How do you set the variable? $ MKL_VERBOSE=1 ./ex1 -ksp_converged_reason MKL_VERBOSE oneMKL 2024.0 Update 1 Product build 20240215 for Intel(R) 64 architecture Intel(R) Advanced Vector Extensions 2 (Intel(R) AVX2) enabled processors, Lnx 2.80GHz lp64 intel_thread MKL_VERBOSE DDOT(10,0x22127c0,1,0x22127c0,1) 2.02ms CNR:OFF Dyn:1 FastMM:1 TID:0 NThr:1 MKL_VERBOSE DSCAL(10,0x7ffc9fb4ff08,0x22127c0,1) 12.67us CNR:OFF Dyn:1 FastMM:1 TID:0 NThr:1 MKL_VERBOSE DDOT(10,0x22127c0,1,0x2212840,1) 1.52us CNR:OFF Dyn:1 FastMM:1 TID:0 NThr:1 MKL_VERBOSE DDOT(10,0x2212840,1,0x2212840,1) 167ns CNR:OFF Dyn:1 FastMM:1 TID:0 NThr:1 [...]
> On 21 Jun 2024, at 7:37 PM, Yongzhong Li <[email protected]> > wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hello all, > > I set MKL_VERBOSE = 1, but observed no print output specific to the use of > MKL. Does PETSc enable this verbose output? > > Best, > Yongzhong > > > > From: Pierre Jolivet <[email protected] <mailto:[email protected]>> > Date: Friday, June 21, 2024 at 1:36 AM > To: Junchao Zhang <[email protected] <mailto:[email protected]>> > Cc: Yongzhong Li <[email protected] > <mailto:[email protected]>>, [email protected] > <mailto:[email protected]> <[email protected] > <mailto:[email protected]>> > Subject: Re: [petsc-users] [petsc-maint] Assistance Needed with PETSc > KSPSolve Performance Issue > > 你通常不会收到来自 [email protected] <mailto:[email protected]> 的电子邮件。了解这一点为什么很重要 > <https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!eXBeeIXo9Yqgp2nypqwKYimLnGBZXnF4dXxgLM1UoOIO6n8nt3XlfgjVWLPWJh4UOa5NNpx-nrJb_H828XRQKUREfR2m69oCbxI$> > > > > > On 21 Jun 2024, at 6:42 AM, Junchao Zhang <[email protected] > <mailto:[email protected]>> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > I remember there are some MKL env vars to print MKL routines called. > > The environment variable is MKL_VERBOSE > > Thanks, > Pierre > > > Maybe we can try it to see what MKL routines are really used and then we can > understand why some petsc functions did not speed up > > --Junchao Zhang > > > On Thu, Jun 20, 2024 at 10:39 PM Yongzhong Li <[email protected] > <mailto:[email protected]>> wrote: > This Message Is From an External Sender > This message came from outside your organization. > > Hi Barry, sorry for my last results. I didn’t fully understand the stage > profiling and logging in PETSc, now I only record KSPSolve() stage of my > program. Some sample codes are as follow, > > // Static variable to keep track of the stage counter > static int stageCounter = 1; > > // Generate a unique stage name > std::ostringstream oss; > oss << "Stage " << stageCounter << " of Code"; > std::string stageName = oss.str(); > > // Register the stage > PetscLogStage stagenum; > > PetscLogStageRegister(stageName.c_str(), &stagenum); > PetscLogStagePush(stagenum); > > KSPSolve(*ksp_ptr, b, x); > > PetscLogStagePop(); > stageCounter++; > > I have attached my new logging results, there are 1 main stage and 4 other > stages where each one is KSPSolve() call. > > To provide some additional backgrounds, if you recall, I have been trying to > get efficient iterative solution using multithreading. I found out by > compiling PETSc with Intel MKL library instead of OpenBLAS, I am able to > perform sparse matrix-vector multiplication faster, I am using MATSEQAIJMKL. > This makes the shell matrix vector product in each iteration scale well with > the #of threads. However, I found out the total GMERS solve time (~KSPSolve() > time) is not scaling well the #of threads. > > From the logging results I learned that when performing KSPSolve(), there are > some CPU overheads in PCApply() and KSPGMERSOrthog(). I ran my programs using > different number of threads and plotted the time consumption for PCApply() > and KSPGMERSOrthog() against #of thread. I found out these two operations are > not scaling with the threads at all! My results are attached as