configure.fv3.nix | 4 +- FV3/gfsphysics/physics/samfdeepcnv.f | 28 +- Makefile | 156 +- README.md | 302 +-- coverage.sh | 63 - docker/Dockerfile | 246 --- run_docker.sh | 42 - tests/pytest/.gitignore | 1 - tests/pytest/README.md | 39 +- ...ession.test_checksum_emulation[repro].out} | 0 ...st_regression.test_gscond_logs[repro].out} | 0 ...regression[debug-baroclinic.yml-False].out | 37 + ...rea-weighted-coarse-graining.yml-True].out | 121 + ...st_regression[debug-default.yml-False].out | 55 + ...-model-level-coarse-graining.yml-True].out | 121 + ...essure-level-coarse-graining.yml-True].out | 121 + ...-extrapolate-coarse-graining.yml-True].out | 121 + ...st_regression[debug-restart.yml-False].out | 55 + ...egression[repro-baroclinic.yml-False].out} | 0 ...ea-weighted-coarse-graining.yml-True].out} | 0 ...t_regression[repro-default.yml-False].out} | 0 ...model-level-coarse-graining.yml-True].out} | 0 ...ssure-level-coarse-graining.yml-True].out} | 0 ...extrapolate-coarse-graining.yml-True].out} | 0 ...t_regression[repro-restart.yml-False].out} | 0 ...n.test_zhao_carr_diagnostics[repro-1].out} | 0 ...n.test_zhao_carr_diagnostics[repro-2].out} | 0 ...n.test_zhao_carr_diagnostics[repro-3].out} | 0 ...n.test_zhao_carr_diagnostics[repro-4].out} | 0 ...n.test_zhao_carr_diagnostics[repro-5].out} | 0 ...n.test_zhao_carr_diagnostics[repro-6].out} | 0 tests/pytest/conftest.py | 80 - .../reference/circleci/baroclinic/md5.txt | 37 - .../md5.txt | 121 - .../pytest/reference/circleci/default/md5.txt | 55 - .../circleci/default/md5_serialize.txt | 480 ---- .../model-level-coarse-graining/md5.txt | 121 - .../pressure-level-coarse-graining/md5.txt | 121 - .../md5.txt | 121 - .../pytest/reference/circleci/restart/md5.txt | 55 - .../circleci/restart/md5_serialize.txt | 1968 ----------------- tests/pytest/run_files/job_jenkins_sarus | 23 - tests/pytest/run_files/submit_job.sh | 9 - tests/pytest/set_reference.sh | 49 - tests/pytest/test_regression.py | 345 +-- tests/test_fv3_exe_restart.py | 142 -- 48 files changed, 1022 insertions(+), 4472 deletions(-) delete mode 100644 .dockerignore delete mode 100755 coverage.sh delete mode 100644 docker/Dockerfile delete mode 100755 run_docker.sh delete mode 100644 tests/pytest/.gitignore rename tests/pytest/_regtest_outputs/{test_regression.test_checksum_emulation[Linux].out => test_regression.test_checksum_emulation[repro].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_gscond_logs.out => test_regression.test_gscond_logs[repro].out} (100%) create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-baroclinic.yml-False].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-blended-area-weighted-coarse-graining.yml-True].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-default.yml-False].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-model-level-coarse-graining.yml-True].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-pressure-level-coarse-graining.yml-True].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-pressure-level-extrapolate-coarse-graining.yml-True].out create mode 100644 tests/pytest/_regtest_outputs/test_regression.test_regression[debug-restart.yml-False].out rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-baroclinic.yml].out => test_regression.test_regression[repro-baroclinic.yml-False].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-blended-area-weighted-coarse-graining.yml].out => test_regression.test_regression[repro-blended-area-weighted-coarse-graining.yml-True].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-default.yml].out => test_regression.test_regression[repro-default.yml-False].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-model-level-coarse-graining.yml].out => test_regression.test_regression[repro-model-level-coarse-graining.yml-True].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-pressure-level-coarse-graining.yml].out => test_regression.test_regression[repro-pressure-level-coarse-graining.yml-True].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-pressure-level-extrapolate-coarse-graining.yml].out => test_regression.test_regression[repro-pressure-level-extrapolate-coarse-graining.yml-True].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_regression_native[Linux-restart.yml].out => test_regression.test_regression[repro-restart.yml-False].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[1].out => test_regression.test_zhao_carr_diagnostics[repro-1].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[2].out => test_regression.test_zhao_carr_diagnostics[repro-2].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[3].out => test_regression.test_zhao_carr_diagnostics[repro-3].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[4].out => test_regression.test_zhao_carr_diagnostics[repro-4].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[5].out => test_regression.test_zhao_carr_diagnostics[repro-5].out} (100%) rename tests/pytest/_regtest_outputs/{test_regression.test_zhao_carr_diagnostics[6].out => test_regression.test_zhao_carr_diagnostics[repro-6].out} (100%) delete mode 100644 tests/pytest/conftest.py delete mode 100644 tests/pytest/reference/circleci/baroclinic/md5.txt delete mode 100644 tests/pytest/reference/circleci/blended-area-weighted-coarse-graining/md5.txt delete mode 100644 tests/pytest/reference/circleci/default/md5.txt delete mode 100644 tests/pytest/reference/circleci/default/md5_serialize.txt delete mode 100644 tests/pytest/reference/circleci/model-level-coarse-graining/md5.txt delete mode 100644 tests/pytest/reference/circleci/pressure-level-coarse-graining/md5.txt delete mode 100644 tests/pytest/reference/circleci/pressure-level-extrapolate-coarse-graining/md5.txt delete mode 100644 tests/pytest/reference/circleci/restart/md5.txt delete mode 100644 tests/pytest/reference/circleci/restart/md5_serialize.txt delete mode 100644 tests/pytest/run_files/job_jenkins_sarus delete mode 100755 tests/pytest/run_files/submit_job.sh delete mode 100755 tests/pytest/set_reference.sh delete mode 100644 tests/test_fv3_exe_restart.py diff --git a/.circleci/config.yml b/.circleci/config.yml index 5da535777..fcd26e192 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,8 +2,7 @@ version: 2.1 orbs: gcp-gcr: circleci/gcp-gcr@0.15.0 commands: - nix: - description: "Build fortran and wrapper in nix environment" + initialize_nix: steps: - run: nix-env -i git openssh google-cloud-sdk - checkout @@ -16,26 +15,62 @@ commands: command: | git submodule init git submodule update - - restore_cache: - name: Restore nix build cache - keys: - - nix-fv3gfs-fortran-{{ .Environment.CIRCLE_SHA1 }} - run: | nix-env -iA cachix -f https://cachix.org/api/v1/install cachix use vulcanclimatemodeling - - run: | nix-build -j 4 -A fms | cachix push vulcanclimatemodeling - nix-shell --run "cd FV3 && bash configure nix && make -j 4" + build_repro: + steps: + - restore_cache: + name: Restore nix build cache + keys: + - nix-fv3gfs-fortran-repro-{{ .Environment.CIRCLE_SHA1 }} + - run: | + nix-shell --run "cd FV3 && bash configure nix && cd .. && make build_repro" - run: name: Build wrapper - command: nix-shell --run "make -j 4 -C FV3 wrapper_build" + command: nix-shell --run "make build_wrapper" + - save_cache: + name: Save nix build cache + key: nix-fv3gfs-fortran-repro-{{ .Environment.CIRCLE_SHA1 }} + paths: + - FV3/ + build_debug: + steps: + - restore_cache: + name: Restore nix build cache + keys: + - nix-fv3gfs-fortran-debug-{{ .Environment.CIRCLE_SHA1 }} + - run: | + nix-shell --run "cd FV3 && bash configure nix && cd .. && make build_debug" - save_cache: name: Save nix build cache - key: nix-fv3gfs-fortran-{{ .Environment.CIRCLE_SHA1 }} + key: nix-fv3gfs-fortran-debug-{{ .Environment.CIRCLE_SHA1 }} paths: - FV3/ + test_fortran_basic: + steps: + - run: + name: Test fortran + command: nix-shell --run "make test_fortran_basic" + test_wrapper_basic: + steps: + - run: + name: Test wrapper + command: nix-shell --run "make -C FV3/wrapper test_basic" + test_fortran_coarse_graining: + steps: + - run: + name: Test fortran + command: nix-shell --run "make test_fortran_coarse_graining" + test_wrapper_coarse_graining: + steps: + - run: + name: Test wrapper + command: nix-shell --run "make -C FV3/wrapper test_coarse_graining" + jobs: - nix-full: + nix-full-repro: docker: - image: nixos/nix environment: @@ -43,14 +78,15 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix + - initialize_nix + - build_repro - run: name: Test fortran - command: nix-shell --run "make test_native_fortran" + command: nix-shell --run "make test_fortran" - run: name: Test wrapper command: nix-shell --run "make -C FV3/wrapper test" - nix-basic: + nix-full-debug: docker: - image: nixos/nix environment: @@ -58,14 +94,12 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix + - initialize_nix + - build_debug - run: name: Test fortran - command: nix-shell --run "make test_native_fortran_basic" - - run: - name: Test wrapper - command: nix-shell --run "make -C FV3/wrapper test_basic" - nix-coarse-graining: + command: nix-shell --run "make test_fortran" + nix-basic-repro: docker: - image: nixos/nix environment: @@ -73,14 +107,45 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix - - run: - name: Test fortran - command: nix-shell --run "make test_native_fortran_coarse_graining" - - run: - name: Test wrapper - command: nix-shell --run "make -C FV3/wrapper test_coarse_graining" - nix-emulation: + - initialize_nix + - build_repro + - test_fortran_basic + - test_wrapper_basic + nix-basic-debug: + docker: + - image: nixos/nix + environment: + FV3CONFIG_CACHE_DIR: /tmp/.fv3config + GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json + FSSPEC_GS_REQUESTER_PAYS: vcm-ml + steps: + - initialize_nix + - build_debug + - test_fortran_basic + nix-coarse-graining-repro: + docker: + - image: nixos/nix + environment: + FV3CONFIG_CACHE_DIR: /tmp/.fv3config + GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json + FSSPEC_GS_REQUESTER_PAYS: vcm-ml + steps: + - initialize_nix + - build_repro + - test_fortran_coarse_graining + - test_wrapper_coarse_graining + nix-coarse-graining-debug: + docker: + - image: nixos/nix + environment: + FV3CONFIG_CACHE_DIR: /tmp/.fv3config + GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json + FSSPEC_GS_REQUESTER_PAYS: vcm-ml + steps: + - initialize_nix + - build_debug + - test_fortran_coarse_graining + nix-emulation-repro: docker: - image: nixos/nix environment: @@ -88,14 +153,15 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix + - initialize_nix + - build_repro - run: name: Test fortran - command: nix-shell --run "make test_native_fortran_emulation" + command: nix-shell --run "make test_fortran_emulation" - run: name: Test wrapper command: nix-shell --run "make -C FV3/wrapper test_emulation" - nix-unmarked: + nix-unmarked-repro: docker: - image: nixos/nix environment: @@ -103,11 +169,12 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix + - initialize_nix + - build_repro - run: name: Test fortran - command: nix-shell --run "make test_native_fortran_unmarked" - nix-wrapper: + command: nix-shell --run "make test_fortran_unmarked" + nix-wrapper-repro: docker: - image: nixos/nix environment: @@ -115,7 +182,8 @@ jobs: GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json FSSPEC_GS_REQUESTER_PAYS: vcm-ml steps: - - nix + - initialize_nix + - build_repro - run: name: Test wrapper command: nix-shell --run "make -C FV3/wrapper test" @@ -126,71 +194,19 @@ jobs: - checkout - run: sudo pip3 install pre-commit==2.15.0 - run: pre-commit - build_default: - machine: - docker_layer_caching: true - image: ubuntu-2004:202111-02 - environment: - FV3CONFIG_CACHE_DIR: /tmp/.fv3config - GOOGLE_APPLICATION_CREDENTIALS: /tmp/key.json - FSSPEC_GS_REQUESTER_PAYS: vcm-ml - steps: - - checkout - - run: - name: "gcloud auth" - command: | - echo $ENCODED_GCR_KEY | base64 -d > $GOOGLE_APPLICATION_CREDENTIALS - echo "export GCLOUD_SERVICE_KEY=\$(echo \$ENCODED_GCR_KEY | base64 --decode)" >> $BASH_ENV - - gcp-gcr/gcr-auth - - run: - name: "Pull dependency images" - command: | - echo "$ENCODED_GCR_KEY" | base64 --decode | docker login --username _json_key --password-stdin https://gcr.io - make pull_deps - - run: - name: "Pull Submodules" - command: | - git submodule init - git submodule update - - run: DOCKER_BUILDKIT=1 BUILDKIT_PROGRESS=plain BUILD_FROM_INTERMEDIATE=y make build build_debug build_serialize - - restore_cache: - keys: - - v1.4-{{ checksum "requirements.txt"}} - - run: - name: "Install Python test dependencies" - command: | - pyenv versions - [ -d /opt/circleci/.pyenv/versions/3.9.7 ] || pyenv install 3.9.7 - pyenv global 3.9.7 - pip install -r requirements.txt - - save_cache: - paths: - - $FV3CONFIG_CACHE_DIR - - /opt/circleci/.pyenv/versions/3.9.7 - key: v1.4-{{ checksum "requirements.txt"}} - # tests - - run: - name: "Run pytest tests" - # -s to avoid capturing stdout/stderr of md5sum call - command: | - make test - no_output_timeout: 1200 - - run: make push_deps - - run: - name: "Delete data files" - command: | - rm ./tests/pytest/output/*/*/INPUT/*.nc - rm ./tests/pytest/output/*/*/*/*.grb - when: on_fail - - store_artifacts: - path: ./tests/pytest/output + workflows: version: 2 build: jobs: - lint - - nix-basic: - name: Minimal native fortran and wrapper tests + - nix-basic-repro: + name: Minimal fortran and wrapper tests in repro mode + filters: + branches: + ignore: master + - nix-basic-debug: + name: Minimal fortran tests in debug mode filters: branches: ignore: master @@ -200,59 +216,71 @@ workflows: filters: branches: ignore: master - - nix-coarse-graining: - name: Coarse graining tests + - nix-coarse-graining-repro: + name: Coarse graining tests in repro mode + requires: + - Minimal fortran and wrapper tests in repro mode + - Launch coarse graining tests + filters: + branches: + ignore: master + - nix-coarse-graining-debug: + name: Coarse graining tests in debug mode requires: - - Minimal native fortran and wrapper tests + - Minimal fortran tests in debug mode - Launch coarse graining tests filters: branches: ignore: master - - hold-nix-emulation: + - hold-nix-emulation-repro: name: Launch emulation tests type: approval filters: branches: ignore: master - - nix-emulation: + - nix-emulation-repro: name: Emulation tests requires: - - Minimal native fortran and wrapper tests + - Minimal fortran and wrapper tests in repro mode - Launch emulation tests filters: branches: ignore: master - - hold-nix-unmarked: + - hold-nix-unmarked-repro: name: Launch unmarked fortran tests type: approval filters: branches: ignore: master - - nix-unmarked: + - nix-unmarked-repro: name: Unmarked fortran tests requires: - - Minimal native fortran and wrapper tests + - Minimal fortran and wrapper tests in repro mode - Launch unmarked fortran tests filters: branches: ignore: master - - hold-nix-wrapper: + - hold-nix-wrapper-repro: name: Launch wrapper tests type: approval filters: branches: ignore: master - - nix-wrapper: + - nix-wrapper-repro: name: Wrapper tests requires: - - Minimal native fortran and wrapper tests + - Minimal fortran and wrapper tests in repro mode - Launch wrapper tests filters: branches: ignore: master - - build_default - - nix-full: - name: "Full native tests" + - nix-full-repro: + name: "Full tests in repro mode" + filters: + branches: + only: master + - nix-full-debug: + name: "Full tests in debug mode" filters: branches: only: master diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index 3bc13a54b..000000000 --- a/.dockerignore +++ /dev/null @@ -1,7 +0,0 @@ -tests/pytest/output/** -*.o -*.mod -*.so -fv3.exe -*.tmp.f90 -coverage_* diff --git a/FV3/conf/configure.fv3.nix b/FV3/conf/configure.fv3.nix index abdbc6c49..d1b369938 100644 --- a/FV3/conf/configure.fv3.nix +++ b/FV3/conf/configure.fv3.nix @@ -16,8 +16,8 @@ NETCDF_DIR = /usr # flags # ######### # default is 64-bit OpenMP non-hydrostatic build -DEBUG = -REPRO = Y +DEBUG ?= N +REPRO ?= Y VERBOSE = OPENMP = Y AVX2 = N diff --git a/FV3/gfsphysics/physics/samfdeepcnv.f b/FV3/gfsphysics/physics/samfdeepcnv.f index 76204ebb4..d29410d2f 100644 --- 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 index 668515239..2ecbc5d55 100644 --- a/Makefile +++ b/Makefile @@ -1,131 +1,44 @@ # setup (use XXX= make to override) -GCR_URL ?= us.gcr.io/vcm-ml -COMMIT_SHA := $(shell git rev-parse HEAD) -DOCKERFILE ?= docker/Dockerfile -ENVIRONMENT_TAG_NAME ?= latest -COMPILE_OPTION ?= -COMPILE_TARGET ?= fv3gfs-compiled -BUILD_ARGS ?= -BUILD_FROM_INTERMEDIATE ?= n -ENVIRONMENT_TARGET ?= fv3gfs-environment -CUDA ?= n -OTHER_MOUNTS ?= - -# base images w/ or w/o CUDA -ifeq ($(CUDA),n) - BASE_IMAGE ?=ubuntu:18.04 - DEP_TAG_NAME ?=gnu7-mpich314-nocuda -else - BASE_IMAGE ?=nvidia/cuda:10.2-devel-ubuntu18.04 - DEP_TAG_NAME ?=gnu7-mpich314-cuda102 -endif -BUILD_ARGS += --build-arg BASE_IMAGE=$(BASE_IMAGE) - -# image names (use XXX_IMAGE= make to override) -COMPILED_TAG_NAME ?=$(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) -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_repro build_debug build_wrapper clean help: @awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z0-9_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST) -build: build_compiled ## build default container image (production) - -build_environment: ## build environment container image - docker build -f $(DOCKERFILE) -t $(ENVIRONMENT_IMAGE) \ - --target $(ENVIRONMENT_TARGET) . - -build_compiled: ## build production container image - docker build \ - --build-arg compile_option=$(COMPILE_OPTION) \ - $(BUILD_ARGS) \ - -f $(DOCKERFILE) \ - -t $(COMPILED_IMAGE) \ - --target $(COMPILE_TARGET) . - -build_debug: ## build container image for debugging - COMPILED_TAG_NAME=$(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) - 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 - -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) - -build_native: ## build FV3 locally (assuming all tools and dependencies are available in the environment) +build: ## build repro and debug mode versions FV3 locally (assuming all tools and dependencies are available in the environment) + $(MAKE) build_repro + $(MAKE) clean_fortran_build_artifacts + $(MAKE) build_debug + +build_repro: ## build repro mode version of FV3 locally (assuming all tools and dependencies are available in the environment) $(MAKE) -j 8 -C FV3 + mkdir -p bin + cp FV3/fv3.exe bin/fv3.repro.exe +build_debug: ## build debug mode version of FV3 locally in debug mode + # Note DEBUG and REPRO cannot be set to Y simultaneously; CALLPYFORT can + # also not currently be set in debug mode without failures (see GitHub issue + # #365). + CALLPYFORT= DEBUG=Y REPRO= $(MAKE) -j 8 -C FV3 + mkdir -p bin + cp FV3/fv3.exe bin/fv3.debug.exe -test_native: DIR=coverage_$(shell date -Is) -test_native: ## run native tests (all tools and build dependencies are assumed to be available in the environment) - find FV3 -type f -name '*.gcda' -delete - pytest --native tests/pytest - pytest -v FV3/wrapper/tests/pytest - pytest -v FV3/wrapper/tests/test_all_mpi_requiring.py - mkdir -p $(DIR) && \ - cd $(DIR) && \ - gcovr -d -r ../FV3 --html --html-details -o index.html +build_wrapper: + $(MAKE) -j 8 -C FV3 wrapper_build -test_native_fortran: - pytest --native tests/pytest -v +test_fortran: + pytest tests/pytest -v -test_native_fortran_basic: - pytest --native tests/pytest -v -m 'basic' +test_fortran_basic: + pytest tests/pytest -v -m 'basic' -test_native_fortran_coarse_graining: - pytest --native tests/pytest -v -m 'coarse' +test_fortran_coarse_graining: + pytest tests/pytest -v -m 'coarse' -test_native_fortran_emulation: - pytest --native tests/pytest -v -m 'emulation' +test_fortran_emulation: + pytest tests/pytest -v -m 'emulation' -test_native_fortran_unmarked: - pytest --native tests/pytest -v -m 'not basic and not coarse and not emulation' +test_fortran_unmarked: + pytest tests/pytest -v -m 'not basic and not coarse and not emulation' test_wrapper: $(MAKE) -C FV3/wrapper/ test @@ -139,10 +52,15 @@ lint: reformat: pre-commit run --all-files -clean: ## cleanup source tree and test output - (cd FV3 && make clean) - $(RM) -f inputdata - $(RM) -rf tests/pytest/output/* +clean_fortran_build_artifacts: + $(MAKE) -C FV3 clean + +clean_executables: + $(RM) -rf bin + +clean: ## cleanup source tree and executables + $(MAKE) clean_fortran_build_artifacts + $(MAKE) clean_executables setup-hooks: pre-commit install diff --git a/README.md b/README.md index 73a4fbe95..90b98e9a5 100644 --- a/README.md +++ b/README.md @@ -13,10 +13,10 @@ repositories associated with different subtrees of this repository: . # ~ https://github.com/ufs-community/ufs-weather-model ├── FMS # https://github.com/NOAA-GFDL/FMS ├── FV3 # https://github.com/NOAA-EMC/fv3atm -│   ├── atmos_cubed_sphere # https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere -│   └── ccpp -│      ├── framework # https://github.com/NCAR/ccpp-framework -│      └── physics # https://github.com/NCAR/ccpp-physics +│ ├── atmos_cubed_sphere # https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere +│ └── ccpp +│ ├── framework # https://github.com/NCAR/ccpp-framework +│ └── physics # https://github.com/NCAR/ccpp-physics ├── serialbox # https://github.com/GridTools/serialbox └── stochastic_physics # https://github.com/noaa-psd/stochastic_physics ``` @@ -24,168 +24,40 @@ repositories associated with different subtrees of this repository: In some cases these are actual submodules, and in other cases they are subtrees. -# How to run fv3gfs via a docker image +## Deprecation of serialize build support -Don't forget to load the submodules in your local copy of the source, i.e. +As September, 2023 we have deprecated the infrastructure for building and +testing the model in a Docker container. All development and testing now occurs +in the nix environment, described below. This means that the latest version of +the repository no longer includes code to