CRIBI. Calcolo Scientifico e Bioinformatica oggi Università di Padova 13 gennaio 2012

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1 CRIBI Calcolo Scientifico e Bioinformatica oggi Università di Padova 13 gennaio 2012

2 what is exact? experience on advanced computational technologies a company lead by IT experts with a strong background in physics and computer science, who have experience in everyday use, maintenance and configuration of high performance computing systems for the scientific community (CNR-IOM DEMOCRITOS, SISSA) international collaborations for training activities and HPC/GRID infrastructure deployments (ICTP) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

3 services for the HPC cluster deployment installation and configuration of HPC and GRID infrastructures high performance storage solution lustre expertise training sys admin and user oriented training programs application tuning optimization, parallelization, porting, development on-demand HPC from raw ssh to highly customized web portals Calcolo Scientifico e Bioinformatica oggi 13 gennaio

4 fill the gap collaboration with Aldebra/HP scientific SW mgmt SW HW END USER optimization / parallelization compilers / scientific libraries deployment / administration / management hardware tuning Aldebra / HP exact Calcolo Scientifico e Bioinformatica oggi 13 gennaio

5 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

6 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

7 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

8 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

9 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

10 HPC CRIBI masternode 32 blades (2x6 cores, 24,48,96GB RAM) GPU node GPU node STORAGE 12x600GB 36x2TB STORAGE 12x600GB 36x2TB FAT node (2TB RAM) 1 GB Ethernet (SP/iLO/mgmt) 1 GB Ethernet (NFS) 40 GB Infiniband (LUSTRE/MPI) 10 GB Ethernet (iscsi) 1 GB (LAN) Calcolo Scientifico e Bioinformatica oggi 13 gennaio

11 challenges heterogeneous environment (GPU, HIMEM/FAT, BLADES w/ or w/o HT, BLADES w/ HIMEM, storage nodes) access policies and queues complex network configuration remote management parallel filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

12 software solution: tools EPICO - exact Procedure for Installation and COnfiguration - LINUX based distributed and unattended installation framework - fully integrated with standard tools and services for HPC torquemaui ganglia and various monitoring tools / utilities standard compilers and scientific libraries LUSTRE parallel filesystem hardware and software tuning needed to increase I/O performance Calcolo Scientifico e Bioinformatica oggi 13 gennaio

13 LUSTRE and storage solution Calcolo Scientifico e Bioinformatica oggi 13 gennaio

14 accessing LUSTRE filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

15 accessing LUSTRE filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

16 accessing LUSTRE filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

17 accessing LUSTRE filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

18 accessing LUSTRE filesystem Calcolo Scientifico e Bioinformatica oggi 13 gennaio

19 accessing LUSTRE filesystem RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

20 accessing LUSTRE filesystem RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

21 accessing LUSTRE filesystem RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

22 accessing LUSTRE filesystem RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

23 why parallel filesystem? Calcolo Scientifico e Bioinformatica oggi 13 gennaio

24 why parallel filesystem? Calcolo Scientifico e Bioinformatica oggi 13 gennaio

25 why parallel filesystem? Calcolo Scientifico e Bioinformatica oggi 13 gennaio

26 why parallel filesystem? Calcolo Scientifico e Bioinformatica oggi 13 gennaio

27 why parallel filesystem? Calcolo Scientifico e Bioinformatica oggi 13 gennaio

28 why parallel filesystem? RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

29 why parallel filesystem? RAID RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

30 why parallel filesystem? RAID RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

31 why parallel filesystem? RAID RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

32 why parallel filesystem? RAID RAID Calcolo Scientifico e Bioinformatica oggi 13 gennaio

33 overall LUSTRE performance Client #1 Client #5 Client #2 Client #6 Client #3 Client #7 Client #4 Client #8 sequential write/read by iozone 1 ~ 8, 1 ~ 4 proc/client 32 GB files writing 64 GB files reading IB QDR Network #1 #2 #3 #4 ~ 1.7 GB/sec writing 32, 32 GB files ~ 1.2 GB/sec reading 32, 64 GB files Calcolo Scientifico e Bioinformatica oggi 13 gennaio

34 LUSTRE can be disappointing too... writing 1 file with variable block size MB/s kb 2 kb 4 kb 8 kb 64 kb 512 kb 1 Mb 2 Mb 4 Mb # Gbytes Calcolo Scientifico e Bioinformatica oggi 13 gennaio

35 tips to use lustre at best identify bottlenecks s, RAID,, volumes and virtual disks, 10GE, iscsi, LUSTRE fs, local caching/buffers, InfiniBand or Gigabit network, LUSTRE client, access patterns when accessing files: read/write in large chunks, not line by line [e.g. mmap instead of readline] when running multiple I/O operations: optimize data distribution and disk access tune cache/buffer size, sync, and priorities Calcolo Scientifico e Bioinformatica oggi 13 gennaio

36 Thanks Calcolo Scientifico e Bioinformatica oggi 13 gennaio

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