High performance computing (HPC)

The scientific computing facility provides the infrastructure and software tools required by researchers (e.g. bioinformaticians and biostatisticians). The goal of the facility is to help investigators with their computational needs allowing them to focus on scientific challenges. These needs range from advice on best practices for scientific computing, software installation, server set-up and even the design of custom solutions for certain computing needs. The platform is continuously updated with the latest technologies in storage, virtualization, automation and software management to offer state-of the art services.

Facility

Cell Explorer - Revity

  • Envision plate reader from Perkin Elmer: compatible with Fluorescence, Ultraluminescence, Absorbance, HTRF and Alpha

  • Echo 650 from Beckman Labcyte: acoustic dispenser from nano-drops of 2.5 nl

  • 2 Multidrop dispensers from Thermo

  • Automated plate incubator (44 plates) temperature, CO2 and humidity control

  • Plate hotel (63 plates); Sealer and peeler

Echo 650 - Beckman Coulter

  • Echo 650 - Beckman Coulter

Multidrop Dispenser - Thermo

Multidrop Dispenser - Thermo

Hamilton Vantage Robotic Laboratory Workstation - Hamilton

  • Liquid handling system with 384 and 8 pipetting heads MagTip: works as a bulk dispenser from 200 nl to 10 ul and for cherry pickings

  • Dianthus pico NANOTEMPER: 384 plate reader for drug-target interaction (TRIC and Spectral Shift)

  • Q50: Automatic freezer under inert atmosphere (735 plates)

  • Plate hotel (180 plates); Sealer and peeler

Q50 automatic freezer - Hamilton

Q50 automatic freezer - Hamilton

Institutional Contacts / Head of Facilities

DAVID IZQUIERDO
DAVID IZQUIERDOCap dels Serveis Científic-Tècnics
IGTP

Provisional Contacts

Francisco Javier Perez Vicente | Scientific System Administrator |  hpc@igtp.cat  | 935 543 079

Francisco Javier Perez Vicente |  hpc@igtp.cat  | 935 543 079

David Izquierdo (Responsible) | Email:  DIZQUIERDO@IGTP.CAT  |

CERCA Institutes

Badalona, Spain

1995

IGTP

Owners

Centres CERCA List

Equipments & Services Offered

The DC has a rotation ventilation system with built-in redundancy, it also has a UPS able to maintain the electricity supply for all servers for several minutes (30+) and multiple power supply lines for each rack. As a protection against fire the CPD has an automatic trifluoromethane gas extinction system. Calculation cluster 16 calculation nodes giving a total of: 240 Nuclei 2 Tb RAM Tb local storage (1Tb/node) Made up of three different types of nodea: HP DL160 G6 : 8 Nuclei (Xeon E5640) and 64 GB RAM (x8) Fujitsu RX200 S7: 12 Nuclei (Xeon E5-2640) and 120 GB RAM (x3) HP DL 360 G9: 28 Nuclei (Xeon E5-2680 v4) and 256 GB RAM (x5) Storage system The main storage system is a high availabililty Isilon (Dell/EMC) Gen 6 with four H400 nodes and four A200 nodes. Usable storage capacity 450Tb Snapshot system available to users Sistema de snapshots accesibles para los usuarios The system provides a unified file system for all users and available from the compute nodes or from workstations, simplifying work for researchers. Backup/Data Recovery The backup/data-recovery system is made up of: HPE 4048 library with two LTO-7 drives and capacity for 48 tapes (768 Tbs capacity) Quantum Scalar i80 two drives LTO-5 with capacity for 50 tapes Both libraries are managed by Bacula backup software The principle library (HPE 4048) is for security copies fo data for groups, virtual machines, data bases and data stored long-term. The secondary library (Quantum Scalar i80) deals with redundant copies of virtual mahcines and work archived on LTO-5 tape. The system makes daily backups of data and with a default 3 month data retention policy. The archive backup jobs are kept indefinitely. Network The DC network is made up of 3 switches of 1Gb 3com 4210G and 3 switches of 10Gb HPE 5700. The switches and connections to the machines are configured for high availability. The Isilon storage system, main backup system and DL 360 compute nodes are connected through 10GB, the rest of the cluster uses 1Gb with aggregated interfaces.

Maintenance and support of the facility Ensuring the computing infrastructure is running 24/7 Installation and management of the operating system (GNU/Linux) in all machines of the scientific computing area Installation and management of the cluster system for the scientific computing area Scientific software installation, maintenance and upgrade Management of the disk infrastructure of the scientific area Management of the network infrastructure of the scientific equipment Management of the backup infrastructure and data recovery strategy Installation and management of diverse servers and services (including but not limited to:) Private and public webservers and services management and installation Databases installation, management FTP(S) services Internal version control system (gitlab) Monitoring tools for performance tuning and alerts Queueing system (SGE) System security (hardening, auditing, patching) Advising bioinformaticians on computational tasks High performance computing Advise and help designing bioinformatics pipelines Advice on hardware purchasing for bioinformatics Open Access to Bioinformatics Portal Open-access to tools developed by the IGTP Maplab Tools (Methylation plotter, Alu ontology, wanderer, Chainy, TrukeTCGA 450k trackhub) Islet Regulome High Ferritin SIRES

Categorització

RIS3CAT domains & other

RIS3CAT Domains
CERCA GINYS Categories

GINYS-IGTP-003

Access procedure & Fares

Open

Institutional Networks