[petsc-users] (percent time in this phase)

Barry Smith bsmith at petsc.dev
Fri Oct 1 10:03:32 CDT 2021 

  What is "max time"? It is best to gather timings with a stage PetscLogStagePush() to get a separate subtable for exactly the part of the code you want timing for. For example if you are studying linear solver time you want only the solver part of the code in the stage, not the time to build the matrix and right hand side.

  It is very difficult to get really correct publishable reliable performance numbers when comparing solvers with similar timings on parallel machines and especially GPUs. Values can be very dependent on particular compilers used, the specific hardware used, generation of memory used etc.

 Barry


> On Oct 1, 2021, at 8:51 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk> wrote:
> 
> Hi Barry,
>  
> Yes, looks like it is computationally faster using GPUs. I used block jacobi as the preconditioner.
> I have attached the output data for cpu and gpu using -ksp_view. I am not sure; what information I should be looking at using -ksp_view?
>  
> I have an outstanding question,
>  
> event time
> T%
> cal = (event/max)*100
> max time
> 2.87E+02
> KSPSolve
> 1.58E+02
> 53
> 55.2
> MatMult 
> 1.08E+01
> 4
> 3.76
> PCApply 
> 1.31E+02
> 37
> 45.6
> VecNorm
> 6.23E+01
> 11
> 21.7
>  
> Matt couple of days back helped breakdown KSPSolve (53 %) ~ PCApply (37%) + VecNorm (11%) + MatMul (4%)
>  
> However, when I calculate T% manually using max time, the numbers for PCApply and VecNorm are way off as you can see from the above table.
> As a result, the cumulative sum of event time don’t match up to KSPSolve. Can you please let me know what I might be doing wrong?
>  
> I will be performing extensive benchmarking of various preconditioners and comparing their performance on cpus and gpus, so this information is critical.
>  
> Many thanks!
> Karthik.
>  
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Thursday, 30 September 2021 at 15:47
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] (percent time in this phase)
>  
>  
>   The MatSolve is no better on the GPUs then on the CPU; while other parts of the computation seem to speed up nicely.  What is the result of -ksp_view ? Are you using ILU(0) as the preconditioner, this will not solve well on the GPU, its solve is essentially sequential. You won't want to use ILU(0) in this way on GPUs.
>  
>   Barry
>  
> 
> 
> On Sep 30, 2021, at 9:41 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
>  
> Based on your feedback from yesterday. I was trying to breakdown KSPSolve.
> Please find the attached bar plot. The numbers are not adding up at least for GPUs.
> Your feedback from yesterday were based on T%.
> I plotted the time spend on each event, hoping that the cumulative sum would add up to KSPSolve time.
>  
> Kind regards,
> Karthik.
>  
> From: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>
> Date: Thursday, 30 September 2021 at 13:52
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>, "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] (percent time in this phase)
>  
> On Thu, Sep 30, 2021 at 8:50 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
> When comparing the MatSolve data for
>  
> GPU
>  
> MatSolve             341 1.0 1.3009e+02 1.6 2.96e+11 1.0 0.0e+00 0.0e+00 0.0e+00 36 34  0  0  0  36 34  0  0  0  4536    4538      1 5.34e+02    0 0.00e+00 100
> MatCUSPARSSolAnl       2 1.0 3.2338e+01 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  9  0  0  0  0   9  0  0  0  0     0       0      0 0.00e+00    0 0.00e+00  0
>  
> and CPU
>  
> MatSolve             352 1.0 1.3553e+02 1.0 1.02e+11 1.0 0.0e+00 0.0e+00 0.0e+00 35 34  0  0  0  35 34  0  0  0  4489
>  
> the time spent is almost the same for this preconditioner.  Look like MatCUSPARSSolAnl is called only twice (since I am running on two cores) 
>  
> mpirun -n 2 ./ex45 -log_summary -da_grid_x 511 -da_grid_y 511 -da_grid_z 511  -dm_mat_type mpiaijcusparse -dm_vec_type mpicuda -ksp_type cg -pc_type bjacobi -ksp_monitor
>  
> So would it be fair to assume MatCUSPARSSolAnl  is not accounted for in MatSolve and it is an exclusive event?
