src/utils/wigTestMaker/timeNotes 1.2
1.2 2010/05/29 22:29:55 kent
SOme more timing measurements.
Index: src/utils/wigTestMaker/timeNotes
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/wigTestMaker/timeNotes,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/utils/wigTestMaker/timeNotes 28 May 2010 16:00:17 -0000 1.1
+++ src/utils/wigTestMaker/timeNotes 29 May 2010 22:29:55 -0000 1.2
@@ -1,168 +1,232 @@
Here's some timings of some of these tests at various machines.
sourceForge: the source forge site. _Very_ slow. You can't wget the files
from it without the connection breaking and resetting several times.
limeconcepts: Steve Benz's machine at home connected via a cable modem
hgwdev: local UCSC machine, the one running the browser
genomebrowser.wustl.edu: Ting Wang's machine in Washington University, St. Louis.
s3.amazonaws.com: Amazon cloud. Cheap S3 storage.
174.129.3.246: Amazon cloud. Storage on genome browser mirror there.
After some experimentation I saw that bedGraphToBigWig files were in practice faster
than wigToBigWig. Attributing this to the zoom levels starting earlier in bedGraphToBigWig
I changed wigToBigWig to begin the zoom levels sooner. This is what the sineSineFixed2 and
sineSineFixed3 are, with sineSineFixed3 beginning earlier than sineSineFixed2, which is
earlier than sineSineFixed.
sourceForge:sineSineFixed.bw:
Initial create - <1 second
100k new chrom 0.796 1.005 fail 1.376
sourceForge:sineSineFixed.wig.gz:
Failed
http://www.limeconcepts.com/sineSineFixed.wig.gz
Initial create - started at 1:16
Timed out after 10 minutes
-http://www.limeconcepts.com/sineSineFixed.bw
- Initial create - <1 second
- Initial draw in brwoser of 100k window: 1.356
- Redraw same window: 0.108
- Scroll right: 1.012 1.014 1.113
- Scroll left: 0.071 0.071 0.111
- Initial 1M window: 14.093
- Scroll right:9.340 9.295 9.482
- Scroll left: 0.281 0.326 0.373
- Initial 5M window: 1.044
- Redraw same window: 0.024
-
http://hgwdev.cse.ucsc.edu/~kent/sineSineFixed.wig.gz
Started at 1:46
Initial draw of 100K window 0.033
Redraw same window 0.032
Scroll right 0.033 0.041 0.051
Scroll left 0.033 0.037 0.038
Initial 1M window: 0.088
Scroll right: 0.077 0.085 0.194
Scroll left: 0.198 0.088 0.070
Initial 5M window: 0.111
Redraw same window: 0.524
Redraw same window: 0.130
http://genomebrowser.wustl.edu/twang_stuff/sineSineFixed.bw
Initial Create < 1 sec
Initial 100k window 1.808
Redraw same window 0.067
Scroll right 1070 1380 1053
Scroll left 89 66 89
Initial 1 M window 4.496
Scroll right 6.028 5.963 5.418
Initial 5M window 1.402
Redraw: 0.023
+http://genomebrowser.wustl.edu/twang_stuff/sineSineFixed3.bw
+ Initial Create < 1 sec
+ Initial 100k window 1321
+ Redraw same window 0.032
+ Scroll right 0.597 0.654 0.976
+ Scroll left 0.036 0.031 0.034
+ Initial 1 M window 1.771
+ Scroll right 0.746 1.641 1.680
+ Scroll left 0.008 0.008 0.008
+ Initial 5M window 1.437
+ Redraw: 0.004
+
+http://genomebrowser.wustl.edu/twang_stuff/sineSineFixed3.bw
+ Initial Create < 1 sec
+ Initial 100k window 1040
+ Redraw same window 0.034
+ Scroll right 0.500 0.572 0.572
+ Scroll left 36 34 28
+ Initial 1 M window 0.919
+ Scroll right 0.467 0.469 0.368
+ Scroll left 0.007 0.008 0.007
+ Initial 5M window 0.382
+ Redraw: 0.004
+
+
http://genomebrowser.wustl.edu/twang_stuff/sineSineFixed.wig.gz
Started at 2:07
Timed out after 10 minutes
http://genomebrowser.wustl.edu/twang_stuff/sineSineBed.bw
Initial Create < 1 sec
Initial 100k window 0.612
Redraw same window 0.026
scroll right 0.504 0.578 0.576
scroll left 0.046 0.034 0.027
Initial 1 M window 1.029
Scroll right 0.713 0.692 0.685
Initial 5M window 1.048
http://s3.amazonaws.com/genome.ucsc.edu/gbdb/hg19/bbi/sineSineBed.bw
Initial create < 1 sec
Initial 100k window 1.067
Redraw same window 0.026
Scroll right 0.685 0.730 0.598
scroll left 0.025 0.040 0.026
Initial 1 M window 1.365
scroll right 0.824 0.684 0.679
scroll left 0.012 0.012 0.011
Initial 5M window 1.180
Redraw same window 0.007
http://s3.amazonaws.com/genome.ucsc.edu/gbdb/hg19/bbi/sineSineFixed.bw
Initial create < 1 sec
Initial 100k window 1.595
Redraw same window 0.092
