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Identify performance hot-spots #1

Open msuchard opened 7 years ago

msuchard commented 7 years ago

Data-source: UCI_NIPS_1987_2015_p-n_10:

                         self.time self.pct total.time total.pct
RcppExports.R#57           2736.30    78.26    2736.30     78.26 # For Marc
RcppExports.R#53            352.14    10.07     352.14     10.07 # For Marc
iterations.R#552            162.00     4.63     162.00      4.63 # For Chiyu/Subha
iterations.R#80              21.82     0.62      21.82      0.62
fast_PDP.functions.R#625     18.78     0.54      18.78      0.54
fast_PDP.functions.R#980     12.04     0.34      12.04      0.34
RcppExports.R#61             11.94     0.34      11.94      0.34
fast_PDP.functions.R#615     11.92     0.34      11.92      0.34
RcppExports.R#45             10.10     0.29      10.10      0.29
fast_PDP.functions.R#644      9.96     0.28       9.96      0.28
msuchard commented 7 years ago

@cgz59 -- can you work on iterations.R#552. The time is either the repeated matrix allocation or the floating-point operations.

cgz59 commented 7 years ago

Sure I'll investigate that.

Thanks! Best, Chiyu

On Tue, Jul 11, 2017 at 10:56 PM Marc Suchard notifications@github.com wrote:

@cgz59 https://github.com/cgz59 -- can you work on iterations.R#552. The time is either the repeated matrix allocation or the floating-point operations.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/suchard-group/NPCluster/issues/1#issuecomment-314637741, or mute the thread https://github.com/notifications/unsubscribe-auth/AcsO2Op--_cdeuaeUN6G4I8KWICAuldmks5sNEQBgaJpZM4OUnJX .

-- Best Regards.

Chiyu Gu

msuchard commented 7 years ago

@SubhaGuha -- glad to see you on-board here. Please check out line-by-line prof above.

msuchard commented 7 years ago

What does the UCI_NIPS_1987_2015_p-n_10 line-by-line profile look like now (after fixes to line 552)?

cgz59 commented 7 years ago

@msuchard we actually disabled the calculation of line 552, which is not necessary for large n. The line-by-line profile now looks like this:

                           self.time self.pct total.time total.pct

RcppExports.R#57 2750.02 81.41 2750.02 81.41 RcppExports.R#53 384.48 11.38 384.48 11.38 iterations.R#80 18.14 0.54 18.14 0.54 fast_PDP.functions.R#625 15.62 0.46 15.62 0.46 fast_PDP.functions.R#615 11.96 0.35 11.96 0.35 fast_PDP.functions.R#644 11.92 0.35 11.92 0.35 fast_PDP.functions.R#980 11.40 0.34 11.40 0.34 RcppExports.R#61 11.14 0.33 11.14 0.33 fast_PDP.functions.R#1054 11.08 0.33 11.08 0.33 fast_PDP.functions.R#1062 8.76 0.26 8.76 0.26 RcppExports.R#45 8.68 0.26 8.68 0.26 iterations.R#149 7.38 0.22 7.38 0.22 fast_PDP.functions.R#100 6.92 0.20 6.92 0.20 fast_PDP.functions.R#104 6.82 0.20 6.82 0.20 fast_PDP.functions.R#452 6.18 0.18 6.18 0.18 RcppExports.R#81 6.02 0.18 6.02 0.18 fast_PDP.functions.R#998 6.00 0.18 6.00 0.18 fast_PDP.functions.R#741 5.94 0.18 5.94 0.18

Please let me know if you need something more.

Thanks!

cgz59 commented 7 years ago 
                               self.time self.pct total.time total.pct
RcppExports.R#57                 2750.02    81.41    2750.02     81.41
RcppExports.R#53                  384.48    11.38     384.48     11.38
iterations.R#80                    18.14     0.54      18.14      0.54
fast_PDP.functions.R#625           15.62     0.46      15.62      0.46
fast_PDP.functions.R#615           11.96     0.35      11.96      0.35
fast_PDP.functions.R#644           11.92     0.35      11.92      0.35
fast_PDP.functions.R#980           11.40     0.34      11.40      0.34
RcppExports.R#61                   11.14     0.33      11.14      0.33
fast_PDP.functions.R#1054          11.08     0.33      11.08      0.33
fast_PDP.functions.R#1062           8.76     0.26       8.76      0.26
RcppExports.R#45                    8.68     0.26       8.68      0.26
iterations.R#149                    7.38     0.22       7.38      0.22
fast_PDP.functions.R#100            6.92     0.20       6.92      0.20
fast_PDP.functions.R#104            6.82     0.20       6.82      0.20
fast_PDP.functions.R#452            6.18     0.18       6.18      0.18
RcppExports.R#81                    6.02     0.18       6.02      0.18
fast_PDP.functions.R#998            6.00     0.18       6.00      0.18
fast_PDP.functions.R#741            5.94     0.18       5.94      0.18
SubhaGuha commented 7 years ago

Thanks for looking into this, Marc. Please let us know if Chiyu or I can help in any way.