the pdf to > give you a clear view. > > My questions is, > > From my understanding, in PCApply, MatSolve() is involved, KSPGMERSOrthog() > will have many vector operations, so why these two parts can’t scale well > with the # of threads when the intel MKL library is linked? > > Thank you, > Yongzhong > > From: Barry Smith <[email protected] <mailto:[email protected]>> > Date: Friday, June 14, 2024 at 11:36 AM > To: Yongzhong Li <[email protected] > <mailto:[email protected]>> > Cc: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, Piero Triverio > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance > Issue > > > I am a bit confused. Without the initial guess computation, there are > still a bunch of events I don't understand > > MatTranspose 79 1.0 4.0598e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatMatMultSym 110 1.0 1.7419e+02 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 > MatMatMultNum 90 1.0 1.2640e+02 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 > MatMatMatMultSym 20 1.0 1.3049e+02 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 > MatRARtSym 25 1.0 1.2492e+02 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 > MatMatTrnMultSym 25 1.0 8.8265e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatMatTrnMultNum 25 1.0 2.4820e+02 1.0 6.83e+10 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 275 > MatTrnMatMultSym 10 1.0 7.2984e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatTrnMatMultNum 10 1.0 9.3128e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > > in addition there are many more VecMAXPY then VecMDot (in GMRES they are each > done the same number of times) > > VecMDot 5588 1.0 1.7183e+03 1.0 2.06e+13 1.0 0.0e+00 0.0e+00 > 0.0e+00 8 10 0 0 0 8 10 0 0 0 12016 > VecMAXPY 22412 1.0 8.4898e+03 1.0 4.17e+13 1.0 0.0e+00 0.0e+00 > 0.0e+00 39 20 0 0 0 39 20 0 0 0 4913 > > Finally there are a huge number of > > MatMultAdd 258048 1.0 1.4178e+03 1.0 6.10e+13 1.0 0.0e+00 0.0e+00 > 0.0e+00 7 29 0 0 0 7 29 0 0 0 43025 > > Are you making calls to all these routines? Are you doing this inside your > MatMult() or before you call KSPSolve? > > The reason I wanted you to make a simpler run without the initial guess code > is that your events are far more complicated than would be produced by GMRES > alone so it is not possible to understand the behavior you are seeing without > fully understanding all the events happening in the code. > > Barry > > > > On Jun 14, 2024, at 1:19 AM, Yongzhong Li <[email protected] > <mailto:[email protected]>> wrote: > > Thanks, I have attached the results without using any KSPGuess. At low > frequency, the iteration steps are quite close to the one with KSPGuess, > specifically > > KSPGuess Object: 1 MPI process > type: fischer > Model 1, size 200 > > However, I found at higher frequency, the # of iteration steps are > significant higher than the one with KSPGuess, I have attahced both of the > results for your reference. > > Moreover, could I ask why the one without the KSPGuess options can be used > for a baseline comparsion? What are we comparing here? How does it relate to > the performance issue/bottleneck I found? “I have noticed that the time taken > by KSPSolve is almost two times greater than the CPU time for matrix-vector > product multiplied by the number of iteration” > > Thank you! > Yongzhong > > From: Barry Smith <[email protected] <mailto:[email protected]>> > Date: Thursday, June 13, 2024 at 2:14 PM > To: Yongzhong Li <[email protected] > <mailto:[email protected]>> > Cc: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, Piero Triverio > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance > Issue > > > Can you please run the same thing without the KSPGuess option(s) for a > baseline comparison? > > Thanks > > Barry > > > On Jun 13, 2024, at 1:27 PM, Yongzhong Li <[email protected] > <mailto:[email