From dbb35b7dba0433ea69837e34d00b7588efcc8121 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Thu, 27 Oct 2022 15:51:28 -0400 Subject: [PATCH 01/82] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 0170421ca..4c7ff9ad6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,7 @@ RUN apt update # Install dependencies RUN apt install -y wget RUN apt install -y vim +RUN apt install -y git # Cleanup RUN rm -rf /var/lib/apt/lists/* && \ apt clean From b11ee391dc0b6d5d817e88aff113cb044fac5363 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:29:13 -0400 Subject: [PATCH 02/82] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index cbc155734..9ee9f6054 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Deploy to ECS,open +name: Deploy to ECS. Build, push image, on: push: From c134a4dc38af7517b010e03a3d257fca43ddbe52 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:31:01 -0400 Subject: [PATCH 03/82] Update main.yml on PR --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9ee9f6054..08afe9f16 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -6,7 +6,7 @@ name: Deploy to ECS. Build, push image, on: - push: + pull_request: branches: - main From e814fc40fff99ed338fc2cf7b024bccb2c3093ee Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 11:49:23 -0400 Subject: [PATCH 04/82] Update Dockerfile env_dir --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4c7ff9ad6..b8b898811 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ - --conda_env_dir ${CONDA_ENV_DIR} + --env_dir ${CONDA_ENV_DIR} # Verify installation RUN ${CODE_ROOT}/mdtf --version # Run mdtf on src/default_tests.jsonc From d64bcb7559ef16d2f24018d285a328457720839a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 14:40:25 -0400 Subject: [PATCH 05/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b8b898811..0d91945c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # Base OS -FROM ubuntu:20.04 +FROM ubuntu:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From e52f0ce25dafe9d97cc5256c02cba12190f236d1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 14:59:29 -0400 Subject: [PATCH 06/82] Update Dockerfile libarchive --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 0d91945c4..b2e445214 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,6 +40,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs +conda install libarchive -n base -c conda-forge #workaround RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 608e9164269bb3759cba465e5bb674ac86635e4d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:04:48 -0400 Subject: [PATCH 07/82] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b2e445214..3bb804fbd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,7 +40,8 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs -conda install libarchive -n base -c conda-forge #workaround +#workaround +conda install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 0e579e0eb2d1d89c9bbbed85d3b69af7dc922671 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:09:49 -0400 Subject: [PATCH 08/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3bb804fbd..bb1450961 100644 --- a/Dockerfile +++ b/Dockerfile @@ -41,7 +41,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs #workaround -conda install libarchive -n base -c conda-forge +mamba install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From fc408a8e1fa37f52fc413cd89581de047013d146 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 22 Aug 2023 15:28:00 -0400 Subject: [PATCH 09/82] Update Dockerfile --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index bb1450961..0d91945c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,8 +40,6 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs -#workaround -mamba install libarchive -n base -c conda-forge RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From 203b19f2326cd274ecece254089cb65d2d67659e Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 11:57:09 -0400 Subject: [PATCH 10/82] Update Dockerfile mamba version --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0d91945c4..585eaad80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash -RUN conda install -c conda-forge mamba +RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From dedfe71611a80634a6196865127b6d77e66e957a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:36:38 -0400 Subject: [PATCH 11/82] Update Dockerfile --- Dockerfile | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 585eaad80..1413b4bea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,6 @@ # Base OS FROM ubuntu:latest +FROM continuumio/miniconda3 # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -17,14 +18,14 @@ RUN rm -rf /var/lib/apt/lists/* && \ apt clean # Install Miniconda3 # Download the latest shell script -RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -# Change permission to execute build script -RUN chmod +x Miniconda3-latest-Linux-x86_64.sh -# Run miniconda installation script -ENV PATH="/root/miniconda3/bin:${PATH}" -ARG PATH="/root/miniconda3/bin:${PATH}" -RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b -RUN rm -f Miniconda3-latest-Linux-x86_64.sh +####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +#### Change permission to execute build script +####RUN chmod +x Miniconda3-latest-Linux-x86_64.sh +#### Run miniconda installation script +####ENV PATH="/root/miniconda3/bin:${PATH}" +####ARG PATH="/root/miniconda3/bin:${PATH}" +####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b +####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash RUN conda install 'mamba<=1.4.5' -n base -c conda-forge @@ -40,6 +41,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/root/miniconda3 ENV CONDA_ENV_DIR=/root/miniconda3/envs +RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation From cfc4362879f19c78183ed6b91cac887f85244b1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:50:05 -0400 Subject: [PATCH 12/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 1413b4bea..b3a21c082 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,7 +28,7 @@ RUN rm -rf /var/lib/apt/lists/* && \ ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN conda info RUN conda init bash -RUN conda install 'mamba<=1.4.5' -n base -c conda-forge +##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From 7478cdf08e75c1ebcb7c1b5c46b3dcd45c0869aa Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 23 Aug 2023 16:57:59 -0400 Subject: [PATCH 13/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index b3a21c082..47776cbaf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -39,8 +39,8 @@ COPY shared ${CODE_ROOT}/shared COPY sites ${CODE_ROOT}/sites COPY tests ${CODE_ROOT}/tests # Install conda environments -ENV CONDA_ROOT=/root/miniconda3 -ENV CONDA_ENV_DIR=/root/miniconda3/envs +ENV CONDA_ROOT=/opt/conda/ +ENV CONDA_ENV_DIR=/opt/conda/envs RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} From 951296d2858102e8b00c9b7bdfd5366ce00dddc7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 17:42:22 -0400 Subject: [PATCH 14/82] Create ecs-task-defn.json --- ecs-task-defn.json | 118 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 ecs-task-defn.json diff --git a/ecs-task-defn.json b/ecs-task-defn.json new file mode 100644 index 000000000..fe676c693 --- /dev/null +++ b/ecs-task-defn.json @@ -0,0 +1,118 @@ +{ + "ipcMode": null, + "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "containerDefinitions": [ + { + "dnsSearchDomains": null, + "environmentFiles": null, + "logConfiguration": { + "logDriver": "awslogs", + "secretOptions": null, + "options": { + "awslogs-group": "/ecs/first-run-task-definition", + "awslogs-region": "us-east-2", + "awslogs-stream-prefix": "ecs" + } + }, + "entryPoint": [], + "portMappings": [], + "command": [], + "linuxParameters": null, + "cpu": 