Container Builds

This document is adapted from an original set of instructions in this document. The original is substantially out of date but has been preserved in case it contains relevant historical information.

Environment Setup

Create a new EC2 instance using a c5n.4xlarge host. Either restore the existing container builder AMI or create a new AMI following the instructions in the spack stack repository.

When building on the remote host, it is recommended that you use the screen session manager in order to save session state since builds can take a long time and may require revisiting past the typical expiration period of a ssh session. Here I have compiled a few useful screen commands

# Start a new named screen session
screen -S spack-stack-container-clang

# Disconnect from active session: "Ctrl+A" then "D"

# Resume a screen session
screen -r spack-stack-container-clang

# List open screen sessions
screen -list

Build notes for specific environments

clang-mpich

After running `spack stack create ctr` you will need to remove `mapl` from your spec.

# After running `spack stack create ctr` from step 5 below.
cd envs/docker-ubuntu-clang-mpich
sed -i '/mapl@/s/^/#/' spack.yaml
spack containerize > Dockerfile
# Continue step 5.

Building spack-stack containers

ssh into your build environment (described earlier) and start a screen session.

Clone the spack stack repo and release

clone -b release/1.7.0 --recursive "https://github.com/climbfuji/spack-stack.git" spack-stack-1.7.0

Setup spack stack
```
cd spack-stack-1.7.0
source setup.sh
```

Create the container:

export DOCKER_ENV=clang-mpich
export DOCKER_CTR_REPO=747101682576.dkr.ecr.us-east-2.amazonaws.com
spack stack create ctr --container=docker-ubuntu-${DOCKER_ENV} \
    --specs=jedi-ci | tee log.create.docker-ubuntu-${DOCKER_ENV}-ci.001
.    Configuring basic directory information ...
.      ... script directory: /home/ubuntu/spack-stack/spack-stack-1.7.1/spack-ext/lib/jcsda-emc/spack-stack/stack
.      ... base directory: /home/ubuntu/spack-stack/spack-stack-1.7.1/spack-ext/lib/jcsda-emc/spack-stack
.      ... spack directory: /home/ubuntu/spack-stack/spack-stack-1.7.1/spack
.    ==> Created container /home/ubuntu/spack-stack/spack-stack-1.7.1/envs/docker-ubuntu-clang-mpich

Use spack to create the docker file and build with docker

cd envs/docker-ubuntu-$DOCKER_ENV/
spack containerize > Dockerfile
docker build -t $DOCKER_CTR_REPO/jedi-${DOCKER_ENV}-dev:test . 2>&1 | tee logdocker.txt

push the built image to ECR

aws ecr get-login-password --profile=jcsda-usaf-aws-us-east-2 \
                           --region us-east-2 \
   | docker login --username AWS \
       --password-stdin $DOCKER_CTR_REPO

docker push ${DOCKER_CTR_REPO}/jedi-${DOCKER_ENV}-dev:test

Update containers on DockerHub

In order to push to dockerhub, an access token is needed. Log into hub.docker.com, go to “Account Settings”, “Security”, “New Access Token”.

# Log into dockerhub using your account token and username.
docker login -u USERNAME

docker image tag \ 469205354006.dkr.ecr.us-east-1.amazonaws.com/jedi-gnu-openmpi-dev:latest \ jcsda/docker-gnu-openmpi-dev:latest
docker image tag jcsda/docker-gnu-openmpi-dev:latest \
jcsda/docker-gnu-openmpi-dev:skylab-vN
docker push jcsda/docker-gnu-openmpi-dev:latest
docker push jcsda/docker-gnu-openmpi-dev:skylab-vN


docker image tag \ 469205354006.dkr.ecr.us-east-1.amazonaws.com/jedi-clang-mpich-dev:latest \ jcsda/docker-clang-mpich-dev:latest
docker image tag jcsda/docker-clang-mpich-dev:latest \
jcsda/docker-clang-mpich-dev:skylab-vN
docker push jcsda/docker-clang-mpich-dev:latest
docker push jcsda/docker-clang-mpich-dev:skylab-vN

Creating Singularity containers

When the image is available in your docker-daemon (you have created it locally, or pulled it from dockerhub or AWS ECR):

singularity build jedi-gnu-openmpi-spack-stack-XYZ.sif docker-daemon:469205354006.dkr.ecr.us-east-1.amazonaws.com/jedi-gnu-openmpi-dev:spack-stack-X.Y.Z

Before uploading to Sylabs make sure to sign the image and authenticate to sylabs.io.

How to sign a singularity image

Generate a new keypair (one-off, does not expire). Open a command line and check for your generated keys:

singularity keys list

If you already have a generated key just skip the next steps (create key, obtain your key's fingerprint). Otherwise, if you need to generate a key just run:

singularity keys newpair

In order to obtain the fingerprint from the key you just created, list again your keys:

singularity keys list

This will list the keys you have created. In this list, you will find your key's fingerprint next to "F:", for example:

0) U: John Doe (my key) <johndoe@sylabs.io>

C: 2018-08-21 20:14:39 +0200 CEST

F: D87FE3AF5C1F063FCBCC9B02F812842B5EEE5934

L: 4096

Copy your fingerprint ( e.g. from the previous example the fingerprint would be D87FE3AF5C1F063FCBCC9B02F812842B5EEE5934 ) and then add it to your keystore by doing:

singularity keys push <Your key's fingerprint>

Now sign the image:

singularity sign jedi-gnu-openmpi-spack-stack-XYZ.sif

How to authenticate for sylabs.io

You need to set your token on Sylabs first:

Go to: https://cloud.sylabs.io/
Click “Sign In” and follow the sign in steps.
Click on your login id (same and updated button as the Sign in one).
Select “Access Tokens” from the drop down menu.
Enter a name for your new access token, such as “test token”
Click the “Create a New Access Token” button.
Click “Copy token to Clipboard” from the “New API Token” page.
Run “singularity remote login” and paste the access token at the prompt.
Once your to token is stored, you can check that you are able to connect to the services with the status subcommand: “singularity remote status”
Note that tokens are only valid for 1 month.

To upload the Singularity container to Sylabs follow instructions here: https://docs.sylabs.io/guides/latest/user-guide/endpoint.html#public-sylabs-cloud

singularity push jedi-clang-mpich-spack-stack-XYZ.sif library://jcsda/public/jedi-clang-mpich-dev:latest

singularity push jedi-gnu-openmpi-spack-stack-XYZ.sif library://jcsda/public/jedi-gnu-openmpi-dev:latest

Note. We don’t have enough free space on the sylabs platform to store the previous AND latest containers for both clang and gnu. Therefore, upload the latest clang container, then go to the website and delete the previous version of the clang container. Then, upload the latest gnu container and once done delete the previous version of the gnu container. The sylabs people offered us in the past to do a writeup of how JCSDA uses sylabs in return for more free storage; but we don’t really need this.

We have an s3 bucket for storing singularity containers … pull the old ones, store them, before uploading new ones (jcsda-noaa account, jcsda containers backup):

# as root
cd /home/ubuntu/spack-stack/keep_singularity
aws s3 sync ./ s3://jcsda-containers-backup/

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