facilitate building the model to +output serialized data through `serialbox`, which previously was done using a +Docker image; if you would still like to use this functionality, be sure to +check out commit +[`b3793303df9800de341a3f8e8b234c6f4dc2b7a1`](https://github.com/ai2cm/fv3gfs-fortran/tree/b3793303df9800de341a3f8e8b234c6f4dc2b7a1) +or earlier. -```bash -cd fv3gfs-fortran -git submodule update --init --recursive -``` - -## Step 1: Create Docker image - -Different docker images are used to build the environment and compile this -model. For development purposes, the software environment is useful, but for -running the model it is most convenient that the docker image contains the -built FV3 model. Both of these images can be built using the following command: - -```bash -make build -``` - -This will make a `fv3gfs-compiled:gnu7-mpich314-nocuda` image with a compiled model executable -that can be used for production simuliations. Other tag names and compile options can be set. For example, to build a debugging executable in a docker image: - -```bash -make build_debug -``` - -Rules are provided for certain compile options. Check the Makefile for a list or simply type `make help`. - -## Step 2: Install fv3config - -FV3 expects to be run within a certain directory structure, which we call a "run directory". These can be prepared using the [fv3config](https://github.com/ai2cm/fv3config). - -This tool can be installed using `pip install fv3config`. To use versions that are guaranteed to work, we provide a `requirements.txt`, that you can use as follows: - -```bash -python3 -m venv venv -source venv/bin/activate -pip install -r requirements.txt -``` - -This command will download required dependencies for running tests and using fv3config. - -In order to use `run_docker.sh` below, you will also need to set the fv3config -cache directory using - -```bash -export FV3CONFIG_CACHE_DIR= -``` - -This should be added to your `~/.bashrc`. If you do not set your cache directory, a default location will be used. You can use the command - -```bash -python -c 'import fv3config; print(fv3config.get_cache_dir())' -``` - -to find out the default location. - -## Step 3: Create run directory - -Create or download an fv3config yaml configuration. Edit the configuration as needed. -Examples of such configurations are included in the tests under `tests/pytest/config`. - -Once you have a configuration file, e.g. `example/config.yml`, you can write a run directory as follows: - - write_run_directory example/config.yml rundirectory - -You will need to be authenticated with google cloud storage to run this command. See instructions below. - -The python API equivalent of this is -```python3 -import fv3config -import yaml -config = yaml.safe_load(open('example/config.yml', 'r')) -fv3config.write_run_directory(config, 'rundir') -``` - -This example is included in `example/create_rundir.py`. - -You also must put a `submit_job.sh` script in the run directory. You can copy the one -included in this repository. - -```bash -cp example/submit_job.sh rundir/ -``` - -Optionally edit `rundir/input.nml` and `rundir/diag_table` to modify the namelist used -for your run and the set of diagnostics the model will output. Ideally this should be -done instead by editing the `config.yml` we used earlier. - - -### Authentication - -The data referred to by this example configuration are stored in a GCS bucket, stored in the `us-central1` region. This data is free to use, but we have enabled requestor-pays to avoid paying for network transfer costs incurred by external users. You will need to authenticate with your own google cloud project credentials to access this data. Detailed instructions are out of scope, but usually involves the setting the following environmental variables -``` -export FSSPEC_GS_REQUESTER_PAYS="on" -export GOOGLE_APPLICATION_CREDENTIALS=/path/to/key.json -``` -For more information see [this documentation](https://gcsfs.readthedocs.io/en/latest/api.html#gcsfs.core.GCSFileSystem). - -## Step 4: Run the model - -## Within container/manual - -Assuming you are in environment with a compiled version of the FV3 model at the path `/absolute/path/to/fv3.exe` and a rundirectory at the path ``, you can run the model like this - - cd - mpirun -n /absolute/path/to/fv3.exe - -The number of processors has to be `6 * num_tiles` where `num_tiles` is the product of the `namelist.fv_core_nml.layout` configurations. - - -## From host via docker - -If you would like to run the model in one of the included docker containers use the command - -```bash -bash run_docker.sh $FV3CONFIG_CACHE_DIR -``` - -where `` is an absolute path to the run directory. `` is the name of the container built by `make build`, typically `us.gcr.io/vcm-ml/fv3gfs-compiled:gnu7-mpich314-nocuda`. - -# Developing the model - -## Docker - -The `fv3gfs-environment` docker image is useful for development purposes where the model code will be recompiled repeatedly in an interactive fashion. To start a bash shell in a docker container with the FV3 source tree mounted at `/FV3`, run the command: - -```bash -make enter -``` - -If necessary, this will build the image, but it will overwrite the compiled sources -with a bind mount to your host filesystem. You will need to compile the model with -the filesystem bind-mounted in this way. Once in the container, you can compile the model using the commands -```bash -cd /FV3 -./configure gnu_docker -make clean -make -j8 -``` +## Developing the model and running tests -## Nix +### Nix +The primary mode of development in this repository now runs through the +[nix](https://nixos.org/) package manager. This package manager is available on +Mac and Linux, and provides a light weight means to distribute isolated software +environments. +To begin, install nix following [these +instructions](https://nixos.org/download.html). -FV3 can also be installed using the [nix](https://nixos.org/) package -manager. This package manager is available on Mac and Linux, and provides a -light weight means to distribute isolated software environments. - - -### Installation - -To begin, install nix following [these instructions](https://nixos.org/download.html). - -(optional) We host binaries using a tool called cachix, and this will greatly speed up any builds. To use our binaries, [install cachix](https://github.com/cachix/cachix#installation) and then run +(optional) We host binaries using a tool called cachix, and this will greatly +speed up any builds. To use our binaries, [install +cachix](https://github.com/cachix/cachix#installation) and then run cachix use vulcanclimatemodeling -Without using the cachix cache, FV3 and all its dependencies will need to build from source (~20 minutes). This only happens once per machine, but it is slow. +Without using the cachix cache, FV3 and all its dependencies will need to build +from source (~20 minutes). This only happens once per machine, but it is slow. -### Developing +#### Developing To develop the model, you can use the environment specified in `shell.nix` by running @@ -197,93 +69,66 @@ Then configure the build to use nix And build the model (from the root directory) - make build_native + make build_repro And the wrapper - make -C FV3 wrapper_build + make build_wrapper + +At this point you can run the tests. -At this point you can run [the native tests](#native-tests). -# Testing the model +## Testing the fortran model -Tests are included in the `tests` subdirectory. You can see which ones run in -continuous integration by inspecting `.circleci/config.yml`. +Tests of the pure fortran model are included in the `tests` subdirectory. You +can see which ones run in continuous integration by inspecting +`.circleci/config.yml`. Regression tests which check the bit-reproducibility of results are performed for a set of reference configurations included in `tests/pytest/config`. Please read the README in `tests/pytest` for more information about these regression tests and how to update the reference checksums. -## Native tests +### Testing the model in different compile modes -Some of the tests can be run in a native environment (e.g. nix, bare metal, -or inside a docker container). A native environment is capable of running the -file `FV3/fv3.exe`. +The fortran model can be built with different sets of compiler flags, defined in +the `FV3/conf/*.configure.fv3` files. These sets of compiler flags facilitate +running the model in different modes. For production workflows, we run the +model with the `repro` set of compiler flags; for debugging it can be useful to +compile and run the model with the `debug` set of compiler flags, which can +facilitate catching array out of bounds errors and the like. -After building the model inside of the `FV3` subdirectory, you can run these -tests like this: +To build the model in `repro` mode use: - make test_native - # or manually - pytest --native tests/pytest - # and - pytest -v FV3/wrapper/tests/pytest - pytest -v FV3/wrapper/tests/test_all_mpi_requiring.py + make build_repro -When using the makefile target, code coverages reports will be saved to the -folder `coverage_`. +To build the model in `debug` mode use: -## Image tests + make build_debug -Certain tests are more convenient or reliable to run within a docker container. -For example, regression tests are only valid within a consistent environment as -represented by a docker container. These test are run from a host environment like this +To build executables in both `repro` and `debug` mode use: - pytest tests/pytest + make build -# Serialization +The test infrastructure is written to detect and run tests only for which the +appropriate executable exists, since regression tests produce different results +when running in `repro` versus `debug` mode. -The model can be compiled for the generation of serialize data which can be used for unit-testing individual components of the model. For more information see the documentation [here](tests/serialized_test_data_generation/README.md). +To run the full suite of fortran model tests for the compiled executables, use: -To build a docker image for serialization use the command + make test_fortran -```bash -make build_serialize -``` +Since the tests are time-consuming, during development it can often be helpful +to select specific tests that pertain to the code you are developing, e.g. with +the `-k` option of `pytest`: -which will create an image where the source files have been pre-processed for serialization. Similarly to default compilation, you can interactively develop -for serialization using the command + pytest -v -k test_use_prescribed_sea_surface_properties tests/pytest/test_regression.py -```bash -make enter_serialize -``` +There are also make rules which select tests to run based on `pytest` marks, +e.g.: -Make sure to set the GT4PY\_DEV flag to `Y' for compilation. This will alter a subset of the code to be more suitable for gt4py in the python