Last modified 11 years ago

  1. Introduction
  2. User Interface Machine
  3. Preparing credentials
  4. Submitting Simple Bash job
  5. MUSCLE job example
  6. Interactive jobs
  7. Further reading

Introduction

The QCG-SimpleClient is a basic client utility used to submit jobs to the QCG-Broker service (a  QosCosGrid meta-scheduler). Its job description format (QCG-Script) and command tools syntax were intentionally modelled after local batch systems "look && feel". Thus, the learning effort needed for a new users (that have some experience with local cluster systems) was very limited. The QCG-SimpleClient allow you to submit MUSCLE job in the coherent way to any single PL-Grid site. Unfortunately current version of QCG-Script do not support description of more advance experiments like co-allocated (cross-cluster) simulations, workflows or parameter sweep. You need to use QCG-AdvancedClient instead.

User Interface Machine

Every cluster in PL-Grid can be accessed from the QCG UI machine: qcg.man.poznan.pl. You can log in there using your PL-Grid account: 

ssh plg[your-id]@qcg.man.poznan.pl

Preparing credentials

  1. Copy your credentials (PKCS12 keystore) to the qcg machine: 
    scp plg[your-id].p12 plg[your-id]@qcg.man.poznan.pl:~/
  2. Create ~/.globus directory 
    mkdir ~/.globus
  3. Convert your credentials to the .pem format 
    $ openssl pkcs12 -nocerts -in usercred.p12 -out ~/.globus/userkey.pem
$ openssl pkcs12 -clcerts -nokeys -in usercred.p12 -out ~/.globus/usercert.pem
$ chmod 644 ~/.globus/usercert.pem
$ chmod 400 ~/.globus/userkey.pem

Submitting Simple Bash job

  • Example job script: 
    $cat hostname.qcg 
#cluster where to run a job
#QCG host=zeus.cyfronet.pl
#QCG output=output.txt
#QCG error=error.txt

/bin/hostname
date
sleep 30
date
sleep 30
date
  • job submission: 
    $qcg-sub hostname.qcg 
https://elder6.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 11 Hours 54 Minutes 8 Seconds

jobId = J1349800941529__3789
  • list all your jobs: 
    $qcg-list 
https://elder6.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 11 Hours 53 Minutes 52 Seconds

JOB IDENTIFIER                  TASK      NOTE                  SUBMISSION TIME  START TIME       FINISH TIME      STATUS            HOSTNAME  

J1349800941529__3789            task                            09.10.12 18:42                                     PENDING           zeus      

Number of tasks:
PENDING : 1
TOTAL: 1
  • get detailed job info: 
    > qcg-info J1349800941529__3789
https://elder6.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 11 Hours 52 Minutes 53 Seconds

Note: 
TaskType: SINGLE
SubmissionTime: Tue Oct 09 18:42:21 CEST 2012
FinishTime: 
ProxyLifetime: P23DT11H52M51S
Status: RUNNING
StatusDesc: 
StartTime: Tue Oct 09 18:42:21 CEST 2012

Allocation: 
HostName: zeus.cyfronet.pl
ProcessesCount: 1
ProcessesGroupId: 
Status: RUNNING
StatusDescription: 
SubmissionTime: Tue Oct 09 18:42:21 CEST 2012
FinishTime: 
LocalSubmissionTime: Tue Oct 09 18:42:24 CEST 2012
LocalStartTime: Tue Oct 09 18:42:54 CEST 2012
LocalFinishTime:
  • peek job output when its running: 
    $  qcg-peek J1349800941529__3789
https://elder6.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 11 Hours 53 Minutes 14 Seconds

n1-3-12.local
Tue Oct  9 18:42:54 CEST 2012
  • when jobs is finished the outputs should be in the directory from where you submitted your job: 
    $ cat output.txt 
n1-3-12.local
Tue Oct  9 18:42:54 CEST 2012
Tue Oct  9 18:43:24 CEST 2012
Tue Oct  9 18:43:54 CEST 2012

MUSCLE job example

#QCG name=SimpleExamples
#QCG host=zeus.cyfronet.pl
#QCG walltime=PT14H

#QCG stage-in-file=SimpleExample.cxa.rb

#QCG application=muscle2
#QCG argument=SimpleExample.cxa.rb

#QCG stage-out-dir=. -> results-${JOB_ID}
#QCG output=output-${JOB_ID}.txt
#QCG error=output-${JOB_ID}.txt

Interactive jobs

With QCG it is possible to start an interactive session with any of the PL-Grid clusters. You can use it to compile your application or to perform some debug runs. Example script: 

#QCG host=inula.man.poznan.pl
#QCG walltime=PT3H

/bin/bash

Example interactive session: 

$ qcg-interactive interactive-reef.qcg 
https://qcg-broker.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 20 Days 2 Hours 28 Minutes 44 Seconds

jobId = J1350912281097__5242
Press Ctrl-C to cancel the task
Interactive session started. Use the 'exit' command to quit.
[r473] /home/plgrid/plgmamonski/reef/J1350912281097__5242_task_1350912283206_133 > module load muscle2
 plgrid/tools/java/jdk1.6.0_23 load complete.
 intel/10.1 load complete.
 'plgrid/tools/openmpi/current' load complete.
[r473] /home/plgrid/plgmamonski/reef/J1350912281097__5242_task_1350912283206_133 > muscle2  --cxa /home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/examples/cxa/SimpleExample.cxa.rb --main r w 
Running both MUSCLE2 Simulation Manager and the Simulation
=== Running MUSCLE2 Simulation Manager ===
...

Other valid #host values:

  • zeus.cyfronet.pl (Cyfronet),
  • galera.task.gda.pl (TASK),
  • hydra.icm.edu.pl (ICM),
  • reef.man.poznan.pl (PSNC),
  • inula.man.poznan.pl (PSNC).

Further reading

Attachments