Cluster

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IIHE local cluster

Deprecated, see T2B wiki

Overview

The cluster is composed by 4 machine types :

  • User Interfaces (UI)

This is the cluster front-end, to use the cluster, you need to log into those machines

Servers : ui01, ui02

  • Computing Element (CE)

This server is the core of the batch system : it run submitted jobs on worker nodes

Servers : ce

  • Worker Nodes (WN)

This is the power of the cluster : they run jobs and send the status back to the CE

Servers : slave*

  • Storage Elements

This is the memory of the cluster : they contains data, software, ...

Servers : datang (/data, /software), lxserv (/user), x4500 (/ice3)



Batch.png

How to connect

To connect to the cluster, you must use your IIHE credentials (same as for wifi)

Rrdns.png
ssh username@icecube.iihe.ac.be

TIP : icecube.iihe.ac.be & lxpub.iihe.ac.be points automatically to available UI's (ui01, ui02, ...)


After a successful login, you'll see this message :

==========================================
Welcome on the IIHE ULB-VUB cluster

Cluster status  http://ganglia.iihe.ac.be
Documentation   http://wiki.iihe.ac.be/index.php/Cluster
IT Help         support-iihe@ulb.ac.be
==========================================

username@uiXX:~$

Your default current working directory is your home folder.


Directory Structure

Here is a description of most useful directories

/user/{username}

Your home folder

/data

Main data repository

/data/user/{username}

Users data folder

/data/ICxx

IceCube datasets

/software

The local software area

/ice3

This folder is the old software area. We strongly recommend you to build your tools in the /software directory

/cvmfs

Centralised CVMFS software repository for IceCube and CERN (see CMFS)

Batch System

Queues

The cluster is decomposed in queues


any lowmem standard highmem express gpu
Description default queue, all available nodes (except GPUs & express)
2 Gb RAM
3 Gb RAM
4 Gb RAM
Limited walltime
GPU's dedicated queue
CPU's (Jobs) 494
88
384
8
24
14
Walltime default/limit 144 hours (6 days) / 240 hours (10 days) 15 hours / 15 hours
50 hours / 50 hours
Memory default/limit 2 Gb
2 Gb
3 Gb
4 Gb
3 Gb
6 Gb


Job submission

To submit a job, you just have to use the qsub command :

qsub myjob.sh

OPTIONS

  • -q queueName : choose the queue (default: any)
  • -N jobName : name of the job
  • -I : (capital i) pass in interactive mode
  • -m mailaddress : set mail address (use in conjonction with -m) : MUST be @ulb.ac.be or @vub.ac.be
  • -m [a|b|e] : send mail on job status change (a = aborted , b = begin, e = end)
  • -l : resources options


Job management

To see all jobs (running / queued), you can use the qstat command or go to the JobMonArch page

qstat

OPTIONS

  • -u username : list only jobs submitted by username
  • -n : show nodes where jobs are running
  • -q : show the job repartition on queues


Backup

/user, /data and /ice3 use snapshot backup system.
They're located in :

  • /backup_user
    • daily : 5
    • weekly : 4
    • monthly : 3
  • /backup_data
    • daily : 6
  • /backup_ice3
    • daily : 5
    • weekly : 4
    • monthly : 3

Each directory contains a snapshot of a specific period. To restore, just copy files from those directory to the location you want.

Useful links

Ganglia Monitoring : Servers status

JobMonArch : Jobs overview