Working with AWS Parallel Cluster

AWS Parallel Cluster version 2

• Install AWS-CLI
• Install Pcluster
• Don't set the spot price. When you do not set a spot price, AWS will give you the spot market price capped at the on-demand price. Setting the spot price makes the instance more prone to being reclaimed and having your job terminated. As there is currently no functionality automatically enabled on EC2 instances for checkpoint/restart, losing an instance is a show-stopper for WRF production runs. For WRF MPI applications it's not worth playing the spot market if the tradeoff is instance reliability.
• Use the base alinux AMI for your version of pcluster; e.g., for v2.4.0 : https://github.com/aws/aws-parallelcluster/blob/v2.4.0/amis.txt

Configure the cluster with a config file:

spot pcluster config

[aws]
aws_region_name = us-east-2
 
[cluster ladcospot]
vpc_settings = ladco
ebs_settings = data,input,apps
scheduler = slurm
master_instance_type = c4.large
compute_instance_type = r4.16xlarge
master_root_volume_size = 40
cluster_type = spot
base_os = alinux2
key_name = ******
s3_read_resource = arn:aws:s3:::ladco-backup/*
s3_read_write_resource = arn:aws:s3:::ladco-wrf/*
post_install = s3://ladco-backup/post_install_users.sh
disable_hyperthreading = true
custom_ami = ami-0c283443a1ebb5c17
max_queue_size = 100
 
# Create a 10 Tb cold storage I/O directory 
[ebs data]
shared_dir = data
volume_type = sc1
volume_size = 10000
volume_iops = 1500
encrypted = false

# Attach an "apps" volume with pre-loaded software
[ebs apps]
shared_dir = ladco
ebs_volume_id = vol-*****

# Attach an "input" data volume with pre-loaded input data
[ebs input]
shared_dir = input
ebs_volume_id = vol-*****

[vpc public]
master_subnet_id = subnet-******
vpc_id = vpc-******

[global]
update_check = true
sanity_check = true
cluster_template = ladcospot

[aliases]
ssh = ssh -Y {CFN_USER}@{MASTER_IP} {ARGS}

on demand pcluster config

[aws]
aws_region_name = us-east-2
 
[cluster ladcowrf]
vpc_settings = public
ebs_settings = ladcowrf
scheduler = sge
master_instance_type = m4.large
compute_instance_type = m5a.4xlarge
placement = cluster
placement_group = DYNAMIC
master_root_volume_size = 40
cluster_type = ondemand
base_os = alinux
key_name = *****
min_vcpus = 0
max_vcpus = 64
desired_vcpus = 0
# Base AMI for pcluster v2.1.0
custom_ami = ami-0381cb7486cdc973f
 
[ebs ladcowrf]
shared_dir = data
volume_type = gp2
volume_size = 10000
volume_iops = 1500
encrypted = false

[vpc public]
master_subnet_id = subnet-******
vpc_id = vpc-******

[global]
update_check = true
sanity_check = true
cluster_template = ladcowrf

[aliases]
ssh = ssh -Y {CFN_USER}@{MASTER_IP} {ARGS}

Cluster Access

Start the cluster

 pcluster create -c config.spot ladcospot

Log in to the cluster

pcluster ssh ladcospot -i {name of your AWS Key}

Fault Tolerance

Script to monitor pcluster system logs for termination notice, and restart WRF.

#!/bin/bash
CASE=LADCO_2016_WRFv39_YNT_NAM
JSTART=2016095
wrk_dir=/data/apps/WRFV3.9.1/sims/LADCO_2016_WRFv39_YNT_NAM
while true
do
  if [ -z $(curl -s http://169.254.169.254/latest/meta-data/spot/termination-time | grep -q .*T.*Z ) ]; then
     echo "terminated"
     break
  else
     echo "Still running fine"
     sleep 3
  fi
done
echo "Restarting WRF job"
#qsub -N WRF_rest $wrk_dir/wrapper_restart_wrf.csh $JSTART 6

~