port. When we have all the features we need on the python side and are confident in the robustness of the new model, we should be able to remove these. The original FV3 sources will be mounted to `/FV3/original`. To compile the model for serialization inside the container, you can use the commands + make test_fortran_basic -```bash -cd /FV3 -make clean -make -C original serialize_preprocess -make -j8 -``` - -If you need to be able to see the preprocessed `atmos_cubed_sphere` sources on your -host filesystem, you can do that with: - -```bash -OTHER_MOUNTS="-v :/FV3/atmos_cubed_sphere" make enter_serialize -``` - -Where `` is replaced with the directory on your host filesystem where you -want to see the preprocessed sources. - -This workflow does not support viewing preprocessed sources in the root `/FV3` directory -on the host filesystem, because `/FV3` has a bind-mounted subdirectory `original` and -it is not possible to contain a bind-mounted subdirectory in a separately bind-mounted -directory. You could see these sources by setting `SERIALBOX_OUTDIR` to a different -directory (it is `/FV3` by default) that you have bind-mounted in to the container. - -# The Python wrapper +## Testing the Python wrapper The `FV3/wrapper` subdirectory contains a python wrappper that can be used to call the fortran model for interactive ML. It's usage docs can be seen [here](TODO/add/path). @@ -302,10 +147,10 @@ dependencies, and is the recommend development environment for iterative development (edit/build/test) of the wrapper. In other environments, e.g. HPC/DOCKER these builds dependencies will need to be manually installed. -Once the dependencies are installed the wrapper and fv3.exe can be built like -this +Once the dependencies are installed, including the `repro`-mode version of the +fortran executable, the wrapper can be built like this - make -C FV3 wrapper_build + make build_wrapper To install the wrapper in some python environment, you can use the wheel built above @@ -320,8 +165,17 @@ To test the wrapper make test_wrapper -# Docker BuildKit - -If you are using a version of docker that supports it, you can enable buildkit by -setting `DOCKER_BUILDKIT=1` as an environment variable. This can be useful when building docker targets in this repo, because it will avoid building mulit-stage targets that are not required for the final image. +## Authentication +The input data files required by our tests are stored in a GCS bucket, stored in +the `us-central1` region. This data is free to use, but we have enabled +requestor-pays to avoid paying for network transfer costs incurred by external +users. You will need to authenticate with your own google cloud project +credentials to access this data. Detailed instructions are out of scope, but +usually involves the setting the following environmental variables +``` +export FSSPEC_GS_REQUESTER_PAYS="on" +export GOOGLE_APPLICATION_CREDENTIALS=/path/to/key.json +``` +For more information see [this +documentation](https://gcsfs.readthedocs.io/en/latest/api.html#gcsfs.core.GCSFileSystem). diff --git a/coverage.sh b/coverage.sh deleted file mode 100755 index 1c750ce48..000000000 --- a/coverage.sh +++ /dev/null @@ -1,63 +0,0 @@ -#!/bin/bash - -# Script which generates coverage information given a configuration *.yml file. -# -# Usage: coverage.sh default.yml -# Output: coverage_default directory which contains coverage in html format -# -# Author: Oliver Fuhrer, Vulcan Inc. - -# stop on errors -set -e - -# arguments -config_file=$1 -if [ -z "${config_file}" -o ! -f "${config_file}" ] ; then - echo "Error: must specify a valid config file as argument (usage: $0 config.yml)" - exit 1 -fi - -# setup -base_dir=`pwd` -config_name=`basename ${config_file} .yml` -coverage_dir=${base_dir}/coverage_${config_name} -rundir=${base_dir}/rundir # must be an absolute path -submit_job=${base_dir}/tests/serialized_test_data_generation/submit_job.sh -count_ranks=${base_dir}/tests/serialized_test_data_generation/count_ranks.py -gcr_url="us.gcr.io/vcm-ml/fv3gfs-compiled" - -# don't overwrite any previous coverage data -if [ -d ${coverage_dir} ] ; then - echo "The directory ${coverage_dir} already exists. Remove and try again." - exit 1 -fi - -# build docker container with model compiled for coverage -COMPILED_TAG_NAME=gcov COMPILED_IMAGE=${gcr_url}:gcov COMPILE_OPTION="OPENMP=\\\nREPRO=\\\nDEBUG=Y\\\nGCOV=Y\\\nGT4PY_DEV=Y\\\nSUBSET_PHYSICS=Y" make -C "${base_dir}" build - -# setup run directory -\rm -rf "${rundir}" -write_run_directory "${config_file}" "${rundir}" -cp "${submit_job}" "${rundir}" -cp "${count_ranks}" "${rundir}" - -# run the model -mkdir -p ${coverage_dir}; \rm -rf ${coverage_dir}/* -mkdir -p ./data; \rm -rf ./data/* -docker run -it --rm --network host -v ${coverage_dir}:/coverage -v `pwd`/rundir:/rundir -v `pwd`/data:/data ${gcr_url}:gcov bash -c "set -ex; cd /rundir; ./submit_job.sh; pip3 install gcovr; cd /coverage; gcovr -d -r /FV3/ --html --html-details -o index.html" -\rm -rf data - -# cleanup run directory -set +e -grep Termination ${rundir}/stdout.out > /dev/null -if [ $? -ne 0 ] ; then - echo "Warning: Run does not seem to have been successfull. Check the rundir!" -else - \rm -rf "${rundir}" -fi -set -e - -# tell user we're done -echo "Open coverage_${config_name}/index.html to view coverage data" -exit 0 - diff --git a/docker/Dockerfile b/docker/Dockerfile deleted file mode 100644 index 95baf151d..000000000 --- a/docker/Dockerfile +++ /dev/null @@ -1,246 +0,0 @@ -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 - -RUN apt-get update && apt-get install -y \ - wget \ - libtool-bin \ - gcc \ - g++ \ - gfortran \ - make - -RUN wget -q http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz && \ - tar xzf mpich-3.1.4.tar.gz && \ - cd mpich-3.1.4 && \ - ./configure --enable-fortran --enable-cxx --prefix=/usr --enable-fast=all,O3 && \ - make -j24 - -FROM $MPI_IMAGE AS mpi_image - -FROM $BASE_IMAGE AS fv3gfs-environment -RUN apt-get update && apt-get install -y \ - wget \ - gcc \ - libtool-bin \ - g++ \ - gfortran \ - make \ - curl \ - git \ - libblas-dev \ - liblapack-dev \ - libnetcdf-dev \ - libnetcdff-dev \ - perl \ - rsync \ - libffi-dev \ - openssl - -COPY --from=mpi_image /mpich-3.1.4 /mpich-3.1.4 - -RUN cd /mpich-3.1.4 && make install && ldconfig - -# download and install NCEP libraries -RUN git config --global http.sslverify false && \ - git clone https://github.com/NCAR/NCEPlibs.git && \ - mkdir /opt/NCEPlibs && \ - cd NCEPlibs && \ - git checkout 3da51e139d5cd731c9fc27f39d88cb4e1328212b && \ - echo "y" | ./make_ncep_libs.sh -s linux -c gnu -d /opt/NCEPlibs -o 1 - -## -## Setup environment for Serialbox -##--------------------------------------------------------------------------------- -FROM fv3gfs-environment as fv3gfs-environment-serialbox -# set TZ -ENV DEBIAN_FRONTEND=noninteractive TZ=US/Pacific -RUN ln -snf /usr/share/zoneinfo/$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 - -ENV CC=/usr/bin/mpicc \ - FC=/usr/bin/mpif90 \ - LDFLAGS="-L/usr/lib" \ - LOG_DRIVER_FLAGS="--comments" \ - CPPFLAGS="-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500 -DGFS_PHYS" \ - FCFLAGS="-fcray-pointer -Waliasing -ffree-line-length-none -fno-range-check -fdefault-real-8 -fdefault-double-8 -fopenmp" - -COPY FMS /FMS -RUN apt-get update && \ - apt-get install -y m4 libtool autoconf bats && \ - cd /FMS && autoreconf --install && ./configure && \ - cd /FMS && make -j8 && \ - mv /FMS/*/*.mod /FMS/*/*.o /FMS/*/*.h /FMS/ - -## Build ESMF -##--------------------------------------------------------------------------------- -FROM fv3gfs-environment AS fv3gfs-esmf - -ENV ESMF_DIR=/esmf \ - ESMF_INSTALL_PREFIX=/usr/local/esmf \ - ESMF_INSTALL_MODDIR=/usr/local/esmf/include \ - ESMF_INSTALL_HEADERDIR=/usr/local/esmf/include \ - ESMF_INSTALL_LIBDIR=/usr/local/esmf/lib \ - ESMF_INSTALL_BINDIR=/usr/local/esmf/bin \ - ESMF_NETCDF_INCLUDE=/usr/include \ - ESMF_NETCDF_LIBS="-lnetcdf -lnetcdff" \ - ESMF_BOPT=O3 - -RUN git clone -b ESMF_8_0_0 --depth 1 https://git.code.sf.net/p/esmf/esmf $ESMF_DIR && \ - cd $ESMF_DIR && \ - make lib -j24 && \ - make install && \ - make installcheck - -## Copy FV3GFS sources for non-serialize image -##--------------------------------------------------------------------------------- -FROM $BASE_IMAGE AS fv3gfs-src-serialize-false - -ARG compile_option -ARG configure_file=configure.fv3.gnu_docker - -COPY stochastic_physics /stochastic_physics -COPY FV3/coarse_graining /FV3/coarse_graining -COPY FV3/conf /FV3/conf -COPY FV3/ccpp /FV3/ccpp -COPY FV3/cpl /FV3/cpl -COPY FV3/gfsphysics /FV3/gfsphysics -COPY FV3/io /FV3/io -COPY FV3/ipd /FV3/ipd -COPY FV3/stochastic_physics /FV3/stochastic_physics -COPY FV3/makefile FV3/mkDepends.pl FV3/atmos_model.F90 FV3/LICENSE.md \ - FV3/coupler_main.F90 FV3/fv3_cap.F90 FV3/module_fcst_grid_comp.F90 \ - FV3/module_fv3_config.F90 FV3/time_utils.F90 /FV3/ - -# copy appropriate configuration file to configure.fv3 -RUN cp /FV3/conf/$configure_file \ - /FV3/conf/configure.fv3 && \ - if [ ! -z $compile_option ]; then sed -i "33i $compile_option" \ - /FV3/conf/configure.fv3; fi - -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 $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 - -ENV ESMFMKFILE=/usr/local/esmf/lib/esmf.mk - -ENV SERIALBOX_DIR=/serialbox \ - SERIALBOX_OUTDIR=/FV3 \ - 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 - -COPY --from=serialbox_image /serialbox/install $SERIALBOX_DIR -COPY --from=fms_image /FMS $FMS_DIR -COPY --from=esmf_image /usr/local/esmf $ESMF_DIR - -COPY --from=fv3gfs-sources /FV3 /FV3 -COPY --from=fv3gfs-sources /stochastic_physics /stochastic_physics - -RUN cd /FV3 && make clean_no_dycore && make libs_no_dycore -j16 - -COPY --from=fv3gfs-sources FV3/atmos_cubed_sphere /FV3/atmos_cubed_sphere - -RUN cd /FV3/atmos_cubed_sphere && make clean && cd /FV3 && make -j16 - -## Define final "user" image for running tests -##--------------------------------------------------------------------------------- -FROM fv3gfs-build AS fv3gfs-compiled - -RUN apt-get update && apt-get install -y \ - python3 \ - python3-pip && \ - ln -s /bin/python3 /bin/python && \ - ln -s /bin/pip3 /bin/pip -# install python packages needed to convert to netcdf data -RUN pip3 install --upgrade setuptools pip && \ - pip3 install --no-cache-dir pyyaml xarray==0.16.2 f90nml==1.1.0 netCDF4 - -# run model -CMD ["bash", "/rundir/submit_job.sh"] diff --git a/run_docker.sh b/run_docker.sh deleted file mode 100755 index b128256fb..000000000 --- a/run_docker.sh +++ /dev/null @@ -1,42 +0,0 @@ -#!