RHRK-Seminar. High Performance Computing with the Cluster Elwetritsch - II. Course instructor : Dr. Josef Schüle, RHRK

Transcription

1 RHRK-Seminar High Performance Computing with the Cluster Elwetritsch - II Course instructor : Dr. Josef Schüle, RHRK

2 Overview Course I Login to cluster SSH RDP / NX Desktop Environments GNOME (default) other desktops Linux Basics Terminal / Shell file systems Tipps & Tricks Course II Cluster Basics Hardware Software Brainware Batch system submitting jobs Monitoring / Accounting AHRP Projects Working on MOGON /Mainz

3 Overview Course III Batchsystem SLURM Array-Jobs Multi-core Jobs SMP MPI Hybrid job resources accellerators file systems Further questions, ideas for the course? Send an to

4 Cluster Basics Hardware Nodes Network File systems Software System Software Module Batch system Brainware

5 Hardware nodes login nodes (headx) compute nodes interactive available not interactive available special different GPU versions/number XEON Phi P5110P 1 TB RAM Infiniband network QDR Ethernet network 1/10GB file systems /scratch Fraunhofer BeeGFS (322 TB) /home NetApp-NFS for HOME (10 TB) /work small files on request /tmp short-time temporary storage

6 Software (1) System software Scientific Linux 7.x periodical updates Module software installed from source ->/software available in several versions -> software modules command: module Is something missing?: to Batch system SLURM jslurm graphical user interface

7 Software (2) Compiler & Tools Intel Cluster Suite Portland PGI GNU Compiler Collection CUDA Toolkit & GPU Programming SDK Totalview Parallel Debugger Various developper environments Libraries MPI Intel Math Kernel Library (MKL) AMD Core Math Library (ACML) Intel MPI Open MPI IBM Platform MPI

8 Brainware Competence in using the cluster at it s best is important for HPC Don t hesitate to contact us and ask questions (Hotline) Direct personal question may be posed to Dr. Josef Schüle Dr. Markus Hillenbrand Sven Daxinger.. if you need help installating programs select best programs compile your programs using the batch system (select parameters and resources) developing your own software (OpenMP, MPI, CUDA) writing scripts to support your work

9 Batch System Job Management submission query ending Monitoring Accounting jslurm

10 Wording (1) Cluster: Number of servers to be seen as unity Bundeling compute power resources and load became balanced commands: sinfo, sacct, sprio, sshare Job: work unit executed by the batch system typical a command or command sequence with options and arguments batch system schedules for execution, controls and protocols commands: squeue, sbatch

11 Wording (2) Jobslot: Smallest execution unit. on Elwetritsch a jobslot corresponds to a CPU core batch system organizes usage of servers commands: sinfo, squeues, rhrk-showqos States for jobs: PEND, RUN, DONE, EXIT, WAIT PSUSP, USUSP, SSUSP, POST_DONE, POST_ERR command: sacct Queue: sorting jobs according to resource requirements after submission, jobs are sorted into waiting queues remain waiting until all resource requirements are available commands: squeue, sbatch Scheduling: algorithm to select and start next jobs Fairshare Scheduling each user has a fair amount - according to project priority - of cluster resources

12 Commands salloc sbatch scancel scontrol sinfo sprio srun sshare sstat sacct SLURM - overview sacctmgr Purpose request interactive job allocations. Better is rhrk-launch submit a batch script cancel a job or job step manage jobs and query information retrieve information about partitions, reservations and nodes job priorities initiate job steps from within a job displays fair share information for each user status information about a running job accounting information. Better is rhrk-accounting query accounting information

13 Further information: SLURM course

14 Monitoring cockpit ELP

15 Accounting Cockpit Kommandozeile sacct [-l] rhrk-accounting -s

16 jslurm - GUI for SLURM Developed at RHRK report errors further improvements? more applications?

17 AHRP General history aims tasks Projects Interaction with MOGON

18 Overview founded April 2010 by TU Kaiserslautern Johannes Gutenberg Universität Mainz aims coordinating HPC activities provisioning of state-of-the-art HPC ressources for research in RLP tasks install, maintain and purchase ressources in common coordinated teaching and support for HPC provisioning of 15% of the ressources for research to all in RLP, load balancing among the sites application based request for ressources

19 Projects three steps fill-in form wait for review follow the sent instruction project sizes XS: < 5 NE / month S: < 30 NE / month M: < 100 NE / month L: < 500 NE / month XL: > 500 NE / month NE = CPU cores * h / 1000 Link:

20 interaction with Mogon Mogon I in Mainz consists of AMD systems with 64 cores more cores in total, but each less powerful source code has to be recompiled interaction will again be realized with common batch system (previous LSF) Usage Premise is an AHRP project to hotline@rhrk.uni-kl.de with a short reasoning

21 High Performance Computing on Elwetritsch Part II Vielen Dank Thank You 25