Genocloud migration to Genostack

Dear Genocloud users,

We just migrated our cloud platform for Genocloud to Genostack.

The new Genouest private cloud is available here:
https://genostack.genouest.org/dashboard/
Please login using the domain “Users” and your Genouest credentials.

For any questions, please check the wiki, or contact the support.

Please note that all virtual machines running on Genocloud will only remain available for a limited time. Make sure to contact the support if you need to transfer your images or your data.

Go-Docker in beta test

Go-Docker is a batch scheduler like SGE, submitting jobs in Docker containers.

With Go-Docker your jobs are isolated in containers with your CPU and memory requirements. You can execute jobs in Docker containers from the Docker hub.

This is a beta-test, and should not use it yet for “production” jobs as it may still experience failures. We would however be glad to get user experience feedbacks on software. All you need is a GenOuest account.

You can request to get your home directory, your omaha-beach directory (/omaha-beach/user-id), as well as /softs and /db in your container.

Access: https://godocker.genouest.org

Official web site: http://www.genouest.org/godocker/index.html

omaha-beach copy and quota

Dear users,
Remember that you have only two weeks left to copy your data from  /old-Omaha-beach to /omaha-beach.
After this period, the Panasas hosting the old-Omaha-beach will be decommissioned and sent back to the  manufacturer. All the data it contains will be lost.
Currently, only 50% of the data has been transferred.
Remember, copying data is YOUR responsibility.
If you have problems over quota please contact support@genouest.org
To see your quota:
$ pan_quota /omaha-beach

New /omaha-beach

A new filesystem /omaha-beach is online since monday, 16 march 2015.

Main features are :

– Data reliability : RAID 6+, controler’s redundancy

– High speed network access : 10 Gb/s

– Parallel NFS with cluster nodes : improved data access

– Users quota : ensure storage for everyone

Until 30th april you can still access to your old data on the front-end servers, they are located in /old-omaha-beach.

Maintenance operation

The platform is suffering storage issues, preventing access to part of the storage and job submissions (online or batch). This is a serious problem we are trying to fix as soon as possible. In the meanwhile, our online services are down and should not be used.

A maintenance operation to fix the issue is planned this week that will prevent access to your home directory. We will inform you when status is operational.

Thank you for your comprehension.

Submit a batch of commands in the cluster

If you need to submit numerous job commands via qsub in the cluster, you can use the joborganizer tool.
JobOrganizer is a utility tool we developped to submit a list of commands as jobs, while limiting the number of simultaneous jobs.
This eases the way to submit numerous jobs without queuing everything at one.

It also provides the possibility to add dependencies between the jobs.

JobOrganizer is available at: /softs/local/utils/joborganizer

More info with:


man /softs/local/utils/man1/joborganizer.1

11th edition of the annual meeting ReNaBI-GO

We are pleased to announce the eleventh edition of ReNaBI-GO meeting. ReNaBI-GO is a federation of core bioinformatics facilities in the West of France. The meeting will take place in Rennes at INRIA/IRISA on November, the 29th.

This year our meeting will focus on the usage of workflows in bioinformatics. A preliminary program and a registration form are available here. Registration to this event is free but mandatory.

This meeting is supported by INRIA, IRISA and Biogenouest.

We hope to see you.