Using Elastic Cloud Computing Cluster (EC3) platform to create an ECAS environment.

The following guide is intended for researchers who want to use ECAS, a complete environment enabling data analysis experiments, in the EGI cloud.

ECAS (ENES Climate Analytics Service) is part of the EOSC-hub service catalog and aims to:

  1. provide server-based computation,
  2. avoid data transfer, and
  3. improve reusability of data and workflows.

It relies on Ophidia, a data analytics framework for eScience, which provides declarative, server-side, and parallel data analysis, jointly with an internal storage model able to efficiently deal with multidimensional data and a hierarchical data organization to manage large data volumes (“datacubes”), and on JupyterHub, to give users access to ready-to-use computational environments and resources.

Thanks to the Elastic Cloud Compute Cluster (EC3) platform, operated by the Polytechnic University of Valencia (UPV), researchers will be able to rely on the EGI Cloud Compute service to scale up to larger simulations without being worried about the complexity of the underlying infrastructure.

This guide will show how to:

  • deploy an ECAS elastic cluster of VMs in order to automatically install and configure the whole ECAS environment services, i.e. JupyterHub, PyOphidia, several Python libraries such as numpy, matplotlib and Basemap;
  • perform data intensive analysis using the Ophidia HPDA framework;
  • access the ECAS JupyterHub interface to create and share documents containing live code, equations, visualizations and explanatory text.

Deploy an ECAS cluster with EC3

In the latest release of the EC3 platform, tailored to support the EGI Applications on Demand (AoD) service, a new Ansible receipt is now available for researchers interested to deploy ECAS cluster on the EGI Infrastuctrure. Additional details on how to configure and deploy an ECAS cluster on EGI resources are provided in the next sections.

ECAS in now available in the latest release of the EC3 platform supporting the EGI Applications on Demand (AoD). The next sections provide details on how to configure and deploy an ECAS cluster on EGI resources.

Configure and deploy the cluster

To configure and deploy a Virtual Elastic Cluster using EC3, access the EC3 platform front page and click on the "Deploy your cluster" link as shown in the figure below:

EC3 front page.

A wizard will guide you through the cluster configuration process. Specifically, the general wizard steps include:

  • LRMS selection: choose ECAS from the list of LRMSs (Local Resource Management System) that can be automatically installed and configured by EC3.

LRMS selection.

  • Endpoint: the endpoints of the providers where to deploy the ECAS elastic cluster. The endpoints serving the VO are dynamically retrieved from the EGI Application DataBase using REST APIs.

Endpoint selection.

  • Operating System: choose EGI CentOS7 as cluster OS.

Operating System selection.

  • Instance details, in terms of CPU and RAM to allocate for the front-end and the working nodes.

Instance details.

  • Cluster’s size and name: the name of the cluster and the maximum number of nodes of the cluster, without including the front-end. This value indicates the maximum number of working nodes that the cluster can scale to. Initially, the cluster is created with the front-end and only one working node: the other working nodes will be powered on on-demand.

Cluster size and name.

  • Resume and Launch: a summary of the chosen cluster configuration. To start the deployment process, click the Submit button.

Resume and Launch.

When the front-end node of the cluster has been successfully deployed, you will be notified with the credentials to access via SSH.

ECAS cluster connection details.

The cluster details are available by clicking on the "Manage your deployed clusters" link on the front page:

Manage your clusters.

Accessing the cluster

To access the front-end of the cluster:

  • download the SSH private key provided by the EC3 portal;
  • change its permissions to 600;
  • access via SSH providing the key as identity file for public key authentication.
[fabrizio@MBP EC3]$ ssh -i key.pem cloudadm@
Last login: Mon Nov 18 11:37:29 2019 from
[cloudadm@oph-server ~]$ sudo su -
[root@oph-server ~]#

Both the front-end and the working node are configured by Ansible. This process usually takes some time. You can monitor the status of the cluster configuration using the is_cluster_ready command-line tool:

[root@oph-server ~]# is_cluster_ready
Cluster is still configuring.

The cluster is successfully configured when the command returns the following message:

[root@oph-server ~]# is_cluster_ready
Cluster configured!

As SLURM is used as workload manager, it is possible to check the status of the working nodes by using the sinfo command, which provides information about Slurm nodes and partitions.

[root@oph-server ~]# sinfo
debug*       up   infinite   1  down* oph-io2
debug*       up   infinite   1   idle oph-io1

Accessing the scientific eco-system

ECAS provides two different ways to get access to its scientific eco-system: Ophidia client (oph_term) and JupyterHub.

Perform some basic operations with Ophidia

Run the Ophidia terminal as ophuser user.

Ophidia terminal.

The default parameters are already defined as environmental variables inside the .bashrc file:

export OPH_SERVER_PORT="11732"
export OPH_PASSWD="abcd"
export OPH_USER="oph-test"

Create an empty container and a new datacube with random data and dimensions.

Create container (1).

Create container (2).

Now, you can submit your first operation of data transformation: let’s reduce the whole datacube in a single value for grid point using the average along the time:

Reduce datacube.

Let’s have a look at the environment by listing the datacubes and containers in the session:

List objects in session.

By default, the Ophidia terminal will use the last output datacube PID. So, you can use the oph_explorecube operator to visualize the first 100 values.

Explorecube operator.

For further details about the Ophidia operators, please refer to the official documentation.

Accessing the Jupyter interface

To access the Jupyter interface, open the browser at https://<YOUR_CLUSTER_IP>:443/jupyter and log in to the system using the username and password specified in the jupyterhub_config.pyp configuration file (see the c.Authenticator.whitelist and c.DummyAuthenticator.password lines) located at the /root folder.

JupyterHub login.

From JupyterHub in ECAS you can do several things such as:

  • create and run a Jupyter Notebook exploiting PyOphidia and Python libraries for visualization and plotting (e.g. matplotlib, basemap, NumPy);
  • browse the directories, download and update the files in the home folder;
  • execute operators and workflows directly from the Ophidia Terminal.

To get started with the ECAS environment capabilities, open the ECAS_Basics.ipynb notebook available under the notebooks/ folder in the home directory.



Last modified November 22, 2020: EC3 review (#151) (88ebfa6)