[petsc-users] Performance question using seq Mat and Vec
Brian Yang
jyang29 at uh.edu
Thu Jul 31 15:24:36 CDT 2014
Hi all,
Here's an abstract of the problem,
I got src and rec, they are 3D images with the same size, say Z, X, Y.
We call one (Z, X) is a panel and then there's Y panels for both src and
rec. BTW, they hold complex numbers.
For example, for the *first* panel (always process the same panel) of src
and rec:
Take the first panel of src as our A (20x20),
take the first column of first panel of rec as our b (20x1),
solve the linear system and get x (20x1),
go to next column of the first panel of rec until finish this panel,
assemble all the solution x column by column (20x20).
After finishing the first panel of src and rec, go to next... repeat.
Hope I explained well of my problem. I used SeqDense matrix for A and Seq
vector for b.
Here's the flow,
- start
- all the nodes will share all the Y panels, each node will get part of them
- each node will read in its own part of src and rec images
- for each node, take a panel of src and rec
*- create Mat and Vec, fill them*
*- create KSP and solve by lsqr*
*- get the solution*
*- destroy all the petsc object, A, b, x (destroying KSP will give me error
here!)*
- repeat for the next panel
Here's the time (seconds) output from node 2 (random choice):
*entire time for this panel* *solving
time*
processing panel 1 *time*= 3.2995000E-02 *solver*=
> 3.0995002E-02
> processing panel 2 time= 3.5994001E-02 solver= 3.4995001E-02
> processing panel 3 time= 3.9994001E-02 solver= 3.8994007E-02
> processing panel 4 time= 4.4993997E-02 solver= 4.3993995E-02
> processing panel 5 time= 4.8991993E-02 solver= 4.6992987E-02
> processing panel 6 time= 5.4991007E-02 solver= 5.3991005E-02
> processing panel 7 time= 5.8990985E-02 solver= 5.7990998E-02
> processing panel 8 time= 6.3990027E-02 solver= 6.1990023E-02
> processing panel 9 time= 6.8989992E-02 solver= 6.6990018E-02
> processing panel 10 time= 7.3989004E-02 solver= 7.1989000E-02
> processing panel 11 time= 7.7987969E-02 solver= 7.6987982E-02
> processing panel 12 time= 8.1988037E-02 solver= 7.9988003E-02
> processing panel 13 time= 8.8985980E-02 solver= 8.6987019E-02
> processing panel 14 time= 9.4985008E-02 solver= 9.2984974E-02
> processing panel 15 time= 0.1009850 solver= 9.8985016E-02
> processing panel 16 time= 0.1119831 solver= 0.1099830
> processing panel 17 time= 0.1269809 solver= 0.1239820
> processing panel 18 time= 0.1469780 solver= 0.1439790
> processing panel 19 time= 0.1709731 solver= 0.1669741
> processing panel 20 time= 0.1909720 solver= 0.1869720
> processing panel 21 time= 0.2019690 solver= 0.1979700
> processing panel 22 time= 0.2239659 solver= 0.2199659
> processing panel 23 time= 0.2369640 solver= 0.2319648
> processing panel 24 time= 0.2499621 solver= 0.2449629
> processing panel 25 time= 0.2709589 solver= 0.2659600
> processing panel 26 time= 0.2869561 solver= 0.2829571
> processing panel 27 time= 0.3129530 solver= 0.3059540
> processing panel 28 time= 0.3389480 solver= 0.3329499
> processing panel 29 time= 0.3719430 solver= 0.3649440
> processing panel 30 time= 0.3949399 solver= 0.3879409
> processing panel 31 time= 0.4249353 solver= 0.4169374
> processing panel 32 time= 0.4549308 solver= 0.4469318
> processing panel 33 time= 0.4859262 solver= 0.4759283
> processing panel 34 time= 0.5119228 solver= 0.5019240
> processing panel 35 time= 0.5449171 solver= 0.5349178
> processing panel 36 time= 0.5689130 solver= 0.5579152
> processing panel 37 time= 0.5959096 solver= 0.5849104
> processing panel 38 time= 0.6199055 solver= 0.6079073
>
You could see the time for solving the panels are increasing all the time.
The panel number here is the local one. If I start to solve from panel 40
(random choice):
processing panel 40 time= 5.5992007E-02 solver= 5.1991999E-02
> processing panel 41 time= 9.1986001E-02 solver= 9.0986013E-02
> processing panel 42 time= 0.1309800 solver= 0.1299810
> processing panel 43 time= 0.1719730 solver= 0.1709740
> processing panel 44 time= 0.2119681 solver= 0.2109680
> processing panel 45 time= 0.2529620 solver= 0.2519621
> processing panel 46 time= 0.2919550 solver= 0.2909551
> processing panel 47 time= 0.3319499 solver= 0.3309500
> processing panel 48 time= 0.3719430 solver= 0.3709428
> processing panel 49 time= 0.4129372 solver= 0.4109371
> processing panel 50 time= 0.4529319 solver= 0.4509320
> processing panel 51 time= 0.4929240 solver= 0.4909239
> processing panel 52 time= 0.5339203 solver= 0.5319204
> processing panel 53 time= 0.5779119 solver= 0.5759130
> processing panel 54 time= 0.6199059 solver= 0.6179061
> processing panel 55 time= 0.6648979 solver= 0.6628990
> processing panel 56 time= 0.7248902 solver= 0.7218900
> processing panel 57 time= 0.7938790 solver= 0.7908792
> processing panel 58 time= 0.8728676 solver= 0.8698678
> processing panel 59 time= 0.9778509 solver= 0.9748516
> processing panel 60 time= 1.125830 solver= 1.122829
> processing panel 61 time= 1.273806 solver= 1.268806
> processing panel 62 time= 1.448780 solver= 1.444779
> processing panel 63 time= 1.647749 solver= 1.643749
> processing panel 64 time= 1.901712 solver= 1.896712
> processing panel 65 time= 2.143673 solver= 2.138674
> processing panel 66 time= 2.437630 solver= 2.431629
> processing panel 67 time= 2.744583 solver= 2.736586
> processing panel 68 time= 3.041536 solver= 3.035538
>
The trend is the same, the time is increasing and also starts from a very
quick one.
Since I have thousands of panels for src and rec, the execution time is
unbearable as it goes.
So I am wondering whether I used the right method? or there's memory issue?
Thanks.
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