Whenever you can get to it is fine. Thanks
Barry > On Jun 6, 2016, at 8:14 AM, Koos Huijssen <[email protected]> wrote: > > Dear Barry, > > Thanks for notifying us of these issues. There seems to be quite a few > fundamental issues with the nested timer functionality and the xml output. We > will have to check the case, reproduce the problems and start looking into > the code. However, currently we are unable to do so. We may be able to look > into the issue in a month or so. Would that be okay for you? If so, then we > will come back on the issue in the beginning of July. > > With kind regards, > > Koos > > From: Barry Smith [mailto:[email protected]] > Sent: zondag 5 juni 2016 1:19 > To: Koos Huijssen <[email protected]>; Richard Mills > <[email protected]> > Cc: [email protected]; Klaij, Christiaan <[email protected]> > Subject: Re: [petsc-dev] Nested event logging and human friendly output > > > We are having some major problems with your xml nested logging on a > slightly more complicated example and I've been trying to debug it with no > success. So I went back to my original commit > bb1d7374b64f295b2ed5ff23b89435d65e905a54 and found something I was not > expecting. When I run src/snes/examples/tutorials/ex19 with logging it > generates the attached image. Which is wrong, note that SNESJacobianEvaluate, > KSPSolve etc are embedded in the SNES solver but this is not properly > displayed. Shouldn't they be in one level from the SNESSolve? Is this a bug, > a feature? Or ...? > > Thanks for any information, > > Barry > > The major problem we are seeing with the nested logging is in the branch > mark/snes-ex56c when we run src/snes/examples/tutorials/ex56 with > > petscmpiexec -n 1 ./ex56 -dm_refine 2 -ne 8 -alpha 1.e-3 -two_solves false > -petscspace_poly_tensor -petscspace_order 1 -ksp_type cg -ksp_monitor_short > -ksp_rtol 1.e-8 -pc_type gamg -pc_gamg_type agg -pc_gamg_agg_nsmooths 1 > -pc_gamg_coarse_eq_limit 100 -pc_gamg_reuse_interpolation true > -pc_gamg_square_graph 1 -pc_gamg_threshold 0.0 -ksp_converged_reason > -use_mat_nearnullspace true -mg_levels_ksp_max_it 2 -mg_levels_ksp_type > chebyshev -mg_levels_esteig_ksp_type cg -mg_levels_esteig_ksp_max_it 10 > -mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05 -mg_levels_pc_type sor > -mat_block_size 3 -petscpartitioner_type chaco -log_view > ascii:ex56-intel2016_knl_fast_64ranks_ne8_dmrefine3_log.xml:ascii_xml > > it messes up the nesting and has total nonsense for the numerical values of > time, for example in the different events, while the traditional -log_summary > prints out reasonable results. It seems somehow either to be not gathering > the data properly into the nested event data structures you have or not > properly processing the data to generate the xml. I tried debugging but the > logic is unclear to me. > > Simple programs such as: > ierr = PetscLogEventRegister("Event1",0,&event1);CHKERRQ(ierr); > > ierr = PetscLogEventBegin(event1,0,0,0,0);CHKERRQ(ierr); > ierr = PetscSleep(1.0);CHKERRQ(ierr); > ierr = PetscLogEventEnd(event1,0,0,0,0);CHKERRQ(ierr); > > produce: > > [0]PETSC ERROR: Petsc has generated inconsistent data > [0]PETSC ERROR: Depth 2 > maxdepth + 1 1 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.1-405-gbb23584 GIT > Date: 2016-06-04 11:37:36 -0500 > [0]PETSC ERROR: ./ex30 on a arch-xmllog named Barrys-MacBook-Pro.local by > barrysmith Sat Jun 4 18:13:00 2016 > [0]PETSC ERROR: Configure options --download-chaco > --with-mpi-dir=/Users/barrysmith/libraries PETSC_ARCH=arch-xmllog > [0]PETSC ERROR: #1 PetscCreateLogTreeNested() line 719 in > /Users/barrysmith/Src/petsc/src/sys/logging/xmllogevent.c > > ierr = PetscLogEventRegister("Event1",0,&event1);CHKERRQ(ierr); > ierr = PetscLogEventRegister("Event2",0,&event2);CHKERRQ(ierr); > ierr = PetscLogEventRegister("Event3",0,&event3);CHKERRQ(ierr); > > ierr = PetscLogEventBegin(event1,0,0,0,0);CHKERRQ(ierr); > ierr = PetscSleep(1.0);CHKERRQ(ierr); > ierr = PetscLogEventBegin(event2,0,0,0,0);CHKERRQ(ierr); > ierr = PetscSleep(1.0);CHKERRQ(ierr); > ierr = PetscLogEventBegin(event3,0,0,0,0);CHKERRQ(ierr); > ierr = PetscSleep(1.0);CHKERRQ(ierr); > ierr = PetscLogEventEnd(event3,0,0,0,0);CHKERRQ(ierr); > ierr = PetscLogEventEnd(event2,0,0,0,0);CHKERRQ(ierr); > ierr = PetscLogEventEnd(event1,0,0,0,0);CHKERRQ(ierr); > > doesn't crash but doesn't nest event2 and 3 in one but does nest 3 into 2. > > If seems that the ordering of the event values mater, if I change the > registration order to > > ierr = PetscLogEventRegister("Event2",0,&event2);CHKERRQ(ierr); > ierr = PetscLogEventRegister("Event1",0,&event1);CHKERRQ(ierr); > ierr = PetscLogEventRegister("Event3",0,&event3);CHKERRQ(ierr); > > then it crashes with > > [0]PETSC ERROR: Petsc has generated inconsistent data > [0]PETSC ERROR: Depth 2 > maxdepth + 1 1 > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.7.1-405-gbb23584 GIT > Date: 2016-06-04 11:37:36 -0500 > [0]PETSC ERROR: ./ex30 on a arch-xmllog named Barrys-MacBook-Pro.local by > barrysmith Sat Jun 4 18:17:40 2016 > [0]PETSC ERROR: Configure options --download-chaco > --with-mpi-dir=/Users/barrysmith/libraries PETSC_ARCH=arch-xmllog > [0]PETSC ERROR: #1 PetscCreateLogTreeNested() line 719 in > /Users/barrