ou supercomputer symposium – september 23, 2015 parallel programming in the classroom analysis of...
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OU Supercomputer Symposium – September 23, 2015 We Started Here... Early Henry!TRANSCRIPT
![Page 1: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/1.jpg)
OU Supercomputer Symposium – September 23, 2015
Parallel Programmingin the Classroom
Analysis of Genome Data
Karl Frinkle - Mike MorrisParallel Programming Seminar CS4973
Spring 2015
![Page 2: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/2.jpg)
OU Supercomputer Symposium – September 23, 2015
We Started Here . . .
![Page 3: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/3.jpg)
OU Supercomputer Symposium – September 23, 2015
We Started Here . . .Early
Henry!
![Page 4: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/4.jpg)
OU Supercomputer Symposium – September 23, 2015
Our first cluster – made from junk – but it
worked!
We Progressed To . . .
![Page 5: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/5.jpg)
OU Supercomputer Symposium – September 23, 2015
Then Found LittleFe . . .
![Page 6: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/6.jpg)
OU Supercomputer Symposium – September 23, 2015
Next We Used Sooner . . .
![Page 7: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/7.jpg)
OU Supercomputer Symposium – September 23, 2015
Now We Have . . .
![Page 8: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/8.jpg)
OU Supercomputer Symposium – September 23, 2015
Analyzing Genome Data
![Page 9: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/9.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 1 – Write Code
![Page 10: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/10.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 1 – Write CodeDefinitions:
SNP: single-nucleotide polymorphismpronounced “snip” is a DNA sequence commonly varying within a population
![Page 11: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/11.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 1 – Write CodeDefinitions:
SNP: single-nucleotide polymorphism
rsid: Reference SNP cluster ID
pronounced “snip” is a DNA sequence commonly varying within a population
access number used to refer to specific SNPs
![Page 12: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/12.jpg)
OU Supercomputer Symposium – September 23, 2015
• Harvard PGP* Database• 23andME
* PGP - Personal Genome Project
# rsid chromosome position genotype. . .rs12564807 1 734462 AArs3131972 1 752721 GGrs148828841 1 760998 CCrs12124819 1 776546 AA . . .
PHASE 1 – Write Code
![Page 13: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/13.jpg)
OU Supercomputer Symposium – September 23, 2015
Harvard PGP DatabasePer person, there were about 1,000,000 snips.
PHASE 1 – Write Code
# rsid chromosome position genotype. . .rs12564807 1 734462 AArs3131972 1 752721 GGrs148828841 1 760998 CCrs12124819 1 776546 AA . . .
![Page 14: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/14.jpg)
OU Supercomputer Symposium – September 23, 2015
• We started with 200 profiles• Then gave ‘em names• That was about 5G of data
Per person, there were about 1,000,000 snips.
PHASE 1 – Write Code
# rsid chromosome position genotype. . .rs12564807 1 734462 AArs3131972 1 752721 GGrs148828841 1 760998 CCrs12124819 1 776546 AA . . .
![Page 15: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/15.jpg)
15
!! Important Info for HPC Instructors !!
• 5G of data isn’t necessarily “big”• Our clusters are significantly small
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16
!! Important Info for HPC Instructors !!
• 5G of data isn’t necessarily “big”• Our clusters are significantly small
• We’re teaching concept and techniques
• We can easily scale up to Boomer
![Page 17: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/17.jpg)
OU Supercomputer Symposium – September 23, 2015
• Search for a particular rsid for a given person• Ditto for many persons• Both of the above for a collection of rsids• Compare 2 persons’ makeup• we used a sliding window algorithm
• Compare many persons’ makeup
PHASE 1 – Write CodeSeveral programs begged to be written, andall were great candidates for parallelization.
![Page 18: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/18.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .PENELOPE KARDASHIANi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AGi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs2340592 1 910935 --rs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 CT
STONEY BURKEi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AAi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs2340592 1 910935 GGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 TT
![Page 19: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/19.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .PENELOPE KARDASHIANi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AGi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs2340592 1 910935 --rs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 CT
STONEY BURKEi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AAi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs2340592 1 910935 GGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 TT
If one person’s rsid was unrecorded, both were
tossed out.
![Page 20: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/20.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .PENELOPE KARDASHIANi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AGi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 CT
STONEY BURKEi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AAi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 TT
FIRSTVARIANCE
![Page 21: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/21.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .PENELOPE KARDASHIANi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AGi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 CT
STONEY BURKEi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AAi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 TT
VARIANCES
![Page 22: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/22.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .PENELOPE KARDASHIANi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AGi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 CT
STONEY BURKEi6019305 1 891343 GGrs13303106 1 891945 AGi6019306 1 894379 GGrs13303010 1 894573 AAi6019308 1 897792 CCi6019309 1 898082 AArs6696281 1 903104 CTi6019310 1 905681 CCi6019311 1 906114 CCi6019312 1 907666 AAi6060381 1 909238 CGrs13303118 1 918384 GTrs78164078 1 921071 GGrs6665000 1 924898 ACrs2341362 1 927309 CCrs9777703 1 928836 TT
VARIANCESA set number of variances
were allowed in a given “block” size w/o causing a
“difference”.