>  
> Looks like that.
>  
>   Thanks
>  
>      Matt
>  
> KSPSolve (53%) + PCSetup (16%) + DMCreateMat (23%) + MatCUSPARSSolAnl (9%) ~ 100 %
>  
> Best,
> Karthik.
>  
>  
> From: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>
> Date: Wednesday, 29 September 2021 at 16:29
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>, "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] %T (percent time in this phase)
>  
> On Wed, Sep 29, 2021 at 10:18 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
> Thank you!
>  
> Just to summarize
>  
> KSPSolve (53%) + PCSetup (16%) + DMCreateMat (23%) + MatCUSPARSSolAnl (9%) ~ 100 %
>  
> You didn’t happen to mention how MatCUSPARSSolAnl is accounted for? Am I right in accounting for it as above?
>  
> I am not sure.I thought it might be the GPU part of MatSolve(). I will have to look in the code. I am not as familiar with the GPU part.
>  
> MatCUSPARSSolAnl       2 1.0 3.2338e+01 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  9  0  0  0  0   9  0  0  0  0     0       0      0 0.00e+00    0 0.00e+00  0
>  
> Finally, I believe the vector events, VecNorn, VecTDot, VecAXPY, and VecAYPX are mutually exclusive?
>  
> Yes.
>  
>   Thanks,
>  
>      Matt
>  
> Best,
>  
> Karthik.
>  
> From: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>
> Date: Wednesday, 29 September 2021 at 11:58
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>, "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] %T (percent time in this phase)
>  
> On Wed, Sep 29, 2021 at 6:24 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
> Thank you Mathew. Now, it is all making sense to me.
>  
> From data file ksp_ex45_N511_gpu_2.txt
>  
> KSPSolve (53%) + KSPSetup (0%) = PCSetup (16%) + PCApply (37%).
>  
> However, you said “So an iteration would mostly consist of MatMult + PCApply, with some vector work”
>  
> 1) You do one solve, but 2 KSPSetUp()s. You must be running on more than one process and using Block-Jacobi . Half the time is spent in the solve (53%)
>  
> KSPSetUp               2 1.0 5.3149e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 2.4e+01  0  0  0  0  1   0  0  0  0  1     0       0      0 0.00e+00    0 0.00e+00  0
> KSPSolve               1 1.0 1.5837e+02 1.1 8.63e+11 1.0 6.8e+02 2.1e+06 4.4e+03 53100100100 95  53100100100 96 10881   11730   1022 6.40e+03 1021 8.17e-03 100
>  
> 
> 2) The preconditioner look like BJacobi-ILU. The setup time is 16%, which is all setup of the individual blocks, and this is all used by the numerical ILU factorization.
>  
> PCSetUp 2 1.0 4.9623e+01 1.3 1.45e+09 1.0 0.0e+00 0.0e+00 0.0e+00 16 0 0 0 0 16 0 0 0 0 58 0 2 6.93e+03 0 0.00e+00 0 PCSetUpOnBlocks 1 1.0 4.9274e+01 1.3 1.45e+09 1.0 0.0e+00 0.0e+00 0.0e+00 15 0 0 0 0 15 0 0 0 0 59 0 2 6.93e+03 0 0.00e+00 0
> MatLUFactorNum         1 1.0 4.6126e+01 1.3 1.45e+09 1.0 0.0e+00 0.0e+00 0.0e+00 14  0  0  0  0  14  0  0  0  0    63       0      2 6.93e+03    0 0.00e+00  0
> MatILUFactorSym        1 1.0 2.5110e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00  1  0  0  0  0   1  0  0  0  0     0       0      0 0.00e+00    0 0.00e+00  0
>  
> 3) The preconditioner application takes 37% of the time, which is all solving the factors and recorded in MatSolve(). Matrix multiplication takes 4%.
