Available HPC resources at CSUC

Available HPC resources at CSUC
Available HPC resources at CSUC Adrián Macía 19 / 02 / 2020
Summary • Who are we? • High performance computing at CSUC • Hardware facilities • Working environment • Development environment
What is the CSUC? • CSUC is a public consortium born from the join of CESCA and CBUC • Institutions part of the consortium: • Associated institutions:
What we do? Scientific computing Communications IT InfrastructuresProcurements Scientific documentation management Joint purchases Electronic administration
HPC matters • Nowadays simulation is a fundamental tool to solve and uderstand problems in science and engineering Theory SimulationExperiment
HPC role in science and engineering • HPC allows the researchers to solve problems that otherwise cannot be afforded • Numerical simulationsare used in a wide variety of fields like: Chemistry and materials sciences Life and health sciences Mathematics, physics and engineering Astronomy, space and Earth sciences
Main applications per knowledge area Chemistry and materials science Vasp Siesta Gaussian ADF CP2K Life and health sciences Amber Gromacs NAMD Schrödinger VMD Mathematics, physics and engineering OpenFOAM FDS Code Aster Paraview Astronomy and Earth sciences WRF WPS
Software available • In the following link you can find a detailed list of the software installed: https://confluence.csuc.cat/display/ HPCKB/Installed+software • If you don't find your application ask for it to the support team and we will be happy to install it for you or help you in the installation process
Demography of the service: users • 32 research projects from 14 different institutions are using our HPC service. • These projects are distributed in: – 11 Large HPC projects (> 500.000 UC) – 3Medium HPC project (250.000 UC) – 13 Small HPC projects (100.000 UC) – 1 XSmall HPC project (40.000 UC)
Demography of the service: jobs (I) Jobs per # cores
Demography of the service: jobs (II) % Jobs vs Memory/core
Top 10 apps per usage (2019)
Usage per knowledge area (2019)
Wait time of the jobs % Jobs vs wait time
Wait time vs Job core count
Hardware facilities Canigo(2018) Bull Sequana X800 384 cores Intel SP Platinum 6148 9 TB RAM memory 33,18 Tflop/s Pirineus II(2018) Bull Sequana X550 2688 cores Intel SP Platinum 6148 4 nodes with 2 GPU + 4 Intel KNL nodes 283,66 TFlop/s
Canigó • Shared memory machines (2 nodes) • 33.18 Tflop/s peak performance (16,59 per node) • 384 cores (8 cpus Intel SP Platinum 8168 per node) • Frequency of 2,7 GHz • 4,6 TB main memory per node • 20 TB disk storage
4 nodes with 2 x GPGPU • 48 cores (2x Intel SP Platinum 8168, 2.7 GHz) • 192 GB main memory • 4.7 Tflop/s per GPGPU 4 Intel KNL nodes • 1 x Xeon-Phi 7250 (68 cores @ 1.5 GHz, 4 hw threads) • 384 GB main memory per node • 3.5 Tflop/s per node Pirineus II
Standard nodes (44 nodes) • 48 cores (2x Intel SP Platinum 6148, 2.7 GHz) • 192 GB main memory (4 GB/core) • 4 TB disk storage per node High memory nodes (6 nodes) • 48 cores (2x Intel SP Platinum 6148, 2.7 GHz) • 384 GB main memory (8 GB/core) • 4 TB disk storage per node Pirineus II
High performace scratch system • High performance storage available based on BeeGFS • 180 TB total space available • Very high read / write speed • Infiniband HDR direct connection (100 Gbps) between the BeeGFS cluster and the compute nodes.
HPC Service infrastructure at CSUC Canigó Pirineus II
Summary of HW infrastructure Canigó Pirineus II TOTAL Cores 384 2 688 3 072 TotalRpeak (TFlop/s) 33.18 283.66 317 Power consumption (kW) 5.24 32.80 38 Efficiency (Tflop/s/kW) 6.33 8.65 8.34
Evolution of the performance of HPC at CSUC 10 x
Working environment • The working environment is shared between all the users of the service. • Each machine is managed by GNU/Linux operating system (Red Had). • Computational resources are managed by the Slurm Workload manager. • Compilers and development tools availble: Intel, GNU and PGI
Batch manager: Slurm • Slurm manages the available resources in order to have an optimal distributionbetween all the jobs in the system • Slurm assign different priority to each job depending on a lot of factors … more on this after the coffee!
Storage units (*) There is a limit per project depending on the project category. Group I: 200 GB, group II 100 GB, group III 50 GB, group IV 25 GB Name Variable Availability Quota Time limit Backup /home/$USER $HOME Global 25- 200 GB (*) Unlimited Yes /scratch/$USER/ − Global 1 TB 30 days No /scratch/$USER/tmp/$JOBI D $SCRATCH / $SHAREDSCRATCH Global 1 TB 7 days No /tmp/$USER/$JOBID $SCRATCH / $LOCALSCRATCH Local node − Job execution No
How to access to our services? • If you are not granted with a RES project or you are not interested in applying for it you can still work with us. More info in https://www.csuc.cat/ca/supercomputacio /sollicitud-d-us
HPC Service price Academic project¹ Initial block - Group I: 500.000 UC 8.333,33 € - Group II: 250.000 UC 5.555,55 € - Group III: 100.000 UC 3.333,33 € - Group IV: 40.000 UC 1.666,66€ Additional 50.000 UC block - When you have paid for 500.000 UC 280 €/block - When you have paid for 250.000 UC 1.100 €/block - When you have paid for 100.000 UC 1.390 €/block - When you have paid for 40.000 UC 2.000 €/block DGR discount for catalan academic groups -10 %
Accounting HPC resources • In order to quantify the used resources we introduce the UC as a unit. • UC: Computational unit. It is defined as UC = HC(Computacional Hour) x factor – For standard nodes, 1HC = 1UC. Factor = 1. – For standard fat nodes, 1HC = 1.5 UC. Factor = 1.5 – For GPU nodes, 1HC = 1UC. Factor = 1. (*) – For KNL nodes, 1HC = 0,5 UC. Factor = 0,5. (**) – Per a canigó (SMP), 1HC = 2UC. Factor = 2 (*) You need to allocate a full socket (24 cores) at minimum (**) You need to allocate the full node (68 cores)
Access through RES project • You can apply for a RES (red española de supercomputación) project asking to work at CSUC (in pirineus II or canigo). More information about this on https://www.res.es/es/acceso-a-la-res
Choosing your architecture: HPC partitions // queues • We have 5 partitions available for the users: std, std-fat, gpu, knl, mem working on standard, standard fat, gpu, knl or shared memory nodes. • Initially the user can only use std and std-fat partition but if any user wants to use a different architecture only need to request permission and it will be granted. … more on this later...
Do you need help? http://hpc.csuc.cat
Documentation: HPC Knowledge Base http://hpc.csuc.cat > Documentation
Problems or requests? Service Desk http://hpc.csuc.cat > Support
Development tools @ CSUC HPC • Compilers available for the users: – Intel compilers – PGI compilers – GNU compilers • MPI libraries: – Open MPI – Intel MPI – MPICH – MVAPICH
Development tools @ CSUC HPC • Intel Advisor, VTune, ITAC, Inspector • Scalasca • Mathematical libraries: – Intel MKL – Lapack – Scalapack – FFTW • If you need anything that is not installed let us know
Questions?
MOLTES GRÀCIES http://hpc.csuc.cat CristianGomollón Adrián Macía Ricard de laVega Ismael Fernàndez VíctorPérez

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