![Page 23: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/23.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .------@@------------------@@--@@----@@--@@------------
![Page 24: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/24.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .This represents rsid
locations. “@@” means difference.
“—” means agreement.
------@@------------------@@--@@----@@--@@------------
![Page 25: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/25.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .This represents rsid
locations. “@@” means difference.
“—” means agreement.
For this example, if 2 or more do not agree in a group of 8, then record a difference.
Otherwise it is recorded as a match.
------@@------------------@@--@@----@@--@@------------
![Page 26: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/26.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .This represents rsid
locations. “@@” means difference.
“—” means agreement.
For this example, if 2 or more do not agree in a group of 8, then record a difference.
Otherwise it is recorded as a match.
------@@------------------@@--@@----@@--@@------------
It’s a “best case” algorithm. If an rsid is ever in a match box of 8, then it is forever a match.
![Page 27: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/27.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
![Page 28: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/28.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 29: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/29.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 30: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/30.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 31: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/31.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 32: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/32.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 33: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/33.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 34: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/34.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 35: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/35.jpg)
OU Supercomputer Symposium – September 23, 2015
Green = MatchRed = Difference
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
![Page 36: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/36.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
It’s a “best case” algorithm. If an rsid is ever in a match box of 8, then it is forever a match.
![Page 37: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/37.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
It’s a “best case” algorithm. If an rsid is ever in a match box of 8, then it is forever a match.
![Page 38: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/38.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 39: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/39.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 40: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/40.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 41: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/41.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 42: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/42.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 43: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/43.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 44: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/44.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 45: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/45.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@------------
Green = MatchRed = Difference
![Page 46: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/46.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@--------------
Green = MatchRed = Difference
![Page 47: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/47.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@--------------
Green = MatchRed = Difference
![Page 48: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/48.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@--------------
Green = MatchRed = Difference
![Page 49: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/49.jpg)
OU Supercomputer Symposium – September 23, 2015
Sliding Window Technique . . .For this example,
if 2 or more do not agree in a
group of 8, then record a
difference. Otherwise it is recorded as a
match.
------@@------------------@@--@@----@@--@@--------------
Green = MatchRed = Difference
![Page 50: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/50.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 2 – Web GUI
![Page 51: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/51.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 2 – Web GUI
![Page 52: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/52.jpg)
OU Supercomputer Symposium – September 23, 2015
PHASE 2 – Web GUI
Currently we have 5 options.
![Page 53: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/53.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Single Person
![Page 54: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/54.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Single Person
![Page 55: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/55.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Multiple Person
![Page 56: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/56.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Multiple Person
![Page 57: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/57.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Group Allele
![Page 58: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/58.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Group Allele
![Page 59: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/59.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Two Person Compare
![Page 60: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/60.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Two Person Compare
![Page 61: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/61.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Two Person Compare
Very different – no connection.
(Blue is no match.)
![Page 62: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/62.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – Two Person Compare
One-allele search.Blue is no match,green is match.
![Page 63: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/63.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System Monitor
![Page 64: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/64.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System Monitor
Group allele – accesses all files on all nodes.
Seeking 2 alleles.
![Page 65: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/65.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System Monitor
Group allele – accesses all files on all nodes.
Seeking 2 alleles.
Head node doing traffic only – not relatively busy.
![Page 66: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/66.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System Monitor
Group allele – accesses all files on all nodes.
Seeking 6 alleles.
Head node doing traffic only – not relatively busy.
![Page 67: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/67.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System MonitorTwo-person compare,
files on same node.
![Page 68: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/68.jpg)
OU Supercomputer Symposium – September 23, 2015
Web GUI – System MonitorTwo-person compare,
files on different nodes.
![Page 69: OU Supercomputer Symposium – September 23, 2015 Parallel Programming in the Classroom Analysis of Genome Data Karl Frinkle - Mike Morris Parallel Programming](https://reader036.vdocuments.site/reader036/viewer/2022070605/5a4d1b277f8b9ab0599978cf/html5/thumbnails/69.jpg)
OU Supercomputer Symposium – September 23, 2015
Thank You!
We especially thank Henry Neeman, Charlie Peck, Tom Murphy, and everyone else associated with OU IT, the
LittleFe project, the SOSU IT guys and all of our colleagues and friends in the educational community involved with
HPC, for all the help we have received.
Karl FrinkleMike Morris