update imi base image to explicitly install gcc in env, use a tagged …

…version of spack, and mamba for python dependencies

resources/containers/base-image/README.md

@@ -8,7 +8,7 @@ Dockerfiles contain a list of instructions to build an image with the necessary
 [Docker](https://www.docker.com/) must be installed to run or build IMI docker containers.
 
 ## Building the Docker image 
-To build the docker image, cd into the benchmarks/environments/ directory and run
+To build the docker image, cd into the resources/containers/base-image directory and run
 `$ docker build -t imi-base-image . --platform=linux/amd64`
 The `--platform=linux/amd64` flag specifies the architecture to mimic while building and ensures consistent builds regardless of whether the build is done on an arm system (apple silicon) or amd system (intel).
 

resources/containers/base-image/install-scripts/geoschem_deps-gnu-openmpi-102.yaml

@@ -11,10 +11,11 @@ spack:
       - spec: [email protected]
         prefix: /usr
   specs:
-    - cmake@3.22.1
+    - cmake%[email protected]
     - [email protected]%[email protected]
     - [email protected]%[email protected]
     - [email protected]%[email protected]
+    - [email protected]%[email protected]
     # - [email protected]%[email protected] +lustre +gpfs fabrics=auto
     # - [email protected] fabrics=sockets,tcp,udp,efa,mlx,shm
     # - [email protected]%[email protected]

resources/containers/base-image/install-scripts/install-imi-env.sh

@@ -6,6 +6,9 @@ set -e
 source /etc/bashrc
 spack env activate compute_env
 
+# install mamba for faster installs
+conda install -c conda-forge mamba
+
 # install the environment
-conda env create -f install-scripts/imi_env.yml
+mamba env create -f install-scripts/imi_env.yml
 conda activate imi_env

resources/containers/base-image/install-scripts/install-spack-env.sh

@@ -16,18 +16,15 @@ source /etc/bashrc
 # name: InstallSpackEnvironment
 echo "Downloading spack environment file"
 umask 022
-# curl $SpackEnvironmentFile -o /spack-manifest.yaml
-# . /opt/spack/share/spack/setup-env.sh
 cat /home/al2/install-scripts/$SpackEnvironmentFile
 spack compiler list
 
 spack env create $SpackEnvironmentName /home/al2/install-scripts/$SpackEnvironmentFile
 spack load $SpackCompiler
 spack env activate $SpackEnvironmentName
-spack install
+spack install --fail-fast --show-log-on-error
 spack clean --all
 
 # AutomaticallyLoadEnvironmentOnLogin
-echo spack load $SpackCompiler >> /etc/bashrc
 echo spack env activate $SpackEnvironmentName >> /etc/bashrc
 chmod -R +r /opt/spack

resources/containers/base-image/install-scripts/install-spack.sh

@@ -4,6 +4,8 @@
 set -x
 set -e # exit 1 if error
 
+# Spack version to install
+SpackVersion="v0.21.0"
 # Spack install spec for desired compiler
 SpackCompiler="[email protected]"
 # Name of spack env
@@ -12,15 +14,19 @@ SpackEnvironmentName="compute_env"
 SpackEnvironmentFile="geoschem_deps-gnu-openmpi-102.yaml"
 # InstallSpack
 source /etc/bashrc
-yum install -y git curl texinfo
+
+yum install -y git curl curl-devel texinfo
 yum groupinstall -y "Development tools"
 umask 022
+# Use spack v0.21.0
 git clone https://github.com/spack/spack /opt/spack
+(cd /opt/spack && git checkout $SpackVersion)
+
 SPACK_ROOT=/opt/spack
 . /opt/spack/share/spack/setup-env.sh
 spack compiler find --scope system
 spack external find --scope system
-spack install $SpackCompiler
+spack install --fail-fast $SpackCompiler
 spack load $SpackCompiler
 spack compiler find --scope system
 

resources/containers/base-image/install-scripts/install-system-deps.sh

@@ -2,7 +2,8 @@
 
 set -e # exit 1 if error
 
-yum install -y emacs wget time jq less glibc which sudo
+yum update
+yum install -y emacs wget time jq less glibc which sudo curl
 
 # install aws-cli
 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"