Commit 09befe84 authored by Ramon Nou's avatar Ramon Nou
Browse files

Merge branch 'mr1_infrastructure' into 'master' 

MR1: Update dependency scripts to 0.9.6

Updated scripts and dockers to 0.9.6

See merge request !274
parents d2adbfb3 9820b6a4

.gitlab-ci.yml

+18 −19
Original line number Diff line number Diff line
@@ -28,14 +28,14 @@ variables: 




# base image

image: gekkofs/core:0.9.5

image: gekkofs/core:0.9.6



################################################################################

## Validating

################################################################################

check format:

  stage: lint

  image: gekkofs/linter:0.9.5

  image: gekkofs/linter:0.9.6

  needs: []

  script:

    - ${SCRIPTS_DIR}/check_format.sh
@@ -49,7 +49,7 @@ check format: 
################################################################################

gkfs:

  stage: build

  image: gekkofs/deps:0.9.5

  image: gekkofs/deps:0.9.6

  interruptible: true

  needs: []

  script:
@@ -88,7 +88,7 @@ gkfs: 
## == tests for scripts ====================

scripts:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  needs: []

  script:

    - mkdir -p ${BUILD_PATH}/tests/scripts
@@ -103,7 +103,7 @@ scripts: 
## == integration tests for gkfs ===========

gkfs:allintegration:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  interruptible: true

  needs: ['gkfs']
@@ -151,12 +151,12 @@ gkfs:allintegration: 
## == integration tests for gkfs ===========

gkfs:integration:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  interruptible: true

  needs: ['gkfs']  # we need to remove gkfs dependencies on manual

  parallel:

    matrix:

      - SUBTEST: [ data, status, syscalls, directories, operations, position, shell, rename ]

      - SUBTEST: [ data, status, syscalls, directories, operations, position, shell, rename, migration, startup, error_handling, resilience, compatibility ]

  rules:

    - if: '$CI_MERGE_REQUEST_EVENT_TYPE == "detached"'

      when: never
@@ -209,7 +209,7 @@ gkfs:integration: 
## == integration tests for gkfwd ==========

gkfwd:integration:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  interruptible: true

  needs: ['gkfs']

  parallel:
@@ -267,7 +267,7 @@ gkfwd:integration: 
## == unit tests for gkfs ==================

gkfs:unit:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  needs: ['gkfs']

  script:

    ## Add path to mkfs.kreon
@@ -307,7 +307,7 @@ gkfs:unit: 
## == unit tests for gkfs ==================

gkfs:app:

  stage: test

  image: gekkofs/apps:0.9.5

  image: gekkofs/apps:0.9.6

  needs: ['gkfs']

  script:

    ## Add path to mkfs.kreon
@@ -348,7 +348,7 @@ gkfs:app: 
## == java tests for gkfs ==================

gkfs:java:

  stage: test

  image: gekkofs/java:0.9.5

  image: gekkofs/java:0.9.6

  needs: ['gkfs']

  script:

    ## Add path to mkfs.kreon
@@ -389,7 +389,7 @@ gkfs:java: 
## == python tests for gkfs ==================

gkfs:python:

  stage: test

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  needs: ['gkfs']

  script:

    ## Add path to mkfs.kreon
@@ -432,7 +432,7 @@ gkfs:python: 
################################################################################

documentation:

  stage: docs

  image: gekkofs/docs:0.9.5

  image: gekkofs/docs:0.9.6

  needs: []

  rules:

    # we only build the documentation automatically if we are on the
@@ -465,7 +465,7 @@ documentation: 
## == coverage baseline ====================

coverage:baseline:

  stage: report

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  interruptible: true

  needs: ['gkfs']
@@ -496,7 +496,7 @@ coverage:baseline: 


coverage:

  stage: report

  image: gekkofs/testing:0.9.5

  image: gekkofs/testing:0.9.6

  #needs: [ 'coverage:baseline', 'gkfs:integration', 'gkfs:unit', 'gkfwd:integration']

  needs: [ 'coverage:baseline', 'gkfs:allintegration', 'gkfs:unit', 'gkfs:app', 'gkfs:java', 'gkfs:python' ]

  script:
@@ -528,12 +528,11 @@ coverage: 


cppcheck:

  stage: report

  image: gekkofs/testing:0.9.5

  needs: [ 'gkfs:allintegration', 'gkfs:unit']

  image: gekkofs/testing:0.9.6

  needs: [ 'gkfs']

  script:

    - cd ${CI_PROJECT_DIR}

    - rm -rf external gkfs

    - cppcheck -I/usr/local/include --xml --enable=warning,style,performance --force ${CI_PROJECT_DIR} 2> cppcheck_out.xml 