/bin/bash - -set -x -if [ "$#" -lt 2 ] ; then - echo "ERROR: You must supply a docker image name and a run directory." - exit 1 -fi -all_args=("$@") -docker_image_name=$1 -rundir_host=$2 -fv3config_cache_dir=$3 - -if [ ! -d $rundir_host ] ; then - echo "ERROR: provided run directory $2 does not exist" - exit 1 -fi -if [ ! -f $rundir_host/submit_job.sh ] ; then - echo "Missing submit_job.sh in $rundir_host. Abort!" - exit 1 -fi - -rundir_container=/rundir - -if [ "$#" -gt 2 ] ; then # mount fv3config cache directory - remaining_args=("${all_args[@]:3}");\ - docker run \ - --rm \ - -v $rundir_host:$rundir_container \ - -v $fv3config_cache_dir:$fv3config_cache_dir \ - -it $1 ${remaining_args[@]} -else # the rundir has real input files, not symlinked to a fv3config_cache dir - if [ -n "`find $rundir_host -type l -ls`" ] ; then - echo "Symbolic links found in run directory but no cache directory specified" - exit 1 - fi - docker run \ - --rm \ - -v $rundir_host:$rundir_container \ - -it $1 ${remaining_args[@]} -fi - -exit 0 diff --git a/tests/pytest/.gitignore b/tests/pytest/.gitignore deleted file mode 100644 index 53752db25..000000000 --- a/tests/pytest/.gitignore +++ /dev/null @@ -1 +0,0 @@ -output diff --git a/tests/pytest/README.md b/tests/pytest/README.md index f85679d0f..1afb3fbc9 100644 --- a/tests/pytest/README.md +++ b/tests/pytest/README.md @@ -1,35 +1,10 @@ -# Image tests +# Tests -Reference files exist in subdirectories of `reference`, e.g. `reference/circleci` for -the baseline md5 checksums for Circle CI. +The tests use [pytest-regtest](https://pypi.org/project/pytest-regtest/) to +store regression information. To update the regression information (e.g. +checksums, ncdump outputs) simply add the `--regtest-reset` flag to the pytest +command invoking the failing test. For example:: -Tests need to be passed a reference directory to use. They can be run with -`pytest --refdir=$(pwd)/reference/circleci`. After running, the output of the -tests will be present in `output`. These output files can be used to update the -references, if non-bit-for-bit changes have occurred and those changes are valid. - -These files can be updated using -`set_reference.sh`, by calling e.g. `./set_reference.sh latest-serialize $(pwd)/reference/circleci`. -This script requires you give it an image tag (e.g. `latest-serialize`) and a -reference directory. The updated references need to be committed into version control. - -Considering whether a non-bit-for-bit change is valid is left to the user. If you -don't expect the model output to be changing, you should probably think hard before -updating the reference md5sum! - -Test configurations are stored in `config` as fv3config yaml files. Adding new -yaml files to this directory will add new regression tests automatically. - -These tests also support running on sarus using the SLURM scheduler, by setting `--image-runner=sarus` -as an argument to `pytest`. - -# Native tests - -The native tests use [pytest-regtest](https://pypi.org/project/pytest-regtest/) -to store regression information. To update the regression information for native -tests (e.g. checksums, ncdump outputs) simply add the `--regtest-reset` flag to -the pytest command invoking the failing test. For example:: - - pytest --regtest-reset --native tests/pytest + pytest --regtest-reset tests/pytest -Then, add any modified/created `.out` files to git. \ No newline at end of file +Then, add any modified/created `.out` files to git. diff --git a/tests/pytest/_regtest_outputs/test_regression.test_checksum_emulation[Linux].out b/tests/pytest/_regtest_outputs/test_regression.test_checksum_emulation[repro].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_checksum_emulation[Linux].out rename to tests/pytest/_regtest_outputs/test_regression.test_checksum_emulation[repro].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_gscond_logs.out b/tests/pytest/_regtest_outputs/test_regression.test_gscond_logs[repro].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_gscond_logs.out rename to tests/pytest/_regtest_outputs/test_regression.test_gscond_logs[repro].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression[debug-baroclinic.yml-False].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[debug-baroclinic.yml-False].out new file mode 100644 index 000000000..ac99fc717 --- /dev/null +++ b/tests/pytest/_regtest_outputs/test_regression.test_regression[debug-baroclinic.yml-False].out @@ -0,0 +1,37 @@ +/rundir/atmos_4xdaily_fine_inst.tile1.nc 131fab4e3cd1feae7cb6bdaff881e725 +/rundir/atmos_4xdaily_fine_inst.tile2.nc fe45eab4a5c25ec93a5a348ee08881a0 +/rundir/atmos_4xdaily_fine_inst.tile3.nc fad54c07bf8692b0bb1296a189306dff +/rundir/atmos_4xdaily_fine_inst.tile4.nc bdf349ecd9d8065fb7bc27d69b438c00 +/rundir/atmos_4xdaily_fine_inst.tile5.nc 1094331a6b0aa718e6509521ae268159 +/rundir/atmos_4xdaily_fine_inst.tile6.nc d4b2fe8b386577cb3d2eeb9d7cd727e2 +/rundir/RESTART/fv_core.res.nc 82157501c5b777a6e51603f36d381a8c +/rundir/RESTART/fv_core.res.tile1.nc 3776fd756dace0f597ec422043c7f118 +/rundir/RESTART/fv_core.res.tile2.nc 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b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-blended-area-weighted-coarse-graining.yml-True].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-blended-area-weighted-coarse-graining.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-blended-area-weighted-coarse-graining.yml-True].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-default.yml].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-default.yml-False].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-default.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-default.yml-False].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-model-level-coarse-graining.yml].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-model-level-coarse-graining.yml-True].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-model-level-coarse-graining.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-model-level-coarse-graining.yml-True].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-pressure-level-coarse-graining.yml].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-pressure-level-coarse-graining.yml-True].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-pressure-level-coarse-graining.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-pressure-level-coarse-graining.yml-True].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-pressure-level-extrapolate-coarse-graining.yml].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-pressure-level-extrapolate-coarse-graining.yml-True].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-pressure-level-extrapolate-coarse-graining.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-pressure-level-extrapolate-coarse-graining.yml-True].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-restart.yml].out b/tests/pytest/_regtest_outputs/test_regression.test_regression[repro-restart.yml-False].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_regression_native[Linux-restart.yml].out rename to tests/pytest/_regtest_outputs/test_regression.test_regression[repro-restart.yml-False].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[1].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-1].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[1].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-1].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[2].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-2].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[2].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-2].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[3].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-3].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[3].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-3].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[4].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-4].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[4].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-4].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[5].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-5].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[5].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-5].out diff --git a/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[6].out b/tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-6].out similarity index 100% rename from tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[6].out rename to tests/pytest/_regtest_outputs/test_regression.test_zhao_carr_diagnostics[repro-6].out diff --git a/tests/pytest/conftest.py b/tests/pytest/conftest.py deleted file mode 100644 index 84ad879dd..000000000 --- a/tests/pytest/conftest.py +++ /dev/null @@ -1,80 +0,0 @@ -from pathlib import Path -import platform -import subprocess -import pytest -import fv3config - -DEFAULT_MODEL_IMAGE = "us.gcr.io/vcm-ml/fv3gfs-compiled" - - -def pytest_addoption(parser): - parser.addoption( - "--refdir", - action="store", - default="reference/circleci", - help="directory for reference files", - ) - parser.addoption( - "--image_version", - action="store", - default="latest", - help="The image version to run", - ) - parser.addoption( - "--image_runner", - action="store", - default="docker", - choices=("docker", "sarus"), - help="The image runner to use", - ) - parser.addoption( - "--image", - action="store", - default=DEFAULT_MODEL_IMAGE, - help="The image name to run, without tags", - ) - parser.addoption( - "--code_root", - action="store", - default="/", - help="The path to the codebase to test", - ) - parser.addoption( - "--native", - action="store_true", - help="Run tests natively. Assumes FV3/fv3.exe exists and is executable. " - "Skips image tests.", - ) - - -@pytest.fixture(params=[platform.system()]) -def system_regtest(regtest): - # A hack to get the system name into the regtest names - # e.g. tests/pytest/test_regression.py::test_checksum_emulation[Linux] - return regtest - - -@pytest.fixture(scope="session") -def run_native(request): - root = Path(__file__).parent.parent.parent - exe = root / "FV3" / "fv3.exe" - - if not request.config.getoption("--native"): - pytest.skip() - - def run_native(config, run_dir: str, error_expected=False): - fv3config.write_run_directory(config, run_dir) - completed_process = subprocess.run( - ["mpirun", "-n", "6", exe.absolute().as_posix()], - cwd=run_dir, - capture_output=True, - ) - if completed_process.returncode != 0 and not error_expected: - print("Tail of Stderr:") - print(completed_process.stderr[-2000:].decode()) - print("Tail of Stdout:") - print(completed_process.stdout[-2000:].decode()) - pytest.fail() - return completed_process - - return run_native diff --git a/tests/pytest/reference/circleci/baroclinic/md5.txt b/tests/pytest/reference/circleci/baroclinic/md5.txt deleted file mode 100644 index 32b0cfc8d..000000000 --- a/tests/pytest/reference/circleci/baroclinic/md5.txt +++ /dev/null @@ -1,37 +0,0 @@ -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 -18eb8d98bb5f0c7a3d8e7817036c3edc RESTART/fv_core.res.tile1.nc -c25a5ba66fbeadcaef8708c14e250271 RESTART/fv_core.res.tile2.nc -a980fe0182890846aeefb6a338f7eac8 RESTART/fv_core.res.tile3.nc -536451d1b0773ab99c839ef8f154227c RESTART/fv_core.res.tile4.nc -2bcd02ecd5fb5564fca637b3639bf48a 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test_data/Generator_rank5_qliquid.dat -4c49057c7463401e30d087dc463d78bf test_data/Generator_rank5_qliquid_js.dat -b75f22ae1a11e4942a1fc519bd85de3f test_data/Generator_rank5_qo3mr.dat -31d5cad96b455b0538f4a2e6fd0c5451 test_data/Generator_rank5_qrain.dat -2b67db8c2ee81d9fc19e26f7f6440508 test_data/Generator_rank5_qrain_js.dat -c81f34e4ac2213e502174c0084c5e03a test_data/Generator_rank5_qs_column_2.dat -6a82d038629b04f783cdeaaeabcfeac0 test_data/Generator_rank5_qsnow.dat -4d23ec92c49d09eaf9f6e8f820b7dd44 test_data/Generator_rank5_qsnow_js.dat -3b5f81cb37b87a67de37b9d64aba6509 test_data/Generator_rank5_qtracers.dat -8be5c47d510797883e3c4aff4a8c7442 test_data/Generator_rank5_qvapor.dat -fe07e8ce5d1d2749ffe7a8d366c529d4 test_data/Generator_rank5_qvapor_js.dat -44a8ec0eafadb079807165b1436a7985 test_data/Generator_rank5_qx.dat -ddc9c16ab5e9efaebb7320ea79d13c90 test_data/Generator_rank5_r_vir.dat -21a3332a0e91d23ad19c50c4371815e4 test_data/Generator_rank5_ra_x.dat 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-3b3902d0d619d4896d720b53c6169f75 test_data/Generator_rank5_rsin_u.dat -f4c5d5b0f7edf50b9c8d6b0835d2ab66 test_data/Generator_rank5_rsin_v.dat -c43cf3d157c38706ad33e40a339958e1 test_data/Generator_rank5_rsina.dat -594b885ff8edd4b0b9d2ceffaf14c9be test_data/Generator_rank5_sin_sg.dat -f3ae0b6a5ca82daa518aa8c16f95c289 test_data/Generator_rank5_sina_u.dat -e8bb17d3363e9cf5a396ba60ccfeef5f test_data/Generator_rank5_sina_v.dat -4352d88a78aa39750bf70cd6f27bcaa5 test_data/Generator_rank5_sphum.dat -93b885adfe0da089cdf634904fd59f71 test_data/Generator_rank5_stretched_grid.dat -c67acbe5a43ee5582f8315a000ea64a2 test_data/Generator_rank5_t_dt.dat -30e6ed6495795c577974619496434ebd test_data/Generator_rank5_table.dat -cffdaf4ee8ffdfcee649f2a7fa503fd2 test_data/Generator_rank5_table2.dat -284d6eb638fdd609ecc435a28e857c5b test_data/Generator_rank5_tablew.dat -5596e83c1fce033c7132b3ff7df75320 test_data/Generator_rank5_te.dat -bac40bb6166f600b837ae5d528b1017e test_data/Generator_rank5_te0_2d.dat -284033e8007616c76cf24e744e921e92 test_data/Generator_rank5_te_2d.dat -dd24e91615f1963a5c64bc9878a0a8d5 test_data/Generator_rank5_teq.dat -680f340d52ce63df1068d44cc648facf test_data/Generator_rank5_tracers.dat -88b387f45d0434f44fb0eb6dc5e96086 test_data/Generator_rank5_u.dat -3244e65495c1dfc7e122d07775f7434b test_data/Generator_rank5_u_dt.dat -92d0190eb1148c028fa9120f3e3ff645 test_data/Generator_rank5_ua.dat -ddc2e8c19e8bf06d140b678b7a88c3e0 test_data/Generator_rank5_uad.dat -b01448662f4e7588df206edd04ba3fc9 test_data/Generator_rank5_ub.dat -0b645b8a5cddb1620e2a640d18db7127 test_data/Generator_rank5_uc.dat -1201a5ce9497e514e110c4e2a3747244 test_data/Generator_rank5_ucd.dat -3fc38062ba00f9b6a9a0c4d484a312f9 test_data/Generator_rank5_ud.dat -9393cf8453fb84b68d15a6afdafa6ab8 test_data/Generator_rank5_update_arr.dat -179d665bdc5cfa976124ee348ec7a9d4 test_data/Generator_rank5_ut.dat -574b43f9e505da7f90e874d5924bdbbe test_data/Generator_rank5_utc.dat -694ccc5bb6c2cec40af1fa2d5150b426 test_data/Generator_rank5_utd.dat -99c03f391406a1cca10c16d965240411 test_data/Generator_rank5_v.dat -3244e65495c1dfc7e122d07775f7434b test_data/Generator_rank5_v_dt.dat -82943dcf7e90f01f8ef3d23b48bcedd8 test_data/Generator_rank5_va.dat -416c5b43ef3dc5c572a87f2d6e0585d2 test_data/Generator_rank5_vad.dat -8d2873cf7b0330feba07030a32019271 test_data/Generator_rank5_var_in.dat -456aa4dfe3ac6cd4f48a37632fdee463 test_data/Generator_rank5_var_in_2.dat -9339322a621212ea07da7703d4cf0f40 test_data/Generator_rank5_var_in_3.dat -5c04aceb6e43f1e57ed05c40a0f5f61f test_data/Generator_rank5_var_inout.dat -4a9c953dcd66c0f40a26008ebf29fded test_data/Generator_rank5_var_inout_2.dat -8db4094bee230607cf1105b081436d79 test_data/Generator_rank5_var_inout_3.dat -009830cbcea285672855a72c3163481d test_data/Generator_rank5_vb.dat -9cf80e0d6ec7d016fdd87c25966082bf test_data/Generator_rank5_vc.dat -383c697613c5d8bd7721c50633e7acf1 test_data/Generator_rank5_vcd.dat -f488c8f67673b43166fc1a2cc31cc88d test_data/Generator_rank5_vd.dat -d436ce5a024655f845ddf9f6a73b598a test_data/Generator_rank5_vort.dat -336c9ff829792083365444e9cdc63bba test_data/Generator_rank5_vort_c.dat -c1ae2d5c2dad0a8de084ddc6166d0366 test_data/Generator_rank5_vt.dat -9916a0fe6eb7a57b91168e87633ac882 test_data/Generator_rank5_vtc.dat -1b44a0a2eefbcca5f97eaf95aaea97bd test_data/Generator_rank5_vtd.dat -a7e6169e3320f68d6f64f5c6b460ea7c test_data/Generator_rank5_w.dat -c96c5cd5e79ad370e42f612c7cd3cab1 test_data/Generator_rank5_w3.dat -63e3e84a8916830b14a65f74e2a4b795 test_data/Generator_rank5_wc.dat -f1bad799e8f9b3c0abd6b3aba688b149 test_data/Generator_rank5_wd.dat -21be478cfd9d3b31360f2db703ada1d7 test_data/Generator_rank5_wd2.dat -922c2e43281a29bbc2d5b15a4c308d96 test_data/Generator_rank5_wk.dat -5309f9845e7db2b3a0c6a5410f9def3b test_data/Generator_rank5_wq.dat -4807f6f4da86bbf4aaa200121d9efcd2 test_data/Generator_rank5_ws.dat -c81f34e4ac2213e502174c0084c5e03a test_data/Generator_rank5_ws_1d.dat -5b2f0ce95fbceb37218ef2171a9bee3d test_data/Generator_rank5_wsd.dat -c86655193a9cf77dd07b11211cdb8760 test_data/Generator_rank5_xflux.dat -0e739d6f625cd70cd17cd3b1c39e657e test_data/Generator_rank5_xflux_2.dat -85553946e4dc81058d2d6cedb6f375f6 test_data/Generator_rank5_xfx.dat -81b98f41da6be06768fc3f68f6a3963a test_data/Generator_rank5_xfx_adv.dat -81b98f41da6be06768fc3f68f6a3963a test_data/Generator_rank5_xfxd.dat -37a113d58588eba4dc164ab0fd8cc56d test_data/Generator_rank5_yflux.dat -f3b6bf97114d0776e4c08737d850ab10 test_data/Generator_rank5_yfx.dat -61becc2e8cfd3e0139f9ae908be1c9ab test_data/Generator_rank5_yfx_adv.dat -61becc2e8cfd3e0139f9ae908be1c9ab test_data/Generator_rank5_yfxd.dat -3244e65495c1dfc7e122d07775f7434b test_data/Generator_rank5_z_rat.dat -c4107198b7d17ea1e2104090dd6ea7ea test_data/Generator_rank5_zh.dat -8f654506af51b708121d06e7799c4bb5 test_data/Generator_rank5_zhd.dat -9fa4765a2dd667c45d02cd4794f948c4 test_data/Generator_rank5_zs.dat -dd24e91615f1963a5c64bc9878a0a8d5 test_data/Generator_rank5_zsum0.dat -98313667a3d992beb0ae0c72cd988ff9 test_data/Generator_rank5_zsum1.dat -ddc9c16ab5e9efaebb7320ea79d13c90 test_data/Generator_rank5_zvir.dat -c49793755dcea6925ecbe12728ec468e test_data/ArchiveMetaData-Generator_rank0.json -4765284ad3676fc09b42c94df7f2d13e test_data/ArchiveMetaData-Generator_rank1.json -8e777c8993c9f5b775f7d55c503899be test_data/ArchiveMetaData-Generator_rank2.json -ea8466ef71823a394c52c9ca2b4273d3 test_data/ArchiveMetaData-Generator_rank3.json -209662842a752b11930d8d7626382333 test_data/ArchiveMetaData-Generator_rank4.json -0383250621a3676f2ab5d99b0b68a696 test_data/ArchiveMetaData-Generator_rank5.json -1d54efccf01022913b0498365ce91147 test_data/MetaData-Generator_rank0.json -ab1139b8d1ab7bcc5ed6510d942503c4 test_data/MetaData-Generator_rank1.json -dbb9a85b94e9b0a017915d37d83eafd9 test_data/MetaData-Generator_rank2.json -de81e2baeada3fd04e2076ea666c0afc test_data/MetaData-Generator_rank3.json -f6eb8b0f594fcbfa96b99d3d3249179a test_data/MetaData-Generator_rank4.json -d397314facb3b1d491998236b751db17 test_data/MetaData-Generator_rank5.json diff --git a/tests/pytest/run_files/job_jenkins_sarus b/tests/pytest/run_files/job_jenkins_sarus deleted file mode 100644 index 7ce20f3cc..000000000 --- a/tests/pytest/run_files/job_jenkins_sarus +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash -l -#SBATCH --job-name="fv3gfs-fortran-test" -#SBATCH --partition=cscsci -#SBATCH --account=s1053m -#SBATCH --constraint=mc -#SBATCH --time=00:04:00 -#SBATCH --nodes=1 -#SBATCH --hint=nomultithread - -## -## Set the compute node environment -## - -module load daint-mc sarus - -export OMP_NUM_THREADS=1 -ulimit -s unlimited - -## -## Perform the c12 test -## - -srun sarus run --mpi --mount=type=bind,source=${SCRATCH_DIR},destination=/scratch --workdir=/scratch load/library/${FV3_CONTAINER} /FV3/fv3.exe diff --git a/tests/pytest/run_files/submit_job.sh b/tests/pytest/run_files/submit_job.sh deleted file mode 100755 index 5d060da14..000000000 --- a/tests/pytest/run_files/submit_job.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -N_PROCESSES=$1 -RUNDIR=/rundir - -ulimit -s unlimited -cp /FV3/fv3.exe $RUNDIR/fv3.exe -cd $RUNDIR -mpirun -np $N_PROCESSES $RUNDIR/fv3.exe diff --git a/tests/pytest/set_reference.sh b/tests/pytest/set_reference.sh deleted file mode 100755 index 4dea177f9..000000000 --- a/tests/pytest/set_reference.sh +++ /dev/null @@ -1,49 +0,0 @@ -#!/bin/bash - -# utility script to generate the md5 hashes used to ensure that the model -# still gives bit-identical results. - -# Note: You must have run `make test` in the top-level directory before being -# able to generate new references. - -# Uage ./set_reference.sh -# Tag of the Docker image to generate md5 sums (e.g. latest, latest-serialize) -# Directory to store the md5 sums - -IMG_TAG=$1 -if [ -z "${IMG_TAG}" ] ; then - echo "Error: You must specify an image tag as the first argument" - exit 1 -fi - -REF_DIR=$2 -if [ -z "${REF_DIR}" ] ; then - echo "Error: You must specify a directory to store the md5 sums as the second argument" - exit 1 -fi -REF_DIR=`realpath ${REF_DIR}` -if [ ! -d "${REF_DIR}" ] ; then - echo "Error: Problem with specified directory to store md5 sums" - exit 1 -fi - -CWD=$(pwd) - -if ! ls $CWD/output/$IMG_TAG/* &>/dev/null ; then - echo "Error: No input directories found in $CWD/output/$IMG_TAG" - exit 1 -fi - -for dir in $CWD/output/$IMG_TAG/* ; do - run_name=$(basename ${dir}) - mkdir -p $REF_DIR/$run_name - echo "Processing $dir, storing md5 sums in $REF_DIR/$run_name" - cd $dir - md5sum *.nc RESTART/*.nc > $REF_DIR/$run_name/md5.txt - if ls test_data/Gen*.dat test_data/*.json >/dev/null 2>&1; then - md5sum test_data/Gen*.dat test_data/*.json > $REF_DIR/$run_name/md5_serialize.txt - fi - cd - -done - -exit 0 diff --git a/tests/pytest/test_regression.py b/tests/pytest/test_regression.py index c59573a02..b53dab4f4 100644 --- a/tests/pytest/test_regression.py +++ b/tests/pytest/test_regression.py @@ -3,12 +3,13 @@ import glob import os from os.path import join -import shutil +from pathlib import Path import pytest +import shutil +import subprocess import fv3config import numpy as np import xarray -import subprocess import typing import hashlib @@ -16,117 +17,99 @@ import prescribed_ssts +EMULATION_DEBUG_MODE_ISSUE = ( + "We do not build the fortran model in debug mode with call_py_fort, because " + "it leads to errors even in non-emulation cases. This means that we cannot " + "run emulation-related tests in debug mode. See GitHub issue #365 for more " + "details." +) +RESTART_REPRODUCIBILITY_DEBUG_MODE_ISSUE = ( + "The model does not restart reproducibly when compiled in debug mode, due to " + "the -finit-logical=true compiler flag. If this flag is removed and all " + "other debug-mode compiler flags are retained, the model restarts " + "reproducibly. See GitHub issue #381 for more details." +) TEST_DIR = os.path.dirname(os.path.realpath(__file__)) -REFERENCE_DIR = os.path.join(TEST_DIR, "reference") -OUTPUT_DIR = os.path.join(TEST_DIR, "output") CONFIG_DIR = os.path.join(TEST_DIR, "config") -SUBMIT_JOB_FILENAME = os.path.join(TEST_DIR, "run_files/submit_job.sh") -STDOUT_FILENAME = "stdout.log" -STDERR_FILENAME = "stderr.log" -MD5SUM_FILENAME = "md5.txt" -SERIALIZE_MD5SUM_FILENAME = "md5_serialize.txt" -GOOGLE_APP_CREDS = os.environ.get("GOOGLE_APPLICATION_CREDENTIALS", None) - -USE_LOCAL_ARCHIVE = True -config_filenames = os.listdir(CONFIG_DIR) - -@pytest.fixture -def image_version(request): - return request.config.getoption("--image_version") - - -@pytest.fixture -def image(request): - return request.config.getoption("--image") - - -@pytest.fixture -def reference_dir(request): - return request.config.getoption("--refdir") +def get_config(filename): + config_filename = os.path.join(CONFIG_DIR, filename) + with open(config_filename, "r") as f: + return fv3config.load(f) -@pytest.fixture -def code_root(request): - return request.config.getoption("--code_root") +def parse_compile_mode(path): + name = path.name + return re.search(r"fv3\.(.*?)\.exe", name).group(1) -@pytest.fixture -def image_runner(request): - if request.config.getoption("--native"): - pytest.skip() - return request.config.getoption("--image_runner") +def get_executables(): + root = Path(__file__).parent.parent.parent / "bin" + executable_paths = root.glob("*.exe") + executables = {} + for executable_path in executable_paths: + compile_mode = parse_compile_mode(executable_path) + executables[compile_mode] = executable_path + return executables -def get_config(filename): - config_filename = os.path.join(CONFIG_DIR, filename) - with open(config_filename, "r") as f: - return fv3config.load(f) +EXECUTABLES = get_executables() -def get_run_dir(model_image_tag, config): - run_name = config["experiment_name"] - return os.path.join(OUTPUT_DIR, model_image_tag, run_name) +def run_executable(executable: Path, config: dict, run_dir: str, error_expected: bool = False): + fv3config.write_run_directory(config, run_dir) + n_processes = fv3config.config.get_n_processes(config) + completed_process = subprocess.run( + ["mpirun", "-n", f"{n_processes}", executable.absolute().as_posix()], + cwd=run_dir, + capture_output=True, + ) + if completed_process.returncode != 0 and not error_expected: + print("Tail of Stderr:") + print(completed_process.stderr[-2000:].decode()) + print("Tail of Stdout:") + print(completed_process.stdout[-2000:].decode()) + pytest.fail() + return completed_process -def get_n_processes(config): - layout = config["namelist"]["fv_core_nml"]["layout"] - return 6 * layout[0] * layout[1] +@pytest.fixture(scope="session", params=EXECUTABLES.keys()) +def executable(request): + return EXECUTABLES[request.param] @pytest.mark.parametrize( - ("config_filename", "tag"), + ("config_filename", "check_layout_invariance"), [ - ("default.yml", "{version}-debug"), - ("baroclinic.yml", "{version}-debug"), - ("default.yml", "{version}"), - ("default.yml", "{version}-serialize"), - ("restart.yml", "{version}"), - ("model-level-coarse-graining.yml", "{version}-debug"), - ("pressure-level-coarse-graining.yml", "{version}-debug"), - ("pressure-level-extrapolate-coarse-graining.yml", "{version}-debug"), - ("blended-area-weighted-coarse-graining.yml", "{version}-debug") + pytest.param("default.yml", False, marks=pytest.mark.basic), + pytest.param("model-level-coarse-graining.yml", True, marks=pytest.mark.coarse), + pytest.param("pressure-level-coarse-graining.yml", True, marks=pytest.mark.coarse), + pytest.param("pressure-level-extrapolate-coarse-graining.yml", True, marks=pytest.mark.coarse), + ("baroclinic.yml", False), + ("restart.yml", False), + pytest.param("blended-area-weighted-coarse-graining.yml", True, marks=pytest.mark.coarse) ], ) -def test_regression( - config_filename, tag, image, image_version, reference_dir, image_runner -): - model_image_tag = tag.format(version=image_version) - model_image = f"{image}:{model_image_tag}" +def test_regression(executable: Path, config_filename: str, check_layout_invariance: bool, tmpdir, regtest): config = get_config(config_filename) - run_dir = get_run_dir(model_image_tag, config) - run_model(config, run_dir, model_image, image_runner) - run_name = config["experiment_name"] - run_reference_dir = os.path.join(reference_dir, run_name) - md5sum_filename = os.path.join(run_reference_dir, MD5SUM_FILENAME) - check_rundir_md5sum(run_dir, md5sum_filename) - if "serialize" in model_image: - serialize_md5sum_filename = os.path.join( - run_reference_dir, SERIALIZE_MD5SUM_FILENAME - ) - check_rundir_md5sum(run_dir, serialize_md5sum_filename) - shutil.rmtree(run_dir) + rundir = tmpdir.join("rundir") + run_executable(executable, config, str(rundir)) + _checksum_rundir(str(rundir), file=regtest) + if check_layout_invariance: + config_modified_layout = get_config(config_filename) + config_modified_layout["namelist"]["fv_core_nml"]["layout"] = [1, 2] + rundir_modified_layout = tmpdir.join("rundir-modified-layout") + run_executable(executable, config_modified_layout, rundir_modified_layout) -@pytest.mark.parametrize( - "config_filename", - [ - pytest.param("default.yml", marks=pytest.mark.basic), - pytest.param("model-level-coarse-graining.yml", marks=pytest.mark.coarse), - pytest.param("pressure-level-coarse-graining.yml", marks=pytest.mark.coarse), - pytest.param("pressure-level-extrapolate-coarse-graining.yml", marks=pytest.mark.coarse), - "baroclinic.yml", - "restart.yml", - pytest.param("blended-area-weighted-coarse-graining.yml", marks=pytest.mark.coarse) - ], -) -def test_regression_native(run_native, config_filename: str, tmpdir, system_regtest): - config = get_config(config_filename) - rundir = tmpdir.join("rundir") - run_native(config, str(rundir)) - _checksum_rundir(str(rundir), file=system_regtest) + expected_checksums = _checksum_restart_files_and_diagnostics(rundir) + result_checksums = _checksum_restart_files_and_diagnostics(rundir_modified_layout) + assert result_checksums == expected_checksums + + shutil.rmtree(rundir_modified_layout) + shutil.rmtree(rundir) @pytest.mark.parametrize( "config_filename", @@ -136,7 +119,13 @@ def test_regression_native(run_native, config_filename: str, tmpdir, system_regt "restart.yml" ], ) -def test_restart_reproducibility(run_native, config_filename, tmpdir): +def test_restart_reproducibility(executable, config_filename, tmpdir): + if config_filename == "emulation.yml" and "debug" in str(executable): + pytest.skip(EMULATION_DEBUG_MODE_ISSUE) + + if "debug" in str(executable): + pytest.skip(RESTART_REPRODUCIBILITY_DEBUG_MODE_ISSUE) + config_template = get_config(config_filename) config_template["diag_table"] = "no_output" config_template["namelist"]["gfs_physics_nml"]["fhswr"] = 900 @@ -153,20 +142,23 @@ def test_restart_reproducibility(run_native, config_filename, tmpdir): segment_2_rundir = str(tmpdir.join("segment-2")) continuous_rundir = str(tmpdir.join("continuous")) - run_native(segmented_config, segment_1_rundir) - run_native(continuous_config, continuous_rundir) + run_executable(executable, segmented_config, segment_1_rundir) + run_executable(executable, continuous_config, continuous_rundir) segment_1_restarts = os.path.join(segment_1_rundir, "RESTART") segmented_config = fv3config.enable_restart(segmented_config, segment_1_restarts) - run_native(segmented_config, segment_2_rundir) + run_executable(executable, segmented_config, segment_2_rundir) continuous_checksums = _checksum_restart_files(continuous_rundir) segmented_checksums = _checksum_restart_files(segment_2_rundir) assert segmented_checksums == continuous_checksums + shutil.rmtree(segment_1_rundir) + shutil.rmtree(segment_2_rundir) + shutil.rmtree(continuous_rundir) -def test_indefinite_physics_diagnostics(run_native, tmpdir): +def test_indefinite_physics_diagnostics(executable, tmpdir): config_template = get_config("default.yml") fdiag = copy.deepcopy(config_template) @@ -182,12 +174,14 @@ def test_indefinite_physics_diagnostics(run_native, tmpdir): fdiag_rundir = str(tmpdir.join("fdiag")) indefinite_rundir = str(tmpdir.join("indefinite")) - run_native(fdiag, fdiag_rundir) - run_native(indefinite, indefinite_rundir) + run_executable(executable, fdiag, fdiag_rundir) + run_executable(executable, indefinite, indefinite_rundir) fdiag_checksums = _checksum_diagnostics(fdiag_rundir) indefinite_checksums = _checksum_diagnostics(indefinite_rundir) assert fdiag_checksums == indefinite_checksums + shutil.rmtree(fdiag_rundir) + shutil.rmtree(indefinite_rundir) def open_tiles(prefix): @@ -199,7 +193,7 @@ def open_tiles(prefix): return xarray.concat(datasets, dim="tile") -def test_use_prescribed_sea_surface_properties(run_native, tmpdir): +def test_use_prescribed_sea_surface_properties(executable, tmpdir): config = get_config("default.yml") prescribed_ssts.create_sst_dataset(tmpdir) @@ -209,10 +203,11 @@ def test_use_prescribed_sea_surface_properties(run_native, tmpdir): config["namelist"]["fv_grid_nml"]["grid_file"] = "INPUT/grid_spec.nc" rundir = os.path.join(str(tmpdir), "rundir") - run_native(config, rundir) + run_executable(executable, config, rundir) results = open_tiles(os.path.join(rundir, "sfc_dt_atmos")) prescribed_ssts.validate_ssts(results) + shutil.rmtree(rundir) PRESCRIBED_SST_ERRORS = { @@ -227,22 +222,26 @@ def test_use_prescribed_sea_surface_properties(run_native, tmpdir): list(PRESCRIBED_SST_ERRORS.items()), ids=list(PRESCRIBED_SST_ERRORS.keys()), ) -def test_use_prescribed_sea_surface_properties_error(run_native, tmpdir, message, patch_files): +def test_use_prescribed_sea_surface_properties_error(executable, tmpdir, message, patch_files): config = get_config("default.yml") config["patch_files"] = patch_files config["namelist"]["gfs_physics_nml"]["use_prescribed_sea_surface_properties"] = True config["namelist"]["fv_grid_nml"]["grid_file"] = "INPUT/grid_spec.nc" rundir = os.path.join(str(tmpdir), "rundir") - result = run_native(config, rundir, error_expected=True) + result = run_executable(executable, config, rundir, error_expected=True) assert message in result.stderr.decode() + shutil.rmtree(rundir) @pytest.fixture(scope="session") -def emulation_run(run_native, tmpdir_factory): +def emulation_run(executable, tmpdir_factory): + if "debug" in str(executable): + pytest.skip(reason=EMULATION_DEBUG_MODE_ISSUE) + config = get_config("emulation.yml") rundir = tmpdir_factory.mktemp("rundir") run_dir = str(rundir) - completed_process = run_native(config, run_dir) + completed_process = run_executable(executable, config, run_dir) return completed_process, run_dir @@ -263,11 +262,14 @@ def test_zhao_carr_diagnostics(emulation_run, regtest, tile): @pytest.mark.emulation -def test_gscond_logs(run_native, regtest, tmpdir): +def test_gscond_logs(executable, regtest, tmpdir): + if "debug" in str(executable): + pytest.skip(reason=EMULATION_DEBUG_MODE_ISSUE) + config = get_config("emulation.yml") config["namelist"]["gfs_physics_nml"]["emulate_gscond_only"] = True rundir = tmpdir.join("rundir") - process = run_native(config, str(rundir)) + process = run_executable(executable, config, str(rundir)) gscond_state_info = re.findall(r"gscond.state:(.