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HPC & HTC User Documentation
All user support documentation related to the Cirrus HPC and HTC service
Users Portal
Generic documentation regarding the INCD user portal
General User Documentation
General documentation regarding the INCD infrastructure. This topic does not cover any services provided by INCD, if looking for information about services follow the other shelves.
Cloud user documentation
User documentation related to the Stratus Openstack Cloud Infrastructure
INCD Institutional Information
Public Information about INCD infrastructure and usage
Training
In this section you will find information related to training and other materials.
Services
Services deployed in the INCD infrastructure
Manage jobs
Submitting and managing jobs in the Cirrus HPC and HTC clusters
Filesystem User Guide
Filesystems and data organization in the Cirrus HPC and HTC clusters
How to access
Guidance to access the INCD services
Compute Node Specs and Information
Compute nodes specs and hardware information for the Cirrus HPC and HTC clusters
Software
How the software is managed in the Cirrus HTC and HPC clusters
Getting Started
Short user guide to request access to the INCD infrastructure
User Support
General user support at INCD
Frequently Asked Questions
Common questions regarding INCD Users Portal usability.
Acknowledgements
How to acknowledge the use of the INCD infrastructure
Openstack users manual
User manuals and tutorials for Openstack
Scientific Publications
Scientific publications which used INCD resources
Organized events
List of events organized by INCD
Dissemination
Participation in dissemination events
Training events
Training events and online material about INCD services and users support
Usage Metrics
Several usefull metrics reporting the Institutional usage of the infrastructure
Cloud Service
Book with links and materials with Cloud user manual, tutorials and training. Includes Virtualization, security considerations for VMs, and resource accounting
Thematic Services Tutorials
Training material for the Thematic Services officially supported by INCD
Containers Tutorials
List of tutorials used in training for using containers for scientific applications and services
Official Reports
INCD official reports and related documents
Customized resources
Customized resources and queues for specific research groups and organizations
Lustre
Lustre basic description on INCD infrastructure
Public access
Public access to the INCD Cirrus HPC and HTC services
Using ssh keys
Basic description on how to use ssh keys
GPU user guide
Troubleshooting information
Login machines
Accessing the login servers with SSH
Applying
Filling the request/registration form
Regarding organizations
* What type of organizations can apply? * Can private companies apply to use the INCD infrastructure? * Research Infrastructures
User Software Installation
Tips and examples on how to install software locally
OpenStack Services
Documentation for INCD Services available for users
Events
Supported Projects
Projects supported by the INCD infrastructure
Supported Institutions
supported institutions per number of ativities
Maturity Evaluation 2019
Documents related to the FCT infrastructures roadmap maturity evaluation of 2019 Documentos relativos à avaliação de maturidade de 2019 das infraestruturas do roteiro da FCT
LNEC users
The information contained on this chapter is complementary information specific for LNEC users that is not covered on the general guidelines
LIP users
The information contained on this chapter is complementary information specific for LIP users that is not covered on the general guidelines
PINFRA/22153/2016
Materials related to the FCT infrastructures roadmap project 01/SAICT/2016 nº 22153
Manage slurm jobs
How to handle jobs management using slurm batch system. Used at Minho and ISEC and Lisbon data center
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Lustre Basics
The latest Lustre documentation is available at Lustre
Lustre best practices
Distributed filesystems such as Lustre are ideal for HPC and HTC environments. In these environments the typical workload consists of large files that have to be accessed from many compute nodes with very high bandwidth and/or low latency. Therefore these file...
How to connect to the HPC and HTC clusters
public login services Access to the INCD clusters is only available to registered users. To use the HPC services users need to login via SSH into a front-end server. The login servers can be customized according to the user requirements (OS, Hardware resource...
Create a ssh key
Access to the INCD computing clusters is performed via SSH and requires the use of SSH keys for authentication. Authentication with passwords is not supported. Each SSH key pair has two components a public key that must be added to the hosts to be remotely acc...
Security
Choose strong passwords - at least 9 characters long, a mixture of alphanumeric mixed case and symbol characters. The password should be completely different from the password you use on any other system. Never use the same password across different systems ...
Configuring SSH
In order to simplify SSH access to remote hosts we recommend INCD users to adopt the following recommendatios and configuration defaults. Enabling SSH agents and X11 forwarding Activate the forwarding of both SSH authentication credentials and X11 graphical ...
Access
INCD is open to all academic and scientific researchers and institutions. In order to use our services please go to the INCD portal and follow the instructions there. For guidance and further information about the access conditions see the FAQ List warning P...
Login and network access
Access to INCD infrastructure is available only to registered users. Access to login machines may be filtered by IP address of origin. During the registration process you may be asked to provide your IP address in order to enable remote access. Access to virt...
My jobs need to run longer than the queues permit
At INCD the default max elapsed time for the queues is 72h. The values for all queues can be consulted here In case you cannot parallelize your job (split one single job into multiple parallel jobs) you can use job dependencies. In this case you creat...
Helpdesk
To contact the INCD user support please send email to: helpdesk (at) incd.pt For other institutional contacts see: contacts web page
Directories and filesystems
The INCD filesystems are based on the Lustre shared filesystem which is mounted in the compute nodes and in the submission/login nodes. Lustre is mostly suited to the storage of large/huge files. For more specific information regarding the Lustre deployment ...
Disk Quota Policy
To prevent storage misuse and problems resulting from filesystems becoming full, INCD has implemented the following data usage policies and limits. File system Hard Limit Exceeded /home Once quota or number of files exceeded, new files will not be all...
How to transfer files between INCD and a local machine
NOTE Please note that INCD Lustre storage is not designed for small files. Attempting to store or retrieve files less than a few megabytes will result in extremely poor performance for all users. If you wish to store lots of small files to massdata, please u...
How to access files belonging to someone else or another project
Users are allowed to change the default permissions file permissions in all folders they own. The default access rights to INCD filesystem is the folllowing: /home All files under /home are only accessible by the user. /data All files under /data/unixgr...
Who can apply to use the INCD infrastructure?
INCD is open to researchers from Portuguese scientific and academic organizations in all areas of knowledge.
Can researchers from foreign organizations apply to use the INCD infrastructure?
Researchers from foreign organizations can be eligible to use INCD when they cooperate with Portuguese researchers in common projects, initiatives and infrastructures. The initial application form must be submitted by a researcher from a Portuguese academic ...
How to apply to use the INCD infrastructure?
Please fill the “New request” form available at: https://portal.incd.pt
How much time will it take to get an answer and gain access?
Depends on the size and specificities of the request. If your project is approved and resources are available the process will take less than one week. Projects requiring fewer compute and storage resources are generally easier and faster to accommodate.
How to contact us?
You can contact us via e-mail to the INCD Computing Services helpdesk address in: INCD
Do I need to specify a research project?
Large requests should be backed by approved peer-reviewed research projects either national or European. Requests without a peer reviewed project will have lower priority, please fill the access request form with the maximum detail to facilitate the evaluati...