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Runtimes and memory use for different runs #96

Closed ole-tange closed 10 years ago

ole-tange commented 10 years ago

Runtime + memory usage for these on 8 core machine:

/usr/bin/time -v bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt

(using ASD) /usr/bin/time -v bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt

/usr/bin/time -v bammds --nosum Gus.Ancient.bam HDGP_hg19.Reference.panel.txt

(using ASD) /usr/bin/time -v bammds --nosum Gus.Ancient.bam HDGP_hg19.Reference.panel.txt

ole-tange commented 10 years ago 
    Command being timed: "bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt"
    User time (seconds): 2834.73
    System time (seconds): 47.41
    Percent of CPU this job got: 282%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 17:01.05
    Maximum resident set size (kbytes): 19003392
ole-tange commented 10 years ago

(with ASD cached)

    Command being timed: "bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt"
    User time (seconds): 307.67
    System time (seconds): 15.81
    Percent of CPU this job got: 83%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 6:28.14
    Maximum resident set size (kbytes): 19003396
ole-tange commented 10 years ago 
    Command being timed: "bammds --nosum Gus.Ancient.bam HDGP_hg19.Reference.panel.txt"
    User time (seconds): 2545.31
    System time (seconds): 35.39
    Percent of CPU this job got: 345%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 12:26.41
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 5500524
ole-tange commented 10 years ago

(With ASDcache)

    Command being timed: "bammds --nosum Gus.Ancient.bam HDGP_hg19.Reference.panel.txt"
    User time (seconds): 61.90
    System time (seconds): 1.19
    Percent of CPU this job got: 107%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 0:58.54
    Maximum resident set size (kbytes): 2414540
sapfo commented 10 years ago

Could you please translate? How many cores, frequency of a core, whats the right unit etc.
are we reporting the wall clock or the user time...? whatever is needed for the average reader? SOmething i could copy paste in the manuscript would be great. Thanks, anna

sapfo commented 10 years ago

could you please also time: /usr/bin/time -v bamdamage Gus.Ancient.bam -s Gus on your machine?

sapfo commented 10 years ago

machine: 8 cores 2.2 GHz

to be used: Elapsed (wall clock) time (h:mm:ss or m:ss) Maximum resident set size (kbytes): 2414540

INCL. SUMMARY no ASD: Command being timed: "bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt" (on an 8 cores, 2.2 GHz machine: running time (wall clock time) 17:01.05, memory usage 18.1 Gb) with ASD: Command being timed: "bammds Gus.Ancient.bam HDGP_hg19.Reference.panel.txt" (on an 8 cores, 2.2 GHz machine: running time (wall clock time) 6:28.14, memory usage 18.1 Gb)

NO SUMMARY Command being timed: "bammds --nosum Gus.Ancient.bam HDGP_hg19.Reference.panel.txt" (on an 8 cores, 2.2 GHz machine: running time (wall clock time) 12:26.41, memory usage 5.2 Gb)

with ASD: (oon an 8 cores, 2.2 GHz machine: running time (wall clock time) 0:58.54, memory usage 2.3 Gb)