*)", process.stderr.decode()) first_state = gscond_state_info[0] print(first_state, file=regtest) @@ -326,6 +328,13 @@ def _checksum_diagnostics(rundir: str): return {os.path.basename(file): checksum_file(file) for file in files} +def _checksum_restart_files_and_diagnostics(rundir: str): + checksums = {} + checksums["restart_files"] = _checksum_diagnostics(rundir) + checksums["diagnostics"] = _checksum_diagnostics(rundir) + return checksums + + def _checksum_rundir(rundir: str, file): """checksum rundir storing output in file""" files = glob.glob(os.path.join(rundir, "*.nc")) @@ -335,133 +344,9 @@ def _checksum_rundir(rundir: str, file): @pytest.mark.emulation -def test_checksum_emulation(emulation_run, system_regtest): +def test_checksum_emulation(emulation_run, regtest): _, run_dir = emulation_run - _checksum_rundir(run_dir, file=system_regtest) - - -def check_rundir_md5sum(run_dir, md5sum_filename): - ensure_reference_exists(md5sum_filename) - subprocess.check_call(["md5sum", "-c", md5sum_filename], cwd=run_dir) - - -def ensure_reference_exists(filename): - if not os.path.isfile(filename): - raise AssertionError( - f"reference md5sum does not exist at " + filename + "," - f" you can create it with `set_reference.sh` -- refer to README.md" - ) - - -def run_model_docker(rundir, model_image, n_processes, additional_env_vars=None): - if USE_LOCAL_ARCHIVE: - archive = fv3config.get_cache_dir() - archive_mount = ["-v", f"{archive}:{archive}"] - else: - archive_mount = [] - - if GOOGLE_APP_CREDS is not None: - secret_mount = ["-v", f"{GOOGLE_APP_CREDS}:/tmp/key.json"] - env_vars = ["--env", "GOOGLE_APPLICATION_CREDENTIALS"] - else: - secret_mount = [] - env_vars = [] - - if additional_env_vars is not None: - env_vars += additional_env_vars - - docker_runpath = "" - docker_run = ["docker", "run", "--rm"] - rundir_abs = os.path.abspath(rundir) - rundir_mount = ["-v", f"{rundir_abs}:" + docker_runpath + "/rundir"] - data_abs = os.path.abspath(os.path.join(rundir_abs, "test_data")) - os.makedirs(data_abs, exist_ok=True) - data_mount = ["-v", f"{data_abs}:" + docker_runpath + "/rundir/test_data"] - fv3out_filename = join(rundir, "stdout.log") - fv3err_filename = join(rundir, "stderr.log") - call = ( - docker_run - + rundir_mount - + archive_mount - + data_mount - + secret_mount - + env_vars - + [model_image] - + ["bash", "/rundir/submit_job.sh", str(n_processes)] - ) - with open(fv3out_filename, "w") as fv3out_f, open(fv3err_filename, "w") as fv3err_f: - subprocess.check_call( - call, - stdout=fv3out_f, - stderr=fv3err_f, - ) - - -def run_model_sarus(rundir, model_image, n_processes): - shutil.copy( - os.path.join(TEST_DIR, "run_files/job_jenkins_sarus"), - os.path.join(rundir, "job_jenkins_sarus"), - ) - # run job_jenkins_sarus with env var FV3_CONTAINER set to model_image - env = os.environ.copy() - env["FV3_CONTAINER"] = model_image - env["SCRATCH_DIR"] = rundir - call = ["sbatch", "--wait", f"--ntasks={n_processes}", "job_jenkins_sarus"] - subprocess.check_call(call, env=env, cwd=rundir) - - -def check_md5sum(run_dir, md5sum_filename): - subprocess.check_call(["md5sum", "-c", md5sum_filename], cwd=run_dir) - - -def write_run_directory(config, dirname): - fv3config.write_run_directory(config, dirname) - shutil.copy(SUBMIT_JOB_FILENAME, os.path.join(dirname, "submit_job.sh")) - - -def run_model(config, run_dir, model_image, image_runner, additional_env_vars=None): - if os.path.isdir(run_dir): - shutil.rmtree(run_dir) - os.makedirs(run_dir) - write_run_directory(config, run_dir) - n_processes = get_n_processes(config) - if image_runner == "docker": - run_model_docker( - run_dir, model_image, n_processes, additional_env_vars=additional_env_vars - ) - elif image_runner == "sarus": - run_model_sarus(run_dir, model_image, n_processes) - else: - raise NotImplementedError("image_runner must be one of 'docker' or 'sarus'") - - -@pytest.mark.parametrize( - ("config_filename", "tag", "layout"), - [ - ("model-level-coarse-graining.yml", "{version}", [1, 2]), - ("pressure-level-coarse-graining.yml", "{version}", [1, 2]), - ("pressure-level-extrapolate-coarse-graining.yml", "{version}", [1, 2]), - ("blended-area-weighted-coarse-graining.yml", "{version}", [1, 2]) - ], - ids=lambda x: str(x), -) -def test_run_reproduces_across_layouts( - config_filename, tag, layout, image, image_version, image_runner, reference_dir -): - model_image_tag = tag.format(version=image_version) - model_image = f"{image}:{model_image_tag}" - config = get_config(config_filename) - config["namelist"]["fv_core_nml"]["layout"] = layout - layout_x, layout_y = layout - run_name = f"{config['experiment_name']}_{layout_x}x{layout_y}" - run_dir = join(OUTPUT_DIR, model_image_tag, run_name) - run_model(config, run_dir, model_image, image_runner) - - reference_run_name = config["experiment_name"] - run_reference_dir = join(reference_dir, reference_run_name) - md5sum_filename = join(run_reference_dir, MD5SUM_FILENAME) - check_rundir_md5sum(run_dir, md5sum_filename) - shutil.rmtree(run_dir) + _checksum_rundir(run_dir, file=regtest) if __name__ == "__main__": diff --git a/tests/test_fv3_exe_restart.py b/tests/test_fv3_exe_restart.py deleted file mode 100644 index af7f44cfc..000000000 --- a/tests/test_fv3_exe_restart.py +++ /dev/null @@ -1,142 +0,0 @@ -import fv3config -import os -from os.path import join -import shutil -from copy import deepcopy -import yaml -import hashlib -import subprocess - -RUN_SCRIPT_FILENAME = 'submit_job.sh' -TEST_DIR = os.path.dirname(os.path.realpath(__file__)) - -RUN_IN_DOCKER_COMMAND = ["bash", os.path.join("/rundir/", RUN_SCRIPT_FILENAME)] - - -def setup_initial_runs(workdir, config_template): - """Set up two run-directories, one for a four-hour run, one for - two-hour run, both initialized from the same state example_restart - state""" - if not os.path.isdir(workdir): - os.mkdir(workdir) - fullrun_config = deepcopy(config_template) - fullrun_config['namelist']['coupler_nml']['hours'] = 4 - fullrun_config['namelist']['coupler_nml']['minutes'] = 0 - firsthalf_config = deepcopy(fullrun_config) - firsthalf_config['namelist']['coupler_nml']['hours'] = 2 - fv3config.write_run_directory(fullrun_config, join(workdir, 'fullrun')) - fv3config.write_run_directory(firsthalf_config, join(workdir, 'firsthalf')) - for run in ['fullrun', 'firsthalf']: - shutil.copy(RUN_SCRIPT_FILENAME, join(workdir, run, RUN_SCRIPT_FILENAME)) - return fullrun_config, firsthalf_config - - -def setup_final_run(workdir, firsthalf_config, remove_phy_data=False): - """Set up run directory for second two-hour run. This must be done after - the first two-hour run has been performed so that the initial conditions - are linked appropriately""" - secondhalf_config = deepcopy(firsthalf_config) - secondhalf_config['initial_conditions'] = os.path.abspath( - join(workdir, 'firsthalf', 'RESTART') - ) - secondhalf_config = fv3config.enable_restart(secondhalf_config) - fv3config.write_run_directory(secondhalf_config, join(workdir, 'secondhalf')) - if remove_phy_data: - for tile in range(1, 7): - os.remove(join(workdir, 'secondhalf', 'INPUT', f'phy_data.tile{tile}.nc')) - shutil.copy(RUN_SCRIPT_FILENAME, join(workdir, 'secondhalf', RUN_SCRIPT_FILENAME)) - return secondhalf_config - - -def run_model(rundir, model_image, mounts): - docker_run = ['docker', 'run', '--rm'] - rundir_abs = os.path.abspath(rundir) - rundir_mount = ['-v', f'{rundir_abs}:/rundir'] - fv3out_filename = join(rundir, 'fv3out') - fv3err_filename = join(rundir, 'fv3err') - with open(fv3out_filename, 'w') as fv3out_f, open(fv3err_filename, 'w') as fv3err_f: - subprocess.check_call( - docker_run + rundir_mount + mounts + [model_image] + RUN_IN_DOCKER_COMMAND, - stdout=fv3out_f, - stderr=fv3err_f - ) - - -def run_full_and_split(workdir, config_template, remove_phy_data=False): - archive = fv3config.get_cache_dir() - archive_mount = ['-v', f'{archive}:{archive}'] - model_image = 'us.gcr.io/vcm-ml/fv3gfs-compiled:latest' - _, firsthalf_config = setup_initial_runs(workdir, config_template) - run_model(join(workdir, 'fullrun'), model_image, archive_mount) - run_model(join(workdir, 'firsthalf'), model_image, archive_mount) - _ = setup_final_run(workdir, firsthalf_config, remove_phy_data=remove_phy_data) - icdir = os.path.abspath(join(workdir, 'firsthalf', 'RESTART')) - ic_mount = ['-v', f'{icdir}:{icdir}'] - run_model(join(workdir, 'secondhalf'), model_image, archive_mount + ic_mount) - - -def compare_restart_files(dir1, dir2, verbose=False): - print(f'Checking diff between restart files in {dir1} and {dir2}.') - restart_files = sorted(os.listdir(join(dir1, 'RESTART'))) - restart_files.remove('coupler.res') # don't expect this file to be the same - file_difference_count = 0 - for file in restart_files: - with open(join(dir1, 'RESTART', file), 'rb') as f: - fullrun_hash = hashlib.md5(f.read()).hexdigest() - with open(join(dir2, 'RESTART', file), 'rb') as f: - secondhalf_hash = hashlib.md5(f.read()).hexdigest() - if fullrun_hash != secondhalf_hash: - file_difference_count +=1 - if verbose: - print(f'{file} differs') - print(f'A total of {file_difference_count} restart files differ.') - - -def get_default_config(): - with open(os.path.join(TEST_DIR, 'pytest/config/default.yml'), 'r') as f: - config = yaml.safe_load(f) - return config - - -def get_restart_config(): - with open(os.path.join(TEST_DIR, 'pytest/config/restart.yml'), 'r') as f: - config = yaml.safe_load(f) - return config - - -def test_gfs_standard(): - workdir = 'rundirs_gfs_standard' - config_standard = get_default_config() - run_full_and_split(workdir, config_standard) - compare_restart_files(join(workdir, 'fullrun'), join(workdir, 'secondhalf')) - - -def test_restart_standard(): - workdir = 'rundirs_restart_standard' - config_standard = get_restart_config() - run_full_and_split(workdir, config_standard) - compare_restart_files(join(workdir, 'fullrun'), join(workdir, 'secondhalf')) - - -def test_isubc_sw_lw_zero(): - workdir = 'rundirs_isubc0' - config_isubc0 = get_restart_config() - config_isubc0['namelist']['gfs_physics_nml']['isubc_sw'] = 0 - config_isubc0['namelist']['gfs_physics_nml']['isubc_lw'] = 0 - run_full_and_split(workdir, config_isubc0) - compare_restart_files(join(workdir, 'fullrun'), join(workdir, 'secondhalf')) - - -def test_dycore_only(): - workdir = 'rundirs_dycore_only' - config_dycore_only = get_restart_config() - config_dycore_only['namelist']['atmos_model_nml']['dycore_only'] = True - run_full_and_split(workdir, config_dycore_only) - compare_restart_files(join(workdir, 'fullrun'), join(workdir, 'secondhalf')) - - -if __name__ == '__main__': - test_dycore_only() - test_gfs_standard() - test_restart_standard() - test_isubc_sw_lw_zero()