EC3 Applications and Tools

How to run scientific applications and tools with EC3

This section documents how to run some applications and use the existing tools with EC3.

How to run scientific applications in EC3

NAMD cluster

To deploy NAMD clusters, please select one of the available LRMS (Local Resource Management System) and choose NAMD from the list of applications.

How to use generic tools/practices in EC3

ECAS cluster

Check the dedicated ECAS documentation.


Check the Cloud Container Compute documentation.

Mesos + Marathon + Chronos

To deploy a virtual cluster with Marathon, Mesos, and Chronos as an orchestration, please select Mesos + Marathon + Chronos from the list of available LRMS.

OSCAR cluster

To deploy Serverless computing for data-processing applications in EGI, please select OSCAR from the list of LRMS (Local Resource Management System). OSCAR supports data-driven serverless computing for file-processing applications. A file upload, to the object storage backend MinIO, will trigger the execution of a chosen shell script running inside a user-defined container. These will be orchestrated as Kubernetes batch jobs. The output data will be uploaded to any object storage backends support. Synchronous invocations are also available.

As external object storage providers, the following services can be used:

  • External MinIO servers, which may be in clusters other than the platform.
  • Amazon S3, the Amazon’s object storage service that offers industry-leading scalability, data availability, security, and performance in the public Cloud.
  • Onedata, the global data access solution for science used in the EGI DataHub.

See the documentation to deploy an elastic Kubernetes cluster with the OSCAR platform with EC3: Deploy OSCAR with EC3

See some use cases of applications that use the OSCAR framework for event-driven high-throughput processing of files (you can found it in the GitHub repository examples folder):

  • Inference of a machine learning model: See full description at OSCAR Blog entry.
  • Mask detection: See full description at OSCAR Blog entry.
  • Plants Classification, an application that performs plant classification using Lasagne/Theano.
  • ImageMagick, a tool to manipulate images.
  • Radiomics, a use case about the handling of Rheumatic Heart Disease (RHD) through image computing and Artificial Intelligence (AI).

More information in the OSCAR web page

SLURM cluster

To deploy SLURM clusters, please select SLURM from the list of available LRMS. See also the dedicated guide on HTC clusters

Next topics:

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


Using Elastic Cloud Computing Cluster (EC3) platform to create elastic virtual clusters on the EGI Cloud.