0, + "environment": [], + "resourceRequirements": null, + "ulimits": null, + "dnsServers": null, + "mountPoints": [], + "workingDirectory": null, + "secrets": null, + "dockerSecurityOptions": null, + "memory": null, + "memoryReservation": null, + "volumesFrom": [], + "stopTimeout": null, + "image": "430073024411.dkr.ecr.us-east-1.amazonaws.com/wrongkindofdoctor/mdtf-test:latest", + "startTimeout": null, + "firelensConfiguration": null, + "dependsOn": null, + "disableNetworking": null, + "interactive": null, + "healthCheck": null, + "essential": true, + "links": [], + "hostname": null, + "extraHosts": null, + "pseudoTerminal": null, + "user": null, + "readonlyRootFilesystem": null, + "dockerLabels": null, + "systemControls": null, + "privileged": null, + "name": "custom" + } + ], + "placementConstraints": [], + "memory": "512", + "taskRoleArn": null, + "compatibilities": [ + "EC2", + "FARGATE" + ], + "taskDefinitionArn": "arn:aws:ecs:us-east-2:430073024411:task-definition/first-run-task-definition:1", + "family": "first-run-task-definition", + "requiresAttributes": [ + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.execution-role-awslogs" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.ecr-auth" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.execution-role-ecr-pull" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" + }, + { + "targetId": null, + "targetType": null, + "value": null, + "name": "ecs.capability.task-eni" + } + ], + "pidMode": null, + "requiresCompatibilities": [ + "FARGATE" + ], + "networkMode": "awsvpc", + "cpu": "256", + "revision": 1, + "status": "ACTIVE", + "inferenceAccelerators": null, + "proxyConfiguration": null, + "volumes": [] +} From 0b67ac4835d7e0ea2adf5c5a820d9b832fba3385 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:20:15 -0400 Subject: [PATCH 15/82] Update ecs-task-defn.json mdtf-test task --- ecs-task-defn.json | 175 ++++++++++++++++----------------------------- 1 file changed, 60 insertions(+), 115 deletions(-) diff --git a/ecs-task-defn.json b/ecs-task-defn.json index fe676c693..b8fefe348 100644 --- a/ecs-task-defn.json +++ b/ecs-task-defn.json @@ -1,118 +1,63 @@ { - "ipcMode": null, - "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", - "containerDefinitions": [ - { - "dnsSearchDomains": null, - "environmentFiles": null, - "logConfiguration": { - "logDriver": "awslogs", - "secretOptions": null, - "options": { - "awslogs-group": "/ecs/first-run-task-definition", - "awslogs-region": "us-east-2", - "awslogs-stream-prefix": "ecs" + "taskDefinitionArn": "arn:aws:ecs:us-east-1:430073024411:task-definition/mdtf-test-a1r:25", + "containerDefinitions": [ + { + "name": "mdtf-test-a1r", + "image": "public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest", + "cpu": 0, + "portMappings": [], + "essential": true, + "environment": [], + "mountPoints": [], + "volumesFrom": [], + "logConfiguration": { + "logDriver": "awslogs", + "options": { + "awslogs-group": "/ecs/mdtf-test-a1r", + "awslogs-region": "us-east-1", + "awslogs-stream-prefix": "ecs" + } + } } - }, - "entryPoint": [], - "portMappings": [], - "command": [], - "linuxParameters": null, - "cpu": 0, - "environment": [], - "resourceRequirements": null, - "ulimits": null, - "dnsServers": null, - "mountPoints": [], - "workingDirectory": null, - "secrets": null, - "dockerSecurityOptions": null, - "memory": null, - "memoryReservation": null, - "volumesFrom": [], - "stopTimeout": null, - "image": "430073024411.dkr.ecr.us-east-1.amazonaws.com/wrongkindofdoctor/mdtf-test:latest", - "startTimeout": null, - "firelensConfiguration": null, - "dependsOn": null, - "disableNetworking": null, - "interactive": null, - "healthCheck": null, - "essential": true, - "links": [], - "hostname": null, - "extraHosts": null, - "pseudoTerminal": null, - "user": null, - "readonlyRootFilesystem": null, - "dockerLabels": null, - "systemControls": null, - "privileged": null, - "name": "custom" - } - ], - "placementConstraints": [], - "memory": "512", - "taskRoleArn": null, - "compatibilities": [ - "EC2", - "FARGATE" - ], - "taskDefinitionArn": "arn:aws:ecs:us-east-2:430073024411:task-definition/first-run-task-definition:1", - "family": "first-run-task-definition", - "requiresAttributes": [ - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.execution-role-awslogs" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.ecr-auth" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.execution-role-ecr-pull" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" - }, - { - "targetId": null, - "targetType": null, - "value": null, - "name": "ecs.capability.task-eni" - } - ], - "pidMode": null, - "requiresCompatibilities": [ - "FARGATE" - ], - "networkMode": "awsvpc", - "cpu": "256", - "revision": 1, - "status": "ACTIVE", - "inferenceAccelerators": null, - "proxyConfiguration": null, - "volumes": [] + ], + "family": "mdtf-test-a1r", + "taskRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "executionRoleArn": "arn:aws:iam::430073024411:role/ecsTaskExecutionRole", + "networkMode": "awsvpc", + "revision": 25, + "volumes": [], + "status": "ACTIVE", + "requiresAttributes": [ + { + "name": "com.amazonaws.ecs.capability.logging-driver.awslogs" + }, + { + "name": "ecs.capability.execution-role-awslogs" + }, + { + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.19" + }, + { + "name": "com.amazonaws.ecs.capability.task-iam-role" + }, + { + "name": "com.amazonaws.ecs.capability.docker-remote-api.1.18" + }, + { + "name": "ecs.capability.task-eni" + } + ], + "placementConstraints": [], + "compatibilities": [ + "EC2", + "FARGATE" + ], + "requiresCompatibilities": [ + "FARGATE" + ], + "cpu": "4096", + "memory": "8192", + "registeredAt": "2022-10-20T16:01:08.915Z", + "registeredBy": "arn:aws:iam::430073024411:user/a1r", + "tags": [] } From bd23c11d07b00c99f0eab21a0d5c1073a56a06f4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:21:42 -0400 Subject: [PATCH 16/82] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 47776cbaf..354bdf507 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,8 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs RUN conda install -c conda-forge -c default libarchive -RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh --all --conda_root ${CONDA_ROOT} \ +#add base only for testing +RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation RUN ${CODE_ROOT}/mdtf --version From d901b70b1bcd587484a9aa3dcb701ee426a8ced9 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:26:04 -0400 Subject: [PATCH 17/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 354bdf507..d8be707ed 100644 --- a/Dockerfile +++ b/Dockerfile @@ -46,6 +46,6 @@ RUN conda install -c conda-forge -c default libarchive RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN ${CODE_ROOT}/mdtf --version +RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] From 9c09ed764325c1730240837475346ef504e7eccc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:46:06 -0400 Subject: [PATCH 18/82] Update Dockerfile --- Dockerfile | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index d8be707ed..3b29e3b4b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM continuumio/miniconda3 +FROM mamba-org/micromamba-docker:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -41,10 +41,12 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -RUN conda install -c conda-forge -c default libarchive +#what-really RUN conda install -c conda-forge -c default