    - cppcheck --enable=all --std=c++17 --suppress=missingIncludeSystem --xml --xml-version=2 src include tests -i external -i builds -i gkfs 2> cppcheck_out.xml

    - cppcheck-codequality --input-file cppcheck_out.xml --output-file cppcheck.json

  #change paths

  after_script:

docker/0.9.6/apps/Dockerfile

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+70 −0
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FROM gekkofs/testing:0.9.6 AS builder



LABEL Description="Build environment for S3D-IO and WaComM++"



ARG DEBIAN_FRONTEND=noninteractive



RUN <<EOF

    apt-get update

    apt-get install -y --no-install-recommends \

    openmpi-bin openmpi-common gfortran libopenmpi-dev pnetcdf-bin libpnetcdf-dev libssl-dev wget nco nghttp2

    rm -rf /var/lib/apt/lists/* 

    apt-get clean

    apt-get autoclean

EOF



# --- Build S3D-IO ---

WORKDIR /build/S3D-IO

RUN git clone https://github.com/wkliao/S3D-IO.git . && \

    # Note: The PNETCDF_DIR and include path might need adjustment if libpnetcdf-dev installs to a different standard location

    # or if the base image structure changes.

    sed -i -e 's/PNETCDF_DIR = ${HOME}\/PNetCDF/PNETCDF_DIR = \/usr/' \

    -e 's/\(INC[[:space:]]*=[[:space:]]*-I\$(PNETCDF_DIR)\/include\)/\1 -I\/usr\/lib\/x86_64-linux-gnu\/fortran\/gfortran-mod-15/' Makefile && \

    make && \

    mv s3d_io.x /usr/local/bin/s3d_io.x



# --- Build wacommplusplus ---

WORKDIR /build/wacommplusplus

RUN git clone https://github.com/CCMMMA/wacommplusplus.git . && \

    sed -i 's|\${LIBCURL}|/usr/lib/x86_64-linux-gnu/libcurl.so|g' CMakeLists.txt && \

    mkdir build && cd build && \

    cmake .. && \

    make -j$(nproc) && \

    mv wacommplusplus /usr/local/bin/wacommplusplus && \

    mv external /usr/local/lib/



# ---- Final Stage ----

FROM gekkofs/testing:0.9.6



LABEL Description="Debian-based environment to test GekkoFS with apps"

ARG DEBIAN_FRONTEND=noninteractive



# Install runtime dependencies

# libpnetcdf13 (or similar, check exact name with 'apt-cache search libpnetcdf')

# libssl might be libssl1.1 or libssl3 depending on Debian version in base image

RUN apt-get update && apt-get install -y --no-install-recommends \

    openmpi-bin openmpi-common libopenmpi-dev pnetcdf-bin libssl3 libcurl4 \

    wget nco nghttp2 \

    && rm -rf /var/lib/apt/lists/* \

    && apt-get clean && \

    mkdir -p /root/wacommplusplus/build/example /root/S3D-IO



# Copy built applications from the builder stage

COPY --from=builder /usr/local/bin/s3d_io.x /root/S3D-IO

COPY --from=builder /usr/local/bin/wacommplusplus /root/wacommplusplus/build

COPY --from=builder /usr/local/lib/external /root/wacommplusplus/build/external/





WORKDIR /root/wacommplusplus/build/example

COPY rms.tar.gz /root/wacommplusplus/build/example/input/

RUN mkdir -p input processed output restarts && \

    cd input && \

    tar xzf rms.tar.gz && \

    rm rms.tar.gz



# Copy configuration files

# These files (sources.json, wacomm.json) should be in the same directory as your Dockerfile

COPY sources.json /root/wacommplusplus/build/example

COPY wacomm.json /root/wacommplusplus/build/example



ENV LD_LIBRARY_PATH=/root/wacommplusplus/build/external/lib/

docker/0.9.6/apps/Makefile

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+10 −0
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.PHONY: all



amd64:

	docker build --platform amd64 -t gekkofs/apps:0.9.6 .



aarch64:

	docker build --platform aarch64 -t gekkofs/apps:0.9.6 .



all:

	docker build -t gekkofs/apps:0.9.6 .

docker/0.9.6/apps/rms.tar.gz

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docker/0.9.6/apps/sources.json

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{

    "type": "FeatureCollection",

    "crs": {

        "type": "name",

        "properties": {

            "name": "urn:ogc:def:crs:OGC:1.3:CRS84"

        }

    },

    "features": [

        {

            "type": "Feature",

            "properties": {

                "start": -1.0,

                "end": -1.0,

                "mode": 1,

                "particlesPerHour": 100,

                "depth": 0.0,

                "id": "1"

            },

            "geometry": {

                "type": "Point",

                "coordinates": [

                    14.972061,

                    40.343286

                ]

            }

        } ] }
 
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