[petsc-users] (percent time in this phase)
Karthikeyan Chockalingam - STFC UKRI
karthikeyan.chockalingam at stfc.ac.uk
Tue Oct 5 13:27:35 CDT 2021
Just to clarify, I am referring to the below -log_view output, where KPSSetUp is called two times
KSPSetUp 2 1.0 1.3278e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 6.0e+00 0 0 0 0 1 0 0 0 0 1 0
By using the following option:
mpirun -n 6 ……… -pc_bjacobi_local_blocks 1 • KSPSetUP is called 2 times
From: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk>
Date: Tuesday, 5 October 2021 at 19:17
To: Barry Smith <bsmith at petsc.dev>
Cc: Matthew Knepley <knepley at gmail.com>, "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] (percent time in this phase)
Thank you very much!
KPS Setup does appear in the flame login it in the far left (and you have to zoom to see it using the browser)
I will look into the debugger option.
You said “. -pc_bjacobi_local_blocks 2 indicates you want to 2 blocks per rank” does it imply on mpi -n 2 that KSPSetUP should be called 4 times?
The below shows a different behaviour?
mpirun -n 6 ……… -pc_bjacobi_local_blocks 1 • KSPSetUP is called 2 times
mpirun -n 6 ……… -pc_bjacobi_local_blocks 2 • KSPSetUP is called 3 times
mpirun -n 6 ……… -pc_bjacobi_local_blocks 3 • KSPSetUP is called 4 times
mpirun -n 3 ……… -pc_bjacobi_local_blocks 1 • KSPSetUP is called 2 times
mpirun -n 3 ……… -pc_bjacobi_local_blocks 2 • KSPSetUP is called 3 times
mpirun -n 3 ……… -pc_bjacobi_local_blocks 3 • KSPSetUP is called 4 times
Thanks,
Karthik.
From: Barry Smith <bsmith at petsc.dev>
Date: Tuesday, 5 October 2021 at 17:47
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk>
Cc: Matthew Knepley <knepley at gmail.com>, "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] (percent time in this phase)
On Oct 5, 2021, at 12:28 PM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Thanks Barry.
Please find the attached screen shoot (flamegraph) and foo.txt which generated that graph (using https://www.speedscope.app<https://www.speedscope.app/>).
If you look at the far right of the flamegraph PCSetUpOnBlock() calls PCSetUp() and not KSPSetup(). Unless, I am not reading the graph right?
For block Jacobi
static PetscErrorCode PCSetUpOnBlocks_BJacobi_Singleblock(PC pc)
{
PetscErrorCode ierr;
PC_BJacobi *jac = (PC_BJacobi*)pc->data;
KSP subksp = jac->ksp[0];
KSPConvergedReason reason;
PetscFunctionBegin;
ierr = KSPSetUp(subksp);CHKERRQ(ierr);
ierr = KSPGetConvergedReason(subksp,&reason);CHKERRQ(ierr);
if (reason == KSP_DIVERGED_PC_FAILED) {
pc->failedreason = PC_SUBPC_ERROR;
}
PetscFunctionReturn(0);
}
I am not sure why the KSPSetUp does not appear in the Flame logging, there may be something that ensures it does not get logged.
KSPSetUpOnBlocks() is not logged so does not appear in the logging.
Sometimes you may need to run in the debugger with break points on certain functions to indicate if they are called and when
Secondly how can I know, how many blocks are being setup? Is there a default flag on the number of blocks being SetUp?
For ASM and block Jacobi the default blocks is one per MPI rank. -pc_bjacobi_local_blocks 2 indicates you want to 2 blocks per rank
From: Barry Smith <bsmith at petsc.dev<mailto:bsmith at petsc.dev>>
Date: Tuesday, 5 October 2021 at 17:15
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>, "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)
PCSetUpOnBlocks() calls KSPSetUp() on each block which calls PCSetUp() on each block. This is why you are getting the confusing logging results. So the "
extra" KSPSetUp() is the one on the blocks.
On Oct 5, 2021, at 12:02 PM, Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Hi Matt,
I have a couple of questions;
1. Weather I run on single core or on multiple cores I find that KSPSetUP (ksp/tutorial/ex.45.c) is always called twice. But why? Is setup not done once?
2. I find PCSetUpOnBlocks is calling PCSetup and not the other way around. Can you shed some light? The preconditioner used is block jacobi.
Thanks,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Sunday, 3 October 2021 at 12:54
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)
On Sun, Oct 3, 2021 at 5:43 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Hi Matt,
Thank you. The flamegraph tool is helpful.
Please find the attached screen shoot and foo.txt which generated that graph (using https://www.speedscope.app<https://www.speedscope.app/>).
I find the following call sequence from the graph
KSPSolve -> PCApply -> KSPSolve -> PCApply -> MatSolve
I have a couple of questions
1. The KSPSolve time listed in the file using -log_summary (or -log_view), is it the time taken by the first KSPSolve (in the above call sequence)?
Yes. When calls are nested, we just do not record the time for the nested call in log_view.
1.
2. What is the unit of measurement in flamegrah?
I believe it is microseconds, but I am not sure.
Thanks,
Matt
1.
Thanks,
Karthik.
From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Friday, 1 October 2021 at 14:51
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?
KSPSolve (53%) + PCSetup (16%) + DMCreateMat (23%) + MatCUSPARSSolAnl (9%) ~ 100 %
I am getting so old. We have a different kind of log output if you are really concerned about inclusion. You can run with
-log_view :foo.txt:ascii_flamegraph
and then there are tools for plotting that output, described here
https://firedrakeproject.org/optimising.html
This output _guarantees_ strict inclusion, so you will not have the problems you have above adding things up.
Thanks,
Matt
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
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:
1. graph.pdf a plot showing overall time and various petsc events.
2. ksp_ex45_N511_cpu_6.txt data file of the log_summary
3. 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
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.
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<ksp_ex45_N511_cpu_6.txt>
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--
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.
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