>  
> PCApply 341 1.0 1.3068e+02 1.6 2.96e+11 1.0 0.0e+00 0.0e+00 0.0e+00 37 34 0 0 0 37 34 0 0 0 4516 4523 1 5.34e+02 0 0.00e+00 100
> MatSolve             341 1.0 1.3009e+02 1.6 2.96e+11 1.0 0.0e+00 0.0e+00 0.0e+00 36 34  0  0  0  36 34  0  0  0  4536    4538      1 5.34e+02    0 0.00e+00 100
> MatMult              341 1.0 1.0774e+01 1.1 2.96e+11 1.0 6.9e+02 2.1e+06 2.0e+00  4 34100100  0   4 34100100  0 54801   66441      2 5.86e+03    0 0.00e+00 100
>  
> 4) The significant vector time is all in norms (11%) since they are really slow on the GPU.
>  
> 
> VecNorm              342 1.0 6.2261e+01129.9 4.57e+10 1.0 0.0e+00 0.0e+00 6.8e+02 11  5  0  0 15  11  5  0  0 15  1466   196884      0 0.00e+00  342 2.74e-03 100
> VecTDot              680 1.0 1.7107e+00 1.3 9.09e+10 1.0 0.0e+00 0.0e+00 1.4e+03  1 10  0  0 29   1 10  0  0 29 106079   133922      0 0.00e+00  680 5.44e-03 100
> VecAXPY              681 1.0 3.2036e+00 1.7 9.10e+10 1.0 0.0e+00 0.0e+00 0.0e+00  1 11  0  0  0   1 11  0  0  0 56728   58367    682 5.34e+02    0 0.00e+00 100
> VecAYPX              339 1.0 2.6502e+00 1.8 4.53e+10 1.0 0.0e+00 0.0e+00 0.0e+00  1  5  0  0  0   1  5  0  0  0 34136   34153    339 2.71e-03    0 0.00e+00 100
>  
> So the solve time is:
>  
>   53% ~ 37% + 4% + 11%
>  
> and the setup time is about 16%. I was wrong about the SetUp time being included, as it is outside the event:
>  
>   https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/interface/itfunc.c#L852 <https://gitlab.com/petsc/petsc/-/blob/main/src/ksp/ksp/interface/itfunc.c#L852>
>  
> It looks like the remainder of the time (23%) is spent preallocating the matrix.
>  
>   Thanks,
>  
>      Matt
>  
> The MalMult event is 4 %. How does this event figure into the above equation; if preconditioning (MatMult + PCApply) is included in KSPSolve?
>  
> Best,
> Karthik.
>  
> From: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>
> Date: Wednesday, 29 September 2021 at 10:58
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>, "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] %T (percent time in this phase)
>  
> On Wed, Sep 29, 2021 at 5:52 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
> That was helpful. I would like to provide some additional details of my run on cpus and gpus. Please find the following attachments:
>  
> graph.pdf a plot showing overall time and various petsc events.
> ksp_ex45_N511_cpu_6.txt data file of the log_summary 
> ksp_ex45_N511_gpu_2.txt data file of the log_summary 
>  
> I used the following petsc options for cpu
>  
> mpirun -n 6 ./ex45 -log_summary -da_grid_x 511 -da_grid_y 511 -da_grid_z 511 -dm_mat_type mpiaij -dm_vec_type mpi -ksp_type cg -pc_type bjacobi -ksp_monitor
>  
> and for gpus
>  
> mpirun -n 1 ./ex45 -log_summary -da_grid_x 511 -da_grid_y 511 -da_grid_z 511  -dm_mat_type mpiaijcusparse -dm_vec_type mpicuda -ksp_type cg -pc_type bjacobi -ksp_monitor
>  
> to run the following problem
>  
> https://petsc.org/release/src/ksp/ksp/tutorials/ex45.c.html <https://petsc.org/release/src/ksp/ksp/tutorials/ex45.c.html>
>  
> From the above code, I see is there no individual function called KSPSetUp(), so I gather KSPSetDM, KSPSetComputeInitialGuess, KSPSetComputeRHS, kSPSetComputeOperators all are timed together as KSPSetUp. For this example, is KSPSetUp time and KSPSolve time mutually exclusive?
