diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 35e32e3d..4cf78ae8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,9 +47,9 @@ jobs: matrix: os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13] fortran: [10, 11] - # exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04 - # - os: ubuntu-20.04 - # fortran: 11 + exclude: # gfortran-11, gfortran-12 not available for ubuntu-20.04 + - os: ubuntu-20.04 + fortran: 12 fail-fast: false # ------------------------------------------------------------- @@ -73,9 +73,9 @@ jobs: # and the AtChem2 dependencies: CVODE, openlibm, numdiff, FRUIT # gfortran on ubuntu - #- name: Install gfortran-11 (ubuntu-20.04) - # if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11 - # run: sudo apt-get install gfortran-11 + - name: Install gfortran-11 (ubuntu-20.04) + if: matrix.os == 'ubuntu-20.04' && matrix.fortran == 11 + run: sudo apt-get install gfortran-11 # gfortran on macos - name: Install gfortran-10 (macos-12) diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh old mode 100644 new mode 100755 index e3c6b618..6c0d8813 --- a/docker/entrypoint.sh +++ b/docker/entrypoint.sh @@ -1,4 +1,4 @@ -#!/usr/bin/bash +#!/bin/sh # ----------------------------------------------------------------------------- # # Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young, @@ -16,41 +16,41 @@ # ----------------------------------------------------------------------------- # ----------------------------------------------------------------------------- -# This script is run everytime the container is run. +# This script is run everytime the container is run. # -# First it copies the /atchem/ directory that is created during the build to +# First it copies the /atchem/ directory that is created during the build to # the home directory of the user running the container. This is for # compatibility with singularity, where the user running the container is not -# root, and therefore cannot modify the model files in place. +# root, and therefore cannot modify the model files in place. # # Next it moves the user configuration from /data_transfer/ and copies it into # the ~/atchem/ directory. This /data_transfer/ directory is created when the # the user mounts a volume when running the container (e.g `docker run -v...`) # # We then move to the ~/atchem directory and build the model using the mechanism -# specified by the user as a runtime argument to `docker run`. +# specified by the user as a runtime argument to `docker run`. # -# Then the model is run by executing the newly built atchem2 file. +# Then the model is run by executing the newly built atchem2 file. # # On completion the atchem model output directory is copied to the data_transfer # directory and as such onto the host filesystem # ----------------------------------------------------------------------------- -# make a copy to home to allow for compatibility with singularity -\command cp -rf /atchem/ ~/ +# Make a copy to home to allow for compatibility with singularity +\command cp -rf /atchem/ ~/ # Transfer in user config \command cp -rf /data_transfer/* ~/atchem/ -# move into atchem dir +# Move into atchem dir cd ~/atchem/ -# build model using user specified mechanism +# Build model using user specified mechanism ./build/build_atchem2.sh $1 echo $1 -# run model +# Run model ./atchem2 -# copy outputs to data_transfer / host filesystem -\command cp -rf ~/atchem/model/output /data_transfer/model/ \ No newline at end of file +# Copy outputs to data_transfer / host filesystem +\command cp -rf ~/atchem/model/output /data_transfer/model/ diff --git a/docker/install.sh b/docker/install.sh old mode 100644 new mode 100755 index e245f073..1c8d0ef7 --- a/docker/install.sh +++ b/docker/install.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/sh # ----------------------------------------------------------------------------- # # Copyright (c) 2009 - 2012 Chris Martin, Kasia Boronska, Jenny Young, @@ -16,34 +16,34 @@ # ----------------------------------------------------------------------------- # ----------------------------------------------------------------------------- -# This is the install script that is run when the container is built. It +# This is the install script that is run when the container is built. It # installs the necessary dependacies for installing AtChem2 (gcc-gfortran, # wget, cmake and python3.11). # -# It then runs the install scripts provided with the model (install_cvode.sh +# It then runs the install scripts provided with the model (install_cvode.sh # and install_openlibm.sh) to install additional dependancies required to build # the model. -# -# Next it produces the Makefile from the skeleton, and amends the dependancy +# +# Next it produces the Makefile from the skeleton, and amends the dependancy # paths. -# +# # Finally it does some housekeeping, updating the build_atchem2.sh to be able -# to find the python installation, and makes the docker entrypoint script -# executable. +# to find the python installation, and makes the docker entrypoint script +# executable. # ----------------------------------------------------------------------------- # Install dependancies from package repository dnf install -y which gcc-gfortran wget cmake python3.11 -# make directories +# Make directories mkdir /atchem-lib # mkdir /atchem -# move to /atchem so the dependacy installation scripts work correctly. +# Move to /atchem so the dependacy installation scripts work correctly. cd atchem # Install dependancies to /atchem-lib -./tools/install/install_cvode.sh /atchem-lib/ +./tools/install/install_cvode.sh /atchem-lib/ ./tools/install/install_openlibm.sh /atchem-lib/ # Change atchem dependancy paths and create Makefile from skeleton @@ -52,4 +52,4 @@ sed -i 's,openlibm-0.8.1,/atchem-lib/openlibm-0.8.1,g' ./Makefile # Fix python command to match installed version sed -i "s/python/python3/g" ./build/build_atchem2.sh -chmod +x docker/entrypoint.sh \ No newline at end of file +chmod +x docker/entrypoint.sh