libarchive +micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + #add base only for testing -RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ - --env_dir ${CONDA_ENV_DIR} +#c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ +#c --env_dir ${CONDA_ENV_DIR} # Verify installation RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc From 1b99e7ab3e3282955553bcf0465c5a078eb311cd Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 18:49:47 -0400 Subject: [PATCH 19/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 3b29e3b4b..52de77b33 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,7 +42,7 @@ COPY tests ${CODE_ROOT}/tests ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #what-really RUN conda install -c conda-forge -c default libarchive -micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #add base only for testing #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ From 7059577b44426749202eea722274be610cf508a2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 19:33:45 -0400 Subject: [PATCH 20/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 52de77b33..fe6b793fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mamba-org/micromamba-docker:latest +FROM mambaorg/micromamba:latest # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From 82ce9c1502b570355d3cbfc48133eeed29934b38 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:36:20 -0400 Subject: [PATCH 21/82] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index fe6b793fe..ee86047a3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,10 +8,10 @@ LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive # Update Ubuntu Software repository -RUN apt update +#RUN apt update # Install dependencies -RUN apt install -y wget -RUN apt install -y vim +#cRUN apt install -y wget +#cRUN apt install -y vim RUN apt install -y git # Cleanup RUN rm -rf /var/lib/apt/lists/* && \ From 068bec561846aa5696efaaf0fd9409f89f115b7d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:40:52 -0400 Subject: [PATCH 22/82] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index ee86047a3..6dc2ad8a1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,10 +12,10 @@ ARG DEBIAN_FRONTEND=noninteractive # Install dependencies #cRUN apt install -y wget #cRUN apt install -y vim -RUN apt install -y git +#c RUN apt install -y git # Cleanup -RUN rm -rf /var/lib/apt/lists/* && \ - apt clean +#c RUN rm -rf /var/lib/apt/lists/* && \ +#c apt clean # Install Miniconda3 # Download the latest shell script ####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh From e17805a6fb92ff9bea5d2a1a1550028eb18cae13 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:43:52 -0400 Subject: [PATCH 23/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6dc2ad8a1..8142742c5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,8 +26,8 @@ ARG DEBIAN_FRONTEND=noninteractive ####ARG PATH="/root/miniconda3/bin:${PATH}" ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh -RUN conda info -RUN conda init bash +RUN micromamba info +RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics From 7ce98546375e0c92c91f98f3e58bfa9b5f3004e1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 20:56:46 -0400 Subject: [PATCH 24/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8142742c5..a2dda45e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN micromamba init bash +#c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics From 58a69c6b708f6b1351350bc666ba7e721d9e5beb Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:03:10 -0400 Subject: [PATCH 25/82] Update Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index a2dda45e4..b41240afb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,4 +50,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml # Verify installation RUN /proj/MDTF-diagnostics/mdtf --version # Run mdtf on src/default_tests.jsonc -CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +# CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +CMD ["/proj/MDTF-diagnostics/mdtf", "-f","/proj/MDTF-diagnostics/src/default_tests.jsonc"] From b4bcd007962b35dda1d88ed0427458f5e0a529b2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:07:49 -0400 Subject: [PATCH 26/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index b41240afb..a10a9248d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,7 +48,7 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN /proj/MDTF-diagnostics/mdtf --version +RUN /proj/MDTF-diagnostics/mdtf_framework --version # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -CMD ["/proj/MDTF-diagnostics/mdtf", "-f","/proj/MDTF-diagnostics/src/default_tests.jsonc"] +CMD ["/proj/MDTF-diagnostics/mdtf_framework", "--version"] From c469dd3e3b9900514ad5496c4750176216d2f614 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Fri, 25 Aug 2023 21:15:59 -0400 Subject: [PATCH 27/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a10a9248d..53e2aecf5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,7 +48,7 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} # Verify installation -RUN /proj/MDTF-diagnostics/mdtf_framework --version +RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -CMD ["/proj/MDTF-diagnostics/mdtf_framework", "--version"] +CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From a9b74d0c28a600751144befe774d44a68a66f9bf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:39:09 -0400 Subject: [PATCH 28/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 53e2aecf5..868e815b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -43,7 +43,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #what-really RUN conda install -c conda-forge -c default libarchive RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml - +RUN micromamba activate _MDTF_base #add base only for testing #c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ #c --env_dir ${CONDA_ENV_DIR} From 102c68794e3836de135788a200528c5b76d8dc32 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:50:22 -0400 Subject: [PATCH 29/82] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 868e815b0..b7a7ad84a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,6 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info +RUN eval "$(micromamba shell hook --shell ) #c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image From 78d8ce5109d63c3b91ae513d708110031f5c28d7 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 09:52:54 -0400 Subject: [PATCH 30/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b7a7ad84a..e7d2a219f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,7 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN eval "$(micromamba shell hook --shell ) +RUN eval "$(micromamba shell hook --shell )" #c RUN micromamba init bash ##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge # Copy the MDTF-diagnostics package contents from local machine to image From a5286cda0dad2a918ec9c07d64f9a3954b8b1128 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:08:40 -0400 Subject: [PATCH 31/82] Update Dockerfile --- Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index e7d2a219f..e389c98c4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,9 +27,7 @@ ARG DEBIAN_FRONTEND=noninteractive ####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b ####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info -RUN eval "$(micromamba shell hook --shell )" -#c RUN micromamba init bash -##RUN conda install 'mamba<=1.4.5' -n base -c conda-forge +RUN micromamba shell hook --shell bash # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src From cea4cef755cf08862701fa04e8a4a6a823a72b25 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:17:50 -0400 Subject: [PATCH 32/82] Update Dockerfile --- Dockerfile | 26 ++------------------------ 1 file changed, 2 insertions(+), 24 deletions(-) diff --git a/Dockerfile b/Dockerfile index e389c98c4..5a71d2b7e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,25 +7,6 @@ LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive -# Update Ubuntu Software repository -#RUN apt update -# Install dependencies -#cRUN apt install -y wget -#cRUN apt install -y vim -#c RUN apt install -y git -# Cleanup -#c RUN rm -rf /var/lib/apt/lists/* && \ -#c apt clean -# Install Miniconda3 -# Download the latest shell script -####RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -#### Change permission to execute build script -####RUN chmod +x Miniconda3-latest-Linux-x86_64.sh -#### Run miniconda installation script -####ENV PATH="/root/miniconda3/bin:${PATH}" -####ARG PATH="/root/miniconda3/bin:${PATH}" -####RUN bash ./Miniconda3-latest-Linux-x86_64.sh -b -####RUN rm -f Miniconda3-latest-Linux-x86_64.sh RUN micromamba info RUN micromamba shell hook --shell bash # Copy the MDTF-diagnostics package contents from local machine to image @@ -40,14 +21,11 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -#what-really RUN conda install -c conda-forge -c default libarchive RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml -RUN micromamba activate _MDTF_base -#add base only for testing -#c RUN bash ${CODE_ROOT}/src/conda/conda_env_setup.sh -e base --conda_root ${CONDA_ROOT} \ -#c --env_dir ${CONDA_ENV_DIR} +#cRUN micromamba activate _MDTF_base # Verify installation RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] +ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From a10e969674dd3ace1172f885ac602e6519b844e5 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:24:46 -0400 Subject: [PATCH 33/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5a71d2b7e..eab8cf723 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ ENV CONDA_ENV_DIR=/opt/conda/envs RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation -RUN /proj/MDTF-diagnostics/mdtf_framework.py --help +#RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] From a573cb346c0b56e163111ea6935d3a8347b3cdd8 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:38:43 -0400 Subject: [PATCH 34/82] Update main.yml --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 08afe9f16..b60094fd0 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -61,7 +61,7 @@ jobs: image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@de0132cf8cdedb79975c6d42b77eb7ea193cf28e + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 with: task-definition: ${{ steps.task-def.outputs.task-definition }} service: ${{ env.ECS_SERVICE }} From d6d8cfea525c0b6f06e45e212fcd489df6d62d9f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Sat, 26 Aug 2023 10:41:01 -0400 Subject: [PATCH 35/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index eab8cf723..639e32a0c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,5 +27,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["micromamba shell hook --shell bash","micromamba activate _MDTF_base"] +ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From 6ade7bcd236a07e1cd3eae40c7411188be260e92 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Mon, 28 Aug 2023 18:31:04 -0400 Subject: [PATCH 36/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 639e32a0c..c974de3d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,5 +27,5 @@ RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] -CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] +#later ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] +#later CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] From ba5b4e3996110b679892142f21e2e77a5d832fca Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Mon, 28 Aug 2023 18:52:18 -0400 Subject: [PATCH 37/82] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index c974de3d9..07e479120 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ # Base OS FROM ubuntu:latest FROM mambaorg/micromamba:latest +USER root # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" From ed09195a7c334d4899771dbdb0ab9a847a8db9e3 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 10:27:11 -0400 Subject: [PATCH 38/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 07e479120..824483d41 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,7 +22,7 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From f59a3cca86afa8e18ab69e1ed08d147e8b97590a Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 10:37:28 -0400 Subject: [PATCH 39/82] Update Dockerfile --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 824483d41..1f6f8742b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,11 +22,11 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -#later ENTRYPOINT ["bash","micromamba shell hook --shell bash","micromamba activate _MDTF_base"] -#later CMD ["/proj/MDTF-diagnostics/mdtf_framework.py", "--help"] +ENTRYPOINT ["micromamba activate _MDTF_base"] +CMD ["/bin/bash", "--help"] From ae547eacdadca8e3e122f74edb123985243a074b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 11:29:44 -0400 Subject: [PATCH 40/82] Update Dockerfile --- Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1f6f8742b..138fc579c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,11 +22,12 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs +USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help # Run mdtf on src/default_tests.jsonc # CMD ["${CODE_ROOT}/mdtf", "-f","${CODE_ROOT}/src/default_tests.jsonc"] -ENTRYPOINT ["micromamba activate _MDTF_base"] -CMD ["/bin/bash", "--help"] +#ENTRYPOINT ["micromamba activate _MDTF_base"] +CMD ["/bin/bash"] From a12ce61040cb1d8b89a39cbaf840178c53ce266d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 11:59:00 -0400 Subject: [PATCH 41/82] Update Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 138fc579c..52178585f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,6 +24,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN export PATH="/proj/MDTF-diagnostics/:$PATH" #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From ff3e22d2d8f0d211dcd6a16117ddb5dfbda922f4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:42:40 -0400 Subject: [PATCH 42/82] Create docker-build-push-to-cloud.yml --- .github/docker-build-push-to-cloud.yml | 69 ++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .github/docker-build-push-to-cloud.yml diff --git a/.github/docker-build-push-to-cloud.yml b/.github/docker-build-push-to-cloud.yml new file mode 100644 index 000000000..b60094fd0 --- /dev/null +++ b/.github/docker-build-push-to-cloud.yml @@ -0,0 +1,69 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Deploy to ECS. Build, push image, + +on: + pull_request: + branches: + - main + +env: + AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 + ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name + ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name + ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name + ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition + # file, e.g. .aws/task-definition.json + CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the + # containerDefinitions section of your task definition MY_CONTAINER_NAME + +jobs: + deploy: + name: push-to-public-ecr-cache-test + runs-on: ubuntu-latest + environment: dev + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ env.AWS_REGION }} + + - name: Build, tag, and push image to Amazon ECR + id: build-image + uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public + env: + ECR_REGISTRY: public.ecr.aws + IMAGE_TAG: "latest" + ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG + with: + registry: public.ecr.aws + username: "${{ secrets.AWS_ACCESS_KEY_ID }}" + password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" + image_name: c6h4h4s8/mdtf/mdtf-test + push_image_and_stages: true + image_tag: latest + + - name: Fill in the new image ID in the Amazon ECS task definition + id: task-def + uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a + with: + task-definition: ${{ env.ECS_TASK_DEFINITION }} + container-name: ${{ env.CONTAINER_NAME }} + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + + - name: Deploy Amazon ECS task definition + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 + with: + task-definition: ${{ steps.task-def.outputs.task-definition }} + service: ${{ env.ECS_SERVICE }} + cluster: ${{ env.ECS_CLUSTER }} + wait-for-service-stability: true From 17d298b3a6422bd0f618c295613c14a145bb072f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:47:22 -0400 Subject: [PATCH 43/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 52178585f..63a7a1d5e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs USER mambauser RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml -RUN export PATH="/proj/MDTF-diagnostics/:$PATH" +ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation #RUN /proj/MDTF-diagnostics/mdtf_framework.py --help From 72d237c451d9586b293ee4b0681db818bf32d73d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:54:38 -0400 Subject: [PATCH 44/82] Delete docker-build-push-to-cloud.yml --- .github/docker-build-push-to-cloud.yml | 69 -------------------------- 1 file changed, 69 deletions(-) delete mode 100644 .github/docker-build-push-to-cloud.yml diff --git a/.github/docker-build-push-to-cloud.yml b/.github/docker-build-push-to-cloud.yml deleted file mode 100644 index b60094fd0..000000000 --- a/.github/docker-build-push-to-cloud.yml +++ /dev/null @@ -1,69 +0,0 @@ -# This workflow uses actions that are not certified by GitHub. -# They are provided by a third-party and are governed by -# separate terms of service, privacy policy, and support -# documentation. - -name: Deploy to ECS. Build, push image, - -on: - pull_request: - branches: - - main - -env: - AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 - ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name - ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name - ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name - ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition - # file, e.g. .aws/task-definition.json - CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the - # containerDefinitions section of your task definition MY_CONTAINER_NAME - -jobs: - deploy: - name: push-to-public-ecr-cache-test - runs-on: ubuntu-latest - environment: dev - - steps: - - name: Checkout - uses: actions/checkout@v2 - - - name: Configure AWS credentials - uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 - with: - aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} - aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - aws-region: ${{ env.AWS_REGION }} - - - name: Build, tag, and push image to Amazon ECR - id: build-image - uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public - env: - ECR_REGISTRY: public.ecr.aws - IMAGE_TAG: "latest" - ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG - with: - registry: public.ecr.aws - username: "${{ secrets.AWS_ACCESS_KEY_ID }}" - password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" - image_name: c6h4h4s8/mdtf/mdtf-test - push_image_and_stages: true - image_tag: latest - - - name: Fill in the new image ID in the Amazon ECS task definition - id: task-def - uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a - with: - task-definition: ${{ env.ECS_TASK_DEFINITION }} - container-name: ${{ env.CONTAINER_NAME }} - image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - - - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 - with: - task-definition: ${{ steps.task-def.outputs.task-definition }} - service: ${{ env.ECS_SERVICE }} - cluster: ${{ env.ECS_CLUSTER }} - wait-for-service-stability: true From 7399c16ffa70797c9efc0f3f3de920a721a0388b Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 12:55:34 -0400 Subject: [PATCH 45/82] Create docker-build-push-aws.yml minus the ECR deployment step --- .github/workflows/docker-build-push-aws.yml | 69 +++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .github/workflows/docker-build-push-aws.yml diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml new file mode 100644 index 000000000..b60094fd0 --- /dev/null +++ b/.github/workflows/docker-build-push-aws.yml @@ -0,0 +1,69 @@ +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Deploy to ECS. Build, push image, + +on: + pull_request: + branches: + - main + +env: + AWS_REGION: us-east-1 # set this to your preferred AWS region, e.g. us-west-1 + ECR_REPOSITORY: mdtf/mdtf-test # set this to your Amazon ECR repository name + ECS_SERVICE: custom-service # MY_ECS_SERVICE set this to your Amazon ECS service name + ECS_CLUSTER: mdtf-east1 # MY_ECS_CLUSTER set this to your Amazon ECS cluster name + ECS_TASK_DEFINITION: ecs-task-defn.json # set this to the path to your Amazon ECS task definition + # file, e.g. .aws/task-definition.json + CONTAINER_NAME: mdtf-test-a1r # set this to the name of the container in the + # containerDefinitions section of your task definition MY_CONTAINER_NAME + +jobs: + deploy: + name: push-to-public-ecr-cache-test + runs-on: ubuntu-latest + environment: dev + + steps: + - name: Checkout + uses: actions/checkout@v2 + + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@13d241b293754004c80624b5567555c4a39ffbe3 + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ${{ env.AWS_REGION }} + + - name: Build, tag, and push image to Amazon ECR + id: build-image + uses: aradhakrishnanGFDL/docker-build-with-cache-action@master #support-aws-ecr-public + env: + ECR_REGISTRY: public.ecr.aws + IMAGE_TAG: "latest" + ECS_IMAGE: $ECR_REGISTRY/ECR_REPOSITORY:$env.IMAGE_TAG + with: + registry: public.ecr.aws + username: "${{ secrets.AWS_ACCESS_KEY_ID }}" + password: "${{ secrets.AWS_SECRET_ACCESS_KEY }}" + image_name: c6h4h4s8/mdtf/mdtf-test + push_image_and_stages: true + image_tag: latest + + - name: Fill in the new image ID in the Amazon ECS task definition + id: task-def + uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a + with: + task-definition: ${{ env.ECS_TASK_DEFINITION }} + container-name: ${{ env.CONTAINER_NAME }} + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + + - name: Deploy Amazon ECS task definition + uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 + with: + task-definition: ${{ steps.task-def.outputs.task-definition }} + service: ${{ env.ECS_SERVICE }} + cluster: ${{ env.ECS_CLUSTER }} + wait-for-service-stability: true From e894826855caced5c1199735af8eaf28116f008f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:00:57 -0400 Subject: [PATCH 46/82] Create docker-run-test.yml --- .github/workflows/docker-run-test.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/workflows/docker-run-test.yml diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml new file mode 100644 index 000000000..6eaf2b9cc --- /dev/null +++ b/.github/workflows/docker-run-test.yml @@ -0,0 +1,15 @@ +name: CI +on: + push: + branches: [ aradhakrishnanGFDL-patch5 ] +jobs: + container-test-job: + runs-on: ubuntu-latest + container: + image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest + env: + NODE_ENV: development + options: --cpus 1 + steps: + - name: Check PATH + run: (echo $PATH) || (echo "No path") From 69c5b3aef059e3f4eff6177d7e0438900824326e Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:03:26 -0400 Subject: [PATCH 47/82] Update docker-build-push-aws.yml --- .github/workflows/docker-build-push-aws.yml | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml index b60094fd0..8976d9908 100644 --- a/.github/workflows/docker-build-push-aws.yml +++ b/.github/workflows/docker-build-push-aws.