SORTING WITH SAS LONG, VERY LONG AND

LARGE, VERY

LARGE DATA

Aldi KrajaDivision of Statistical Genomics

SAS seminar seriesJune 02, 2008

SORT AND MERGE EXAMPLE data a; input id m1 $ m2 $ m3 $ DNAreserve; datalines; 1 1/1 1/2 1/1 12 2 1/2 1/1 2/2 14 3 2/2 1/1 1/1 15 4 1/2 1/2 1/2 16 5 1/1 2/2 1/1 15 ; run; proc sort data=a; by id; run;

SORT AND MERGE EXAMPLE (CONT.) data b; input id age sex SBP DBP; datalines; 1 23 1 128 95 2 25 2 115 84 3 30 1 120 85 4 27 1 130 90 5 35 2 122 82 ; run; proc sort data=b; by id; run;

SORT AND MERGE EXAMPLE (CONT.) data ab; merge a (in=in1) b (in=in2); by id ; if in1 and in2; run;

proc print data=ab; title "A and B merged"; run; A and B merged Monday, June 2, 2008

Obs id m1 m2 m3 DNAreserve age sex SBP DBP

1 1 1/1 1/2 1/1 12 23 1 128 95 2 2 1/2 1/1 2/2 14 25 2 115 84 3 3 2/2 1/1 1/1 15 30 1 120 85 4 4 1/2 1/2 1/2 16 27 1 130 90 5 5 1/1 2/2 1/1 15 35 2 122 82

EXAMPLE 2: JOIN TABLES WITH SQL

proc sql; create table sqlab as select * from a, b where a.id=b.id; quit; proc print data=sqlab; title "SQL joined tables"; run;

TIME:

Merge: sorting a: real time 0.01 seconds cpu time 0.01 seconds sorting b: real time 0.01 seconds cpu time 0.01 seconds Merge: real time 0.01 seconds cpu time 0.01 seconds

NOTE: PROCEDURE SQL used (Total process time): real time 0.01 seconds cpu time 0.01 seconds

Test it with large and long data if there is any advantage of using proc sql

EXAMPLE 3: SORT FLAGS (IN THE DESCRIPTOR PORTION OF A DATASET)

The CONTENTS Procedure

Data Set Name WORK.A Observations 5

Member Type DATA Variables 5 Sort Information

Sortedby id Validated YES

EXAMPLE 3: SORT FLAGS (CONT.) data one (sortedby=id); input id; datalines; 1 4 3 5 2 ; run; proc contents data=one; title " data one with option sortedby=id "; run;

EXAMPLE 3: SORT FLAGS (CONT.) proc sort data=one; by id; run;

data two; set one; by id; run;

proc sql; create index id on one(id); quit;

proc datasets nolist; modify one; index create id; run;

SORTING LARGE DATA ON MANY KEYS

Problems: Disk space or temporary space may be

inadequate Time needed may be quite long The software or the operating system may not

work correct during the sorting of large data

Work directory normally is located under /tmp of a server. If my data to be sorted is 3 GB and the /tmp is set to 1GB can SAS do the SORT?

What about if 8-jobs run in parallel in the same server with 8 processors, and try to do SORT on different very large and long sets , but for different purposes?

EXAMPLE 4: TAGSORT OPTION data a; input pedid id m1 $ m2 $ m3 $ DNAreserve; datalines; 1 1 1/1 1/2 1/1 12 1 2 1/2 1/1 2/2 14 1 3 2/2 1/1 1/1 15 2 6 1/2 1/2 1/2 16 2 5 1/1 2/2 1/1 15 2 4 2/2 2/2 1/2 12 ; run;

proc sort tagsort data=a nodupkey out=sorted_a;

by pedid id ; run;

TAGSORT

Introduced in versin 6.07 Can produce important improvements in

clock time but increases the cpu time Internally sort will store in the temporary files

only the sort-keys and observation numbers These sort-keys and the observation

numbers are the “tags” of tagsort. At the end of the sort, the tags are used to

retrieve the entire record from the entire set, but now ordering them in sorted order.

Potential gains when the set is very large

EXAMPLE 5: GENESTAR PROJECT PROBLEM

8 large text files Read into SAS 8 SAS datasets

The data are very large

S1-S400By

1,044,977

S1-S400By

1,044,977

S1-S149By

1,044,977

S1-S687By

1,044,977

GENESTAR PROJECT PROBLEM A. split data for each subject as a new

dataset d1-d3236 B. split data for each subject into 25

chromosomes d1c1-d1c25 …….. d3236c1-d3236c25 Transpose markers by batches of 200

markers at a time and place data together for a chromosome

Finally with proc append, place together subjects of the same chromosome.Subject marker geno

genocall1 m1 1/1 0.75601 m2 1/2 0.76899

………………started ended

Subject m1 m2 …1 0.7560 0.768992 0.9999 0.98999

………………Subject m1 m2 …

1 1/1 1/32 1/2 3/3

………………

SORT IN THE GENESTAR PROJECT

sas -memsize 16G pgm.sas & MPRINT(SORTIT): proc sort

data=in1.rawdataf8 nodupkey out=a (keep=barcoden) ; SYMBOLGEN: Macro variable BYL resolves to barcoden MPRINT(SORTIT): by barcoden ; MPRINT(SORTIT): run;

NOTE: There were 718126154 observations read from the data set IN1.MYDATA. ERROR: Insufficient memory. NOTE: The SAS System stopped processing this step because of errors. NOTE: SAS set option OBS=0 and will continue to check

SORT ON LARGE DATA, IS IT NECESSARY? I resolved the problem in the following way: a)

removed from the data every other variable and kept only the by variable in the set. b) only after a), the sorting with nodupkey worked.

In addition where I had another similar sorting, I removed the sorting and used steps that do the same thing without sorting.

Only now the program does not run out of memory, which means that SAS did not have limit toward the number of observations, but the limit was on the memory use in our server (needed more than 16GB of mem) ???. (32/64b issues and -memsize 0)

EXAMPLE 6, SORT WITH SQL

proc sql; create table sql_a as select * from a order by pedid, id; quit;

EXAMPLE 7: MERGE WITH INDEX WITHOUT SORTING DATA proc contents data=a; title "a is not sorted"; run; proc contents data=b; title "b is not sorted"; run; data a_index (index=(id)); set a; run; data b_index (index=(id)); set b; run;

data final; set b_index ; set a_index key=id; run; proc print data=final; title "Merged data based on index= id"; run;

PROBLEMS WITH INDEXING

Indexing can be faster than sorting The difference can be significant in large data SAS will create an extra file for the index and

this will be a large file. For example in a 1.2GB dataset SAS may create an index file of ~ 340 MB

Advantage: a set indexed on many variables can be used as just sorted in one of the variables

Proc datasets has an index, also SQL has indexing: for example

proc datasets library=work; modify a; create index idlist=(pedid id); run;

READINGS:

Paul M. Dorfman. QuickSorting an array. Paper 96-26.

Paul M. Dorfman. Table look-up by direct addressing: key indexing – Bitmapping – Hashing. Paper 8-26

Paper 075-29 Randomly Selecting Observations Robert Patten, Lands’ End, Dodgeville, WI http://www2.sas.com/proceedings/sugi29/075-

29.pdf