Scroll right 1.414 1.680 1.420
Scroll left 0.123 0.074 0.091
Initial 1 M window 2.298
Redraw same window 0.350
scroll right 3.269 2.974 4.662
Initial 5M window 1.221
Redraw same window 0.032
http://s3.amazonaws.com/genome.ucsc.edu/gbdb/hg19/bbi/sineSineFixed.wig.gz
Initial create - started 5:07 - timed out after 10 minutes, but track succeeded
http://174.129.3.246/testFile/sineSineBed.bw (amazon)
Initial create < 1 sec
Inital 100k window 1.005
Redraw same window 0.035
Scroll right 0.627 0.628 0.525
Scroll left 23 34 31
Initial 1M window 1.009
Redraw same window 0.010
Scroll right 0.716 0.716 0.715
Scroll left 0.011 0.010 0.011
Initial 5M window 1.1110
Redraw same window 0.007
http://174.129.3.246/testFile/sineSineFixed.bw (amazon)
Initial create < 1 sec
Initial 100k window 1.728
Redraw same window 0.076
Scroll right 0.978 1.298 0.980
Scroll left 0.121 0.063 0.077
Initial 1M window 2.798
Redraw same window 0.311
Scroll right 2.825 2.734 2.676
Scroll left 0.332 0.372 0.339
Initial 5M window 1.220
Redraw same window 0.030
http://174.129.3.246/testFile/sineSineFixed.bw (amazon) after 2x change
Initial create < 1 sec
Initial 100k window 1.012
Redraw same window 0.076
Scroll right 0.971 1.284 0.965
Scroll left 0.099 0.051 0.074
Initial 1M window 2.787
Redraw same window 0.309
Scroll right 2.807 2.815 2.791
Scroll left 0.338 0.374 0.317
Initial 5M window 1.220
Redraw same window 0.030
http://174.129.3.246/testFile/sineSineFixed2.bw (amazon) after 2x change
- Initial create
- Initial 100k window
- Redraw same window
- Scroll right
- Scroll left
- Initial 1M window
- Redraw same window
- Scroll right
- Scroll left
- Initial 5M window
- Redraw same window
+ Initial create < 1 sec
+ Initial 100k window 1.723
+ Redraw same window 0.065
+ Scroll right 0.973 1.299 0.972
+ Scroll left 0.115 0.058 0.068
+ Initial 1M window 1.319
+ Redraw same window 0.039
+ Scroll right 0.835 0.847 0.846
+ Scroll left 0.046 0.042 0.036
+ Initial 5M window 1.110
+ Redraw same window 0.011
http://174.129.3.246/testFile/sineSineFixed3.bw (amazon) after 2x change
- Initial create
- Initial 100k window
- Redraw same window
- Scroll right
- Scroll left
- Initial 1M window
- Redraw same window
- Scroll right
- Scroll left
- Initial 5M window
- Redraw same window
+ Initial create < 1 sec
+ Initial 100k window 1.005
+ Redraw same window 0.046
+ Scroll right 0.640 0.545 0.544
+ Scroll left 0.037 0.046 0.044
+ Initial 1M window 1.114
+ Redraw same window 0.048
+ Scroll right 0.750 0.749 0.750
+ Scroll left 0.049 0.046 0.039
+ Initial 5M window 1.210
+ Redraw same window 0.015
+
+http://www.limeconcepts.com/sineSineFixed.bw
+ Initial create - <1 second
+ Initial draw in brwoser of 100k window: 1.356
+ Redraw same window: 0.108
+ Scroll right: 1.012 1.014 1.113
+ Scroll left: 0.071 0.071 0.111
+ Initial 1M window: 14.093
+ Scroll right:9.340 9.295 9.482
+ Scroll left: 0.281 0.326 0.373
+ Initial 5M window: 1.044
+ Redraw same window: 0.024
+
+http://www.limeconcepts.com/sineSineFixed.bw (after 2x oversampling reduction)
+ Initial create - <1 second
+ Initial draw in browser of 100k window: 1.330
+ Redraw same window: 0.063
+ Scroll right: 1.005 1.114 0.980
+ Scroll left: 0.075 0.056 0.052
+ Initial 1M window: 9.732
+ Redraw same window: 0.311
+ Scroll right: 9.272 9.240 9.207
+ Scroll left: 0.364 0.358 0.305
+ Initial 5M window: 1.167
+ Redraw same window: 0.029
+
+http://www.limeconcepts.com/sineSineFixed2.bw
+ Initial create < 1 sec
+ Initial 100k window 1.349
+ Redraw same window 0.070
+ Scroll right 1.002 1.125 0.982
+ Scroll left 0.095 0.056 0.069
+ Initial 1M window 1.045
+ Redraw same window 0.040
+ Scroll right 0.806 0.764 0.808
+ Scroll left 0.033 0.033 0.031
+ Initial 5M window 0.668
+ Redraw same window 0.011
+
+http://www.limeconcepts.com/sineSineFixed3.bw
+ Initial create < 1 sec
+ Initial 100k window 0.943
+ Redraw same window 0.044
+ Scroll right 0.262 0.183 0.219
+ Scroll left 0.022 0.024 0.027
+ Initial 1M window 0.749
+ Redraw same window 0.026
+ Scroll right 0.412 0.452 0.478
+ Scroll left 0.030 0.025 0.036
+ Initial 5M window 0.712
+ Redraw same window 0.011