[petsc-users] Performance question using seq Mat and Vec
Brian Yang
jyang29 at uh.edu
Thu Jul 31 16:43:26 CDT 2014
I found one thing, as long as I don't destroy the vector that holds the
solution from KSPGetSolution, I could successfully destroy all other
objects (including KSP) for each panel.
On Thu, Jul 31, 2014 at 4:36 PM, Brian Yang <jyang29 at uh.edu> wrote:
> Here's the message (all the nodes are the same):
>
> [8]PETSC ERROR:
> ------------------------------------------------------------------------
> [8]PETSC ERROR: VecDestroy() line 539 in src/vec/vec/interface/vector.c
> [8]PETSC ERROR: KSPReset() line 740 in src/ksp/ksp/interface/itfunc.c
> [8]PETSC ERROR: KSPDestroy() line 783 in src/ksp/ksp/interface/itfunc.c
> [6]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [6]PETSC ERROR: Invalid argument!
> [6]PETSC ERROR: Wrong type of object: Parameter # 1!
> [6]PETSC ERROR:
> ------------------------------------------------------------------------
> [6]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013
> [6]PETSC ERROR: See docs/changes/index.html for recent updates.
> [6]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [6]PETSC ERROR: See docs/index.html for manual pages.
> [6]PETSC ERROR:
> ------------------------------------------------------------------------
>
>
> On Thu, Jul 31, 2014 at 4:31 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> On Jul 31, 2014, at 3:24 PM, Brian Yang <jyang29 at uh.edu> wrote:
>>
>> > 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!)
>>
>> If you do not destroy the KSP then the other objects won't get
>> destroyed (since the KSP reference counts them). You need to determine why
>> the KSP cannot be destroyed. What is the error message? Run with valgrind?
>>
>>
>> > - 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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