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AWS EC2 Usage Instructions

The following instructions give a step-by-step guide to launching an AWS virtual machine with all the required prerequisites to run openproblems.

Code of conduct

Please be respectful of our finite resources!

  • The use of the openproblems AWS account is a privilege, not a right.
  • This privilege is given solely for the purposes of testing methods with openproblems-cli test.
  • Developers who have their own compute resources should use them; please help us conserve our resources for those who need them.
  • If developers are found to be using resources irresponsibly, we may have to revoke this privilege.

Requirements

Instructions

The following instructions are for bash, other shell users may need to modify commands slightly.

First, if you have recieved openproblems AWS credentials, configure AWS to use them. Note: openproblems uses us-west-2 as default region. If you have other AWS accounts, you can configure AWS with multiple accounts by using the AWS_PROFILE environment variable.

export AWS_PROFILE=openproblems
aws configure

Second, create a key pair (only do this once):

KEY_NAME="my_openproblems_key" # name this whatever you like, but it must be unique
aws ec2 create-key-pair --key-name $KEY_NAME --key-format pem \
--query "KeyMaterial" --output text > ${KEY_NAME}.pem
chmod 400 ${KEY_NAME}.pem

Now, create an instance with your key pair:

OWNER_NAME="this_is_your_name"
AWS_EC2_INSTANCE_TYPE="t2.micro"
INSTANCE_ID=$(
aws ec2 run-instances --count 1 --image-id ami-01219569b1bbf9fb2 \
  --instance-type $AWS_EC2_INSTANCE_TYPE --key-name $KEY_NAME \
  --security-group-ids sg-002d2b9db29bb43dd \
  --tag-specifications "ResourceType=instance,Tags=[{Key=owner,Value=${OWNER_NAME}}]" |
  jq '.["Instances"][0]["InstanceId"]' |
  tr -d '"'
)

Get the public DNS address for your instance

sleep 30 # wait for boot
PUBLIC_DNS_NAME=$(
aws ec2 describe-instances --instance-id $INSTANCE_ID |
  jq '.["Reservations"][0]["Instances"][0]["PublicDnsName"]' |
  tr -d '"'
)

Now you can SSH into your instance:

# check the status of your instance
aws ec2 describe-instance-status --instance-id ${INSTANCE_ID} | \
jq '.["InstanceStatuses"][0]["SystemStatus"]'
ssh -i ${KEY_NAME}.pem ubuntu@${PUBLIC_DNS_NAME}

The instance will by default contain all dependencies to use openproblems. You can run openproblems with

git clone https://github.com/openproblems-bio/openproblems
cd openproblems
sudo docker run \
  -v $(pwd):/usr/src/singlecellopenproblems -v /tmp:/tmp \
  -it singlecellopenproblems/openproblems bash
openproblems-cli --help

For more information on using the CLI, see CONTRIBUTING.md.

When you are done, make sure to shut down your instance:

aws ec2 terminate-instances --instance-ids ${INSTANCE_ID}

Finally, make sure you don't have any instances left running:

aws ec2 describe-instances --filters "Name=tag:owner,Values=${OWNER_NAME}"