Clusters and accounts

Get account and sharing data

• RequestAccount? - How to request an account for access to GCC maintained infrastructure (Cloud & HPC clusters)
• DataSharing? - How to up-/download data via SFTP
• TransparentMultiHopSSH? - How to connect via the proxy
• PortForwarding? - How to use port forwarding on Mac to use Filezilla and Komodo Edit

High Performance Computing (HPC) infra

For Users

How to compute on the HPC generation 2.x clusters Calculon, Zinc-Finger and Leucine-Zipper Clusters.

• Overview? - Description of the different HPC environments
• Login? - How to start a session.
• Analyses SOP? - How to manage your jobs on the cluster.
• Available resources? - What is available and where.
• Storage SOP? - What is stored where.
• Support? - FAQs, mailinglists, courses and contact info to get in touch with an admin.
• Scheduled Maintenance? - Policy and dates for scheduled maintenance.

How to compute on the HPC generation 3.x clusters

• Analyses SOP for beta testers? - New Gearshift cluster online!

For Admins

• SOP Accounts? - Managing users and groups for the HPC infrastructure.
• Deploy Apps & Data - SOP for central deployment of software and reference data sets.
• Shared Storage Config? - How are logical file systems related to physical ones.
• Compute Config? - SLURM schedulers, partitions and nodes.

Molgenis and VMs

Cloud VMs / Jenkins / WordPress

• Molgenis Servers? - List of all VMs in our cloud.
• ​Create a new MOLGENIS instance - You can create a new MOLGENIS VM based on CentOS running this Ansible script
• Install SOP / Deploy MOLGENIS via Jenkins - How to deploy MOLGENIS on a VM using Jenkins.
• SOP WordPress - How to manage WordPress websites

Deploy MOLGENIS v2.x server based on PostGreSQL Golden VM

• Deploy a PostGreSQL based MOLGENIS server - How to deploy a MOLGENIS server compatible with MOLGENIS v2.0 and higher

Internal GCC SOPs

• SOP UMCG network - How to connect to UMCG network
• SOP new Employee (employee) - Manual for employee
• SOP New Employee (team) - Manual for team
• GccSopMolgenisRelease - How to create a MOLGENIS release
• GccSopMolgenisBugfixRelease - How to create a MOLGENIS Bugfix-release
• GccSopSystemsGeneticsRelease - How to create a Systems Genetics release
• GccSopMolgenisComputeRelease - How to create a MOLGENIS Compute release