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Deploy to ECS. Build, push image, +name: Build and push image to Amazon ECR on: pull_request: @@ -51,19 +51,3 @@ jobs: image_name: c6h4h4s8/mdtf/mdtf-test push_image_and_stages: true image_tag: latest - - - name: Fill in the new image ID in the Amazon ECS task definition - id: task-def - uses: aws-actions/amazon-ecs-render-task-definition@97587c9d45a4930bf0e3da8dd2feb2a463cf4a3a - with: - task-definition: ${{ env.ECS_TASK_DEFINITION }} - container-name: ${{ env.CONTAINER_NAME }} - image: public.ecr.aws/c6h4h4s8/mdtf/mdtf-test:latest - - - name: Deploy Amazon ECS task definition - uses: aws-actions/amazon-ecs-deploy-task-definition@v1.4.10 - with: - task-definition: ${{ steps.task-def.outputs.task-definition }} - service: ${{ env.ECS_SERVICE }} - cluster: ${{ env.ECS_CLUSTER }} - wait-for-service-stability: true From d4890eadc9b2fda3c8917881273edd6811d3dba1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:06:22 -0400 Subject: [PATCH 48/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 6eaf2b9cc..e748e3245 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -1,7 +1,7 @@ -name: CI +name: docker-run-minitest on: - push: - branches: [ aradhakrishnanGFDL-patch5 ] + pull_request: + branches: [ main ] jobs: container-test-job: runs-on: ubuntu-latest From 13b503d90da86ce7bb32fd095bbd16b438466856 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:17:50 -0400 Subject: [PATCH 49/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e748e3245..5e0580268 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,3 +13,7 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") + - name: Activate environment + run: (micromamba activate _MDTF_base) || (echo "Unable to activate environment") + - name: Get version of mdtf_framework.py + run: (mdtf_framework.py --version) From 31218a0683570fc34a0d061eaf5f3aad5ff90f48 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:27:19 -0400 Subject: [PATCH 50/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 5e0580268..4856418ff 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate _MDTF_base) || (echo "Unable to activate environment") + run: (eval "$(micromamba shell hook --shell )" + micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 060efab5e714213baa005b328912b95bb3f38c91 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:28:59 -0400 Subject: [PATCH 51/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 4856418ff..3eed90770 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (eval "$(micromamba shell hook --shell )" + run: (eval "$(micromamba shell hook --shell bash)" micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 65c4fa8c8251335b561a51e8eea338b7c9ff8dfc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:31:35 -0400 Subject: [PATCH 52/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 3eed90770..0ada44cb7 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (eval "$(micromamba shell hook --shell bash)" - micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook --shell bash))" + micromamba activate _MDTF_base - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 225a0ab1733f3e63a94ed0d413303fffdcb85b3c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:35:27 -0400 Subject: [PATCH 53/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 0ada44cb7..e4205fb06 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,8 +13,9 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") - - name: Activate environment + - name: Shell init for micromamba run: (eval "$(micromamba shell hook --shell bash))" + - name: Activate environment micromamba activate _MDTF_base - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 6b5a7dc016ecabf8e48382f883852807530862fb Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 13:38:19 -0400 Subject: [PATCH 54/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e4205fb06..e0cbed4b9 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,6 +16,6 @@ jobs: - name: Shell init for micromamba run: (eval "$(micromamba shell hook --shell bash))" - name: Activate environment - micromamba activate _MDTF_base + run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py - run: (mdtf_framework.py --version) + run: (mdtf_framework.py --version) From 542e6fc50f6cb0e7cd615966974bca7216ae7b1c Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:32:18 -0400 Subject: [PATCH 55/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index e0cbed4b9..2ae85cc9f 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Shell init for micromamba - run: (eval "$(micromamba shell hook --shell bash))" + run: (eval "$(micromamba shell hook --shell bash)") - name: Activate environment run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py From 2556a392a6a1d93451401ceacce576ee77cf1ce4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:35:34 -0400 Subject: [PATCH 56/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2ae85cc9f..0bf0564f6 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,7 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Shell init for micromamba - run: (eval "$(micromamba shell hook --shell bash)") + run: (micromamba shell hook --shell bash) - name: Activate environment run: (micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py From 3756eac88f9cb262c505df4f40f58bd60685b2fa Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:45:07 -0400 Subject: [PATCH 57/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 0bf0564f6..2cc3acac5 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,6 +16,6 @@ jobs: - name: Shell init for micromamba run: (micromamba shell hook --shell bash) - name: Activate environment - run: (micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 74acf422e68e5d1c5b0ff5dac02f7e857d75d732 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:47:32 -0400 Subject: [PATCH 58/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2cc3acac5..f758a4f43 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -13,9 +13,7 @@ jobs: steps: - name: Check PATH run: (echo $PATH) || (echo "No path") - - name: Shell init for micromamba - run: (micromamba shell hook --shell bash) - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell hook --shell bash; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 437c175153384074f2e049b94c37c31dc09c6979 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 14:53:32 -0400 Subject: [PATCH 59/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index f758a4f43..2f5fd8d8b 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell hook --shell bash; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From bb7fc1fd1723bf7675ceb5c3686f3c7b65385886 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 15:39:47 -0400 Subject: [PATCH 60/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 2f5fd8d8b..edaa45656 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell bash --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 576070a38b0bf519fd40b46c1f32fc95a0435f90 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 15:47:06 -0400 Subject: [PATCH 61/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index edaa45656..129ac99e4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell