SGI InfiniteStorage 3500 Manual de usuario

EIC system user manual how to use system Feb 28th 2013 SGI Japan Ltd.

10 ©2012 SGI How to login(Windows）  how to login – Please use Windows’ SSH software (TeraTerm,Putty) • HOST:eic.eri.u-tokyo.ac.jp • username:username

11 ©2012 SGI job script  Creating job script file – Create job script file to submit a batch job, sample is in a right square. – You must define .. –

12 ©2012 SGI Submitting job  Use “bsub” to submit a batch job. – Re-direct a job script to bsub command. $ cat sample.csh #!/usr/bin/csh #BSUB -q A #

13 ©2012 SGI Displaying job status  bstatus – bstatus displays status of jobs you submitted. $ bstatus JOBID USER STAT QUEUE FROM_HOST

14 ©2012 SGI Canceling, Deleting job  bkill – bkill can cancel or delete jobs. – define job ID. $ bjobs JOBID USER STAT QUEUE FROM_HOST

15 ©2012 SGI Queue configuration Queue name： Queue name Runtime： Wallclock time limitation per job（only queue A limits cputime） Memory limit：

16 ©2012 SGI MPI job script sample – 24 mpi parallel job(sample) – Define 24(number of parallel) on “BSUB –n” and “mpirun -np” – Insert “dplace -s1”

17 ©2012 SGI Submitting MPI job – 24 parallel job runs on 4CPU（24cores） – EIC servers have 12cores on local memory, all jobs are automatically set to

18 ©2012 SGI OpenMP job script sample – 48 OpenMP parallel job(sample) – Define 48(number of parallel) on “BSUB –n” and environment variable ”OMP_NUM_

19 ©2012 SGI Submitting OpenMP job – 48 parallel job runs on 8CPU（48cores） – EIC servers have 12cores on local memory, all jobs are automatically set

2 ©2012 SGI Index  EIC system overview  File system, Network  User environment  job script  Submitting job  Displaying status of job  Canceling

20 ©2012 SGI MPI+OpenMP Hybrid Parallel job  What is hybrid parallel ? – MPI processes boot OpenMP threads. – recommends 2,3, or 6 as number of OpenM

21 ©2012 SGI MPI+OpenMP Hybrid job script(sample) – 24 hybrid parallel job(8MPI x 3 threads) – Define number of MPI for np, number of threads per MPI

22 ©2012 SGI Core Hopping  What is core hopping? – Normally job occupies all 6cores and local memory on same CPU socket. – You can reduce used cores

23 ©2012 SGI Queue option for core hopping – Define not only normal “-n” , but also “-P” how many cores you use per CPU. （define –P from 1 to 6) – You

24 ©2012 SGI Core hopping MPI job script 32 parallel MPI job(4 cores per CPU) #BSUB -n number of parallel #BSUB -P cores per cpu（1~6） source /opt/lsf

25 ©2012 SGI Core hopping OpenMP job script 32 parallel OpenMP job(4 cores per CPU) #BSUB -n number of parallel #BSUB -P cores per cpu（1~6） omplace -

26 ©2012 SGI Core hopping hybrid job script BSUB -n number of parallel #BSUB -P cores per cpu（1~6） setenv OMP_NUM_THREADS [number of OpenMP threads] m

27 ©2012 SGI Displaying core hopping job  qstatus – qstatus displays core hopping job or normal job. $ bjobs JOBID USER STAT QUEUE FROM_HO

28 ©2012 SGI How to use printer – how to print from eic, eicxx Use “lpr” eic%lpr -Pprinter_name PSfile_name ex) eic%lpr –Pxdp1-6f test.ps – how to

29 ©2012 SGI How to use DAT drive  DAT drive – connect to eic00 and eic01. • /dev/st0------rewinding • /dev/nst0----no rewinding – Use tar or cpio –

3 ©2012 SGI EIC system overview frontend server 1 node high spec server 2 nodes parallel server 2 nodes Altix UV 100 Xeon X7542 2.66GHｚ 8CPU/128GB Alt

30 ©2012 SGI How to use DAT – Writing tape $ mt -f /dev/st0 rewind rewinding tape media $ mt -f /dev/st0 compression 0

31 ©2012 SGI How to use Blu-ray drive  Blu-ray drive – connect to eic02 and eic03 – “bdr” command boots GUI writing software. $ bdr – confirm target

32 ©2012 SGI Application software  AVS – is available on workstations（eic00~eic05）. – login to workstation, use “express” command. eic00$ express

33 ©2012 SGI MATLAB  MATLAB – you can use matlab on eic Login to eic % ssh -X [email protected] run matlab % matlab limitation CPU TIM

34 ©2012 SGI MATLAB  MATLAB via LSF – how to use matlab via LSF(batch) Login to eic % ssh -X [email protected] submit a job % bsub -q M

35 ©2012 SGI Attention – When you finish MATLAB, you have to • % exit • if you don’t exit, MATLAB license will be still used, other user will not be a

©2012 SGI

4 ©2012 SGI File system, network LAN User workstation 6 nodes High spec server UV 1000 Frontend server UV 100 Parallel serever UV 1000 CXFS server Al

5 ©2012 SGI User environment  EIC user can login and use the following servers. hostname Hardware IP address notice eic SGI UV 100 133.11.57.80

6 ©2012 SGI User environment  File system – /home(home area) is total 40TB, you can use 150GB as default quota limit. – /work(temporary area)

7 ©2012 SGI User environment  TSS（interactive job） limitation ※Please use LSF batch software if you will run a job over TSS limitation. limit

8 ©2012 SGI User environment  environment variable – On EIC system your environment variable was already set to use. – You don’t have to set environm

9 ©2012 SGI How to login  How to login – Please login a frontend server “eic” for making a program, compiling, interactive debugging, submitting a ba