>  
> No, KSPSetUp() will be contained in KSPSolve() if it is called automatically.
>  
> In your response you said that
>  
>    “PCSetUp() time may be in KSPSetUp() or it maybe in PCApply() it depends on how much of the preconditioner construction can take place early, so depends exactly on the preconditioner used.”
>  
> I don’t see a explicit call to PCSetUp() or  PCApply() in ex45; so for this particular preconditioner (bjacobi) how can I tell how they are timed?
>  
> They are all inside KSPSolve(). If you have a preconditioned linear solve, the oreconditioning happens during the iteration. So an iteration would mostly
> consist of MatMult + PCApply, with some vector work.
>  
> I am hoping to time KSP solving and preconditioning mutually exclusively.
>  
> I am not sure that concept makes sense here. See above.
>  
>   Thanks,
>  
>      Matt
>  
>  
> Kind regards,
> Karthik.
>  
>  
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Tuesday, 28 September 2021 at 19:19
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] %T (percent time in this phase)
>  
>  
>  
> 
> On Sep 28, 2021, at 12:11 PM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
>  
> Thanks for Barry for your response.
>  
> I was just benchmarking the problem with various preconditioner on cpu and gpu. I understand, it is not possible to get mutually exclusive timing.
> However, can you tell if KSPSolve time includes both PCSetup and PCApply? And if KSPSolve and KSPSetup are mutually exclusive? Likewise for PCSetUp and PCApply.
>  
>    If you do not call KSPSetUp() separately from KSPSolve() then its time is included with KSPSolve().
>  
>    PCSetUp() time may be in KSPSetUp() or it maybe in PCApply() it depends on how much of the preconditioner construction can take place early, so depends exactly on the preconditioner used.
>  
>    So yes the answer is not totally satisfying. The one thing I would recommend is to not call KSPSetUp() directly and then KSPSolve() will always include the total time of the solve plus all setup time. PCApply will contain all the time to apply the preconditioner but may also include some setup time.
>  
>   Barry
>  
>  
> Best,
> Karthik.
>  
>  
>  
>  
> From: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>
> Date: Tuesday, 28 September 2021 at 16:56
> To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>>
> Cc: "petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>>
> Subject: Re: [petsc-users] %T (percent time in this phase)
>  
>  
>  
> 
> On Sep 28, 2021, at 10:55 AM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk <mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
>  
> Hello,
>  
> I ran ex45 in the KPS tutorial, which is a 3D finite-difference Poisson problem. I noticed from the output from using the flag -log_summary that for various events their respective %T (percent time in this phase) do not add up to 100 but rather exceeds 100. So, I gather there is some overlap among these events. I am primarily looking at the events KSPSetUp, KSPSolve, PCSetUp and PCSolve. Is it possible to get a mutually exclusive %T or Time for these individual events? I have attached  the log_summary output file from my run for your reference.
>  
>  
>   For nested solvers it is tricky to get the times to be mutually exclusive because some parts of the building of the preconditioner is for some preconditioners delayed until the solve has started. 
>  
>   It looks like you are using the default preconditioner options which for this example are taking more or less no time since so many iterations are needed. It is best to use -pc_type mg to use geometric multigrid on this problem.
>  
>   Barry
>  
>  
>  
> 
> Thanks!
> Karthik.
>  
> This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. 
> <ksp_ex45_N511_cpu_6.txt>
>  
> 
> 
>  
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>  
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> 
>  
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>  
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> 
>  
> --
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>  
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> 
>  
> -- 
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> -- Norbert Wiener
>  
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
> <KSPSolve.pdf>
>  
> <ksp_ex45_N511_cpu_6.txt><ksp_ex45_N511_gpu_2.txt>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20211001/4fddc570/attachment-0001.html>

More information about the petsc-users mailing list