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WestGrid Seminar Series Copyright © 2006 University of Alberta. All rights reserved Integrating Gridstore Into The Job Submission Process With GSUB Edmund.

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Presentation on theme: "WestGrid Seminar Series Copyright © 2006 University of Alberta. All rights reserved Integrating Gridstore Into The Job Submission Process With GSUB Edmund."— Presentation transcript:

1 WestGrid Seminar Series Copyright © 2006 University of Alberta. All rights reserved Integrating Gridstore Into The Job Submission Process With GSUB Edmund Sumbar University of Alberta

2 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 2  Gridstore… close proximity to vizserver does not impose quotas has a large capacity performs backups

3 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 3  time gcp gridstore:largefile. glacierlattice*matrixnexuscortex 10MB45865 100MB1477040170 1GB12055~600440~4000 Data collected January 11, 2006. * Using scp, gcp not installed yet.

4 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 4  Job submission protocol… copy files from gridstore to execution site (gcp) submit job (qsub) wait for job to end (qstat) copy files from execution site to gridstore (gcp)

5 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 5 desktop user

6 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 6 { execution nodes desktop user head node exec site

7 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 7 { execution nodes desktop user head node exec site gridstore

8 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 8 { execution nodes desktop user head node exec site head node home site gridstore

9 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 9 ssh { execution nodes desktop user head node exec site head node home site gridstore

10 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 10 ssh { execution nodes desktop user head node exec site head node home site grid-proxy-init gridstore

11 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 11 ssh { execution nodes desktop user head node exec site head node home site grid-proxy-init ssh gridstore

12 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 12 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init ssh gcp

13 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 13 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshqsub gcp

14 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 14 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshqsub gcp

15 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 15 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshqsub gcp 123456

16 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 16  Becomes tedious/inefficient/error-prone  Automate process with scripts…

17 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 17  Consider gsub…

18 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 18  Consider gsub… No changes are required to your existing Torque (PBS) job scripts

19 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 19  Consider gsub… No changes are required to your existing Torque (PBS) job scripts All qsub command-line options are supported

20 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 20 { execution nodes desktop user head node exec site gridstore head node home site

21 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 21 ssh { execution nodes desktop user head node exec site head node home site gridstore

22 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 22 ssh { execution nodes desktop user head node exec site head node home site grid-proxy-init gridstore

23 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 23 ssh { execution nodes desktop user head node exec site head node home site grid-proxy-init ssh gridstore

24 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 24 { execution nodes head node exec site ssh desktop user gridstore head node home site grid-proxy-init sshgsub

25 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 25 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshgsub gcp

26 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 26 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshgsub gcp stage in

27 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 27 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshqsub gcp

28 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 28 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshqsub gcp stage out

29 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 29 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshgsub gcp 1234

30 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 30  Demonstration…

31 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 31

32 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 32 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshgsub gcp

33 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 33 ssh { execution nodes desktop user head node exec site gridstore head node home site grid-proxy-init sshgsub gcp blackhole (gridstore head node) ssh prepare input analyze output

34 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 34  Submit jobs directly from blackhole…

35 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 35 desktop user { execution nodes head node gridstore head node home site

36 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 36 desktop user { execution nodes head node gridstore head node home site 

37 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 37 desktop user { execution nodes head node blackholegridstore

38 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 38 desktop user { execution nodes head node blackhole ssh gridstore

39 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 39 desktop user { execution nodes head node blackhole ssh myproxy-get-delegation gridstore

40 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 40 head node blackhole desktop user { execution nodes ssh myproxy-get-delegation gridstore gsub

41 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 41 desktop user { execution nodes head node blackhole ssh myproxy-get-delegation gsub gridstore

42 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 42 desktop user { execution nodes head node blackhole ssh myproxy-get-delegation gsub gridstore gcp

43 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 43 desktop user { execution nodes head node blackhole ssh myproxy-get-delegation gsub gridstore gcp

44 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 44 desktop user { execution nodes head node blackhole ssh myproxy-get-delegation gsub gridstore gcp 123

45 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 45  Demonstration…

46 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 46

47 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 47  Tools for monitoring and managing jobs gstat gdel glog

48 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 48  Demonstration…

49 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 49

50 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 50  View WestGrid like a scaled-up execution site…

51 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 51 desktop user { execution nodes head node

52 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 52 desktop user {

53 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 53 desktop user {

54 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 54 desktop user { {

55 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 55 desktop user { { {

56 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 56 { desktop user { { {

57 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 57 { desktop user { { {

58 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 58 { desktop user { { {

59 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 59 { desktop user { { { blackhole super head node

60 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 60 { desktop user { { { blackhole super head node myproxy credential server

61 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 61 { desktop user { { { blackhole super head node myproxy credential server gridstore file system

62 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 62 { desktop user { { { blackhole super head node myproxy credential server gridstore file system

63 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 63 { desktop user { { { blackhole super head node myproxy credential server gridstore file system WestGrid

64 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 64  DISCLAIMER The opinions expressed herein are those of the author and do not necessarily represent the views of WestGrid management.

65 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 65  Gsub implements programmable workflow  Specify actions to be executed at various times (phases) during the life of a job before stage in after stage in job start job end before stage out after stage out

66 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 66  Workflow programmed as a case statement case $phase in beforestagein ) exit ;; afterstagein ) exit ;; jobstarted ) exit ;; jobended ) exit ;; beforestageout ) exit ;; afterstageout ) if some condition is true; then resubmit fi exit ;; esac

67 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 67  Predefined workflows email prevent tidy autoresub exclusive aggressive

68 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 68  No script modifications required  Specified at submission time gsub jobscript=workflow  Cascade workflows gsub jobscript=workflow1+workflow2

69 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 69  Demonstration…

70 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 70

71 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 71

72 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 72  Gsub is unsuitable for… very short jobs developing, testing, debugging programs staging very large or very many files

73 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 73  Gsub is not officially accepted by WestGrid  Still needs testing in the real world…

74 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 74  Gsub is not officially accepted by WestGrid  Still needs testing in the real world… …any volunteers?

75 createdelete GSUB Copyright © 2006 University of Alberta. All rights reserved January 25, 2006 75  Questions…

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