bash --root-prefix=/usr/bin/micromamba; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 96f398cdf799ee04020a83e1c0458036df3b4c36 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 21:10:30 -0400 Subject: [PATCH 62/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 129ac99e4..1e314ca17 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; source ~/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From aef473c3cea0247f4655fb987ead76b1b951ed27 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Tue, 29 Aug 2023 21:18:59 -0400 Subject: [PATCH 63/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 1e314ca17..c367979d4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; source ~/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 73b2f10667f93b8daff0a2cb01b883af8feb4963 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 16:45:08 -0400 Subject: [PATCH 64/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c367979d4..959540718 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -11,9 +11,15 @@ jobs: NODE_ENV: development options: --cpus 1 steps: - - name: Check PATH - run: (echo $PATH) || (echo "No path") + - uses: mamba-org/setup-micromamba@v1 + with: + micromamba-version: '1.3.1-0' + init-shell: >- + bash + powershell + cache-environment: true + post-cleanup: 'all' - name: Activate environment - run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 325a87b6512623f67ea70a3de56c01441a47224f Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 16:47:12 -0400 Subject: [PATCH 65/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 959540718..a29caeb60 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -17,7 +17,6 @@ jobs: init-shell: >- bash powershell - cache-environment: true post-cleanup: 'all' - name: Activate environment run: (micromamba activate; micromamba activate _MDTF_base) From c2f5de60c21b7e8388ae0b3ffe3088cb7349a3fc Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:00:59 -0400 Subject: [PATCH 66/82] Update Dockerfile --- Dockerfile | 47 +++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 43 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 63a7a1d5e..99637024d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,15 +1,53 @@ # Base OS FROM ubuntu:latest FROM mambaorg/micromamba:latest + +#micromamba set up + USER root + +# if your image defaults to a non-root user, then you may want to make the +# next 3 ARG commands match the values in your image. You can get the values +# by running: docker run --rm -it my/image id -a +ARG MAMBA_USER=mambauser +ARG MAMBA_USER_ID=57439 +ARG MAMBA_USER_GID=57439 +ENV MAMBA_USER=$MAMBA_USER +ENV MAMBA_ROOT_PREFIX="/opt/conda" +ENV MAMBA_EXE="/bin/micromamba" + +COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" +COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh +COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh +COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh + +RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ + /usr/local/bin/_dockerfile_setup_root_prefix.sh + +USER $MAMBA_USER + +SHELL ["/usr/local/bin/_dockerfile_shell.sh"] + +ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] +# Optional: if you want to customize the ENTRYPOINT and have a conda +# environment activated, then do this: +# ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] + +RUN micromamba info +RUN micromamba shell hook --shell bash +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + +## + # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation ARG DEBIAN_FRONTEND=noninteractive -RUN micromamba info -RUN micromamba shell hook --shell bash + # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics COPY src ${CODE_ROOT}/src @@ -22,8 +60,9 @@ COPY tests ${CODE_ROOT}/tests # Install conda environments ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs -USER mambauser -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + +#USER mambauser +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation From d8c08d1a2a03410e8b63055f1bee3ed0e7773736 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:02:01 -0400 Subject: [PATCH 67/82] Update docker-build-push-aws.yml --- .github/workflows/docker-build-push-aws.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-build-push-aws.yml b/.github/workflows/docker-build-push-aws.yml index 8976d9908..3f400a384 100644 --- a/.github/workflows/docker-build-push-aws.yml +++ b/.github/workflows/docker-build-push-aws.yml @@ -3,7 +3,7 @@ # separate terms of service, privacy policy, and support # documentation. -name: Build and push image to Amazon ECR +name: Build and push image to Amazon ECR. on: pull_request: From eca019da68b70ce20fa9e1f95d50654d7e172acf Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:05:12 -0400 Subject: [PATCH 68/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index a29caeb60..c367979d4 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -11,14 +11,9 @@ jobs: NODE_ENV: development options: --cpus 1 steps: - - uses: mamba-org/setup-micromamba@v1 - with: - micromamba-version: '1.3.1-0' - init-shell: >- - bash - powershell - post-cleanup: 'all' + - name: Check PATH + run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 33a59a5364bcb2225cda3875814e894a686ea917 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 17:11:24 -0400 Subject: [PATCH 69/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 99637024d..d68cd2f55 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mambaorg/micromamba:latest +FROM mambaorg/micromamba:1.5.0 as micromamba #micromamba set up From dc8dab268f3a7fd50bcf34c41e16793bb0da8c6d Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:12:01 -0400 Subject: [PATCH 70/82] Update Dockerfile --- Dockerfile | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index d68cd2f55..29b09f8b9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,8 +8,9 @@ USER root # if your image defaults to a non-root user, then you may want to make the # next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a -ARG MAMBA_USER=mambauser +# by running: docker run --rm -it my/image id -a + +ARG MAMBA_USER=mambauser ARG MAMBA_USER_ID=57439 ARG MAMBA_USER_GID=57439 ENV MAMBA_USER=$MAMBA_USER @@ -28,6 +29,7 @@ RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ USER $MAMBA_USER + SHELL ["/usr/local/bin/_dockerfile_shell.sh"] ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] @@ -36,6 +38,8 @@ ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] # ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] RUN micromamba info +RUN "echo done" + RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml @@ -46,7 +50,7 @@ LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" LABEL description="This is a docker image for the MDTF-diagnostics package" # Disable Prompt During Packages Installation -ARG DEBIAN_FRONTEND=noninteractive +#ARG DEBIAN_FRONTEND=noninteractive # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics @@ -63,6 +67,7 @@ ENV CONDA_ENV_DIR=/opt/conda/envs #USER mambauser #RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml + ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base # Verify installation From 5ba6cfd2459a9cc50339e4f69ee029e24829d6b4 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:13:06 -0400 Subject: [PATCH 71/82] Update Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 29b09f8b9..0d82f1fd5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # Base OS FROM ubuntu:latest -FROM mambaorg/micromamba:1.5.0 as micromamba +FROM mambaorg/micromamba:latest as micromamba #micromamba set up From 8498b796ba08612dd33c0dd1b3dfb3546b723804 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:14:29 -0400 Subject: [PATCH 72/82] Update Dockerfile --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index 0d82f1fd5..da1694b04 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,6 +17,8 @@ ENV MAMBA_USER=$MAMBA_USER ENV MAMBA_ROOT_PREFIX="/opt/conda" ENV MAMBA_EXE="/bin/micromamba" +######### + COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh From b118a1b96f698826f86eade79ce9039c5b824806 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 19:26:10 -0400 Subject: [PATCH 73/82] Update Dockerfile --- Dockerfile | 36 ++---------------------------------- 1 file changed, 2 insertions(+), 34 deletions(-) diff --git a/Dockerfile b/Dockerfile index da1694b04..048f6bf57 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,38 +6,7 @@ FROM mambaorg/micromamba:latest as micromamba USER root -# if your image defaults to a non-root user, then you may want to make the -# next 3 ARG commands match the values in your image. You can get the values -# by running: docker run --rm -it my/image id -a - -ARG MAMBA_USER=mambauser -ARG MAMBA_USER_ID=57439 -ARG MAMBA_USER_GID=57439 -ENV MAMBA_USER=$MAMBA_USER -ENV MAMBA_ROOT_PREFIX="/opt/conda" -ENV MAMBA_EXE="/bin/micromamba" - -######### - -COPY --from=micromamba "$MAMBA_EXE" "$MAMBA_EXE" -COPY --from=micromamba /usr/local/bin/_activate_current_env.sh /usr/local/bin/_activate_current_env.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_shell.sh /usr/local/bin/_dockerfile_shell.sh -COPY --from=micromamba /usr/local/bin/_entrypoint.sh /usr/local/bin/_entrypoint.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_initialize_user_accounts.sh /usr/local/bin/_dockerfile_initialize_user_accounts.sh -COPY --from=micromamba /usr/local/bin/_dockerfile_setup_root_prefix.sh /usr/local/bin/_dockerfile_setup_root_prefix.sh - -RUN /usr/local/bin/_dockerfile_initialize_user_accounts.sh && \ - /usr/local/bin/_dockerfile_setup_root_prefix.sh - -USER $MAMBA_USER - - -SHELL ["/usr/local/bin/_dockerfile_shell.sh"] - -ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"] -# Optional: if you want to customize the ENTRYPOINT and have a conda -# environment activated, then do this: -# ENTRYPOINT ["/usr/local/bin/_entrypoint.sh", "my_entrypoint_program"] +USER $MAMBA_USER RUN micromamba info RUN "echo done" @@ -46,7 +15,6 @@ RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ## - # Container Metadata LABEL maintainer="20195932+wrongkindofdoctor@users.noreply.github.com" LABEL version="alpha-01" @@ -56,7 +24,7 @@ LABEL description="This is a docker image for the MDTF-diagnostics package" # Copy the MDTF-diagnostics package contents from local machine to image ENV CODE_ROOT=/proj/MDTF-diagnostics -COPY src ${CODE_ROOT}/src +COPY src ${CODE_ROOT}/src COPY data ${CODE_ROOT}/data #COPY diagnostics ${CODE_ROOT}/diagnostics COPY mdtf_framework.py ${CODE_ROOT} From af8d669df83028222184ff76f903f4ed9f9671d8 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 20:41:53 -0400 Subject: [PATCH 74/82] Update Dockerfile --- Dockerfile | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 048f6bf57..a8e4ecead 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,10 +6,8 @@ FROM mambaorg/micromamba:latest as micromamba USER root -USER $MAMBA_USER - RUN micromamba info -RUN "echo done" + RUN micromamba shell hook --shell bash RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml From c3edd04553389e52b6492ba667c24ae8771c27e5 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 20:46:25 -0400 Subject: [PATCH 75/82] Update Dockerfile --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index a8e4ecead..f0db5afac 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN micromamba info RUN micromamba shell hook --shell bash -RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ## # Container Metadata @@ -34,7 +34,7 @@ ENV CONDA_ROOT=/opt/conda/ ENV CONDA_ENV_DIR=/opt/conda/envs #USER mambauser -#RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml +RUN micromamba create -f /proj/MDTF-diagnostics/src/conda/env_base.yml ENV PATH="${PATH}:/proj/MDTF-diagnostics/" #cRUN micromamba activate _MDTF_base From 4fd92fe70796c60bcf8c5660fdc198241da399f3 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:02:40 -0400 Subject: [PATCH 76/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c367979d4..433ff5594 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -1,4 +1,4 @@ -name: docker-run-minitest +name: docker-run-minitest1 on: pull_request: branches: [ main ] From 7e0bffec9c2e12ab711d66dd1215bb6f46fd5ca2 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:04:11 -0400 Subject: [PATCH 77/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 433ff5594..b314ca799 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,6 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba shell init --shell=bash; /github/home/.bashrc; micromamba activate; micromamba activate _MDTF_base) + run: (micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 1a5687f5df249e9c4e1cb307073ebb8e361a4dee Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:15:29 -0400 Subject: [PATCH 78/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index b314ca799..c7578c5f0 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -14,6 +14,7 @@ jobs: - name: Check PATH run: (echo $PATH) || (echo "No path") - name: Activate environment - run: (micromamba activate; micromamba activate _MDTF_base) + shell: bash + run: (micromamba shell hook -s bash -p ~/conda; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 618ae853e70aed6b6721401922b9a944602a9776 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:20:02 -0400 Subject: [PATCH 79/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c7578c5f0..c425cb78a 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (micromamba shell hook -s bash -p ~/conda; micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda); micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From e0ee8e1f1386263a466b7f4fa42b0443145dc253 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:25:46 -0400 Subject: [PATCH 80/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index c425cb78a..b656beeb5 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (eval "$(micromamba shell hook -s bash -p ~/conda); micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From aee3f551ee4973a0a39e7db343add38b2b57d1ae Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:32:37 -0400 Subject: [PATCH 81/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index b656beeb5..381362187 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -15,6 +15,6 @@ jobs: run: (echo $PATH) || (echo "No path") - name: Activate environment shell: bash - run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base) + run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base;mdtf_framework.py --version) - name: Get version of mdtf_framework.py run: (mdtf_framework.py --version) From 2701f37ad3ed3f92dc8af6a5c334f3ccfe42d7b1 Mon Sep 17 00:00:00 2001 From: Aparna Radhakrishnan Date: Wed, 30 Aug 2023 21:35:15 -0400 Subject: [PATCH 82/82] Update docker-run-test.yml --- .github/workflows/docker-run-test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/docker-run-test.yml b/.github/workflows/docker-run-test.yml index 381362187..dfddcb24c 100644 --- a/.github/workflows/docker-run-test.yml +++ b/.github/workflows/docker-run-test.yml @@ -16,5 +16,3 @@ jobs: - name: Activate environment shell: bash run: (eval "$(micromamba shell hook -s bash -p ~/conda)"; micromamba activate; micromamba activate _MDTF_base;mdtf_framework.py --version) - - name: Get version of mdtf_framework.py - run: (mdtf_framework.py --version)