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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