protected]>> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hi Matt, > > I have rerun the program with the keys you provided. The system output when > performing ksp solve and the final petsc log output were stored in a .txt > file attached for your reference. > > Thanks! > Yongzhong > > From: Matthew Knepley <[email protected] <mailto:[email protected]>> > Date: Wednesday, June 12, 2024 at 6:46 PM > To: Yongzhong Li <[email protected] > <mailto:[email protected]>> > Cc: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>>, Piero Triverio > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-maint] Assistance Needed with PETSc KSPSolve Performance > Issue > > 你通常不会收到来自 [email protected] <mailto:[email protected]> 的电子邮件。了解这一点为什么很重要 > <https://urldefense.us/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!G_uCfscf7eWS!djGfJnEhNJROfsMsBJy5u_KoRKbug55xZ64oHKUFnH2cWku_Th1hwt4TDdoMd8pWYVDzJeqJslMNZwpO3y0Et94d31qk-oCEwo4$> > > On Wed, Jun 12, 2024 at 6:36 PM Yongzhong Li <[email protected] > <mailto:[email protected]>> wrote: > Dear PETSc’s developers, I hope this email finds you well. I am currently > working on a project using PETSc and have encountered a performance issue > with the KSPSolve function. Specifically, I have noticed that the time taken > by KSPSolve is > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > Dear PETSc’s developers, > I hope this email finds you well. > I am currently working on a project using PETSc and have encountered a > performance issue with the KSPSolve function. Specifically, I have noticed > that the time taken by KSPSolve is almost two times greater than the CPU time > for matrix-vector product multiplied by the number of iteration steps. I use > C++ chrono to record CPU time. > For context, I am using a shell system matrix A. Despite my efforts to > parallelize the matrix-vector product (Ax), the overall solve time remains > higher than the matrix vector product per iteration indicates when multiple > threads were used. Here are a few details of my setup: > Matrix Type: Shell system matrix > Preconditioner: Shell PC > Parallel Environment: Using Intel MKL as PETSc’s BLAS/LAPACK library, > multithreading is enabled > I have considered several potential reasons, such as preconditioner setup, > additional solver operations, and the inherent overhead of using a shell > system matrix. However, since KSPSolve is a high-level API, I have been > unable to pinpoint the exact cause of the increased solve time. > Have you observed the same issue? Could you please provide some experience on > how to diagnose and address this performance discrepancy? Any insights or > recommendations you could offer would be greatly appreciated. > > For any performance question like this, we need to see the output of your > code run with > > -ksp_view -ksp_monitor_true_residual -ksp_converged_reason -log_view > > Thanks, > > Matt > > Thank you for your time and assistance. > Best regards, > Yongzhong > ----------------------------------------------------------- > Yongzhong Li > PhD student | Electromagnetics Group > Department of Electrical & Computer Engineering > University of Toronto > https://urldefense.us/v3/__http://www.modelics.org__;!!G_uCfscf7eWS!dyMF1oRvr6dKSgMF8DY1CbNZpPH1TLs6jQQPaBSD91BavByk95ynHW8SxAFI8F3BNIxHhs0HO2I4dpeIlVq2fQ$ > > <https://urldefense.us/v3/__http://www.modelics.org__;!!G_uCfscf7eWS!cuLttMJEcegaqu461Bt4QLsO4fASfLM5vjRbtyNhWJQiInbjgNwkGNdkFE1ebSbFjOUatYB0-jd2yQWMWzqkDFFjwMvNl3ZKAr8$> > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener > > https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dyMF1oRvr6dKSgMF8DY1CbNZpPH1TLs6jQQPaBSD91BavByk95ynHW8SxAFI8F3BNIxHhs0HO2I4dpfRK52EeQ$ > > <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!djGfJnEhNJROfsMsBJy5u_KoRKbug55xZ64oHKUFnH2cWku_Th1hwt4TDdoMd8pWYVDzJeqJslMNZwpO3y0Et94d31qkNOuenGA$> > <ksp_petsc_log.txt> > > <ksp_petsc_log.txt><ksp_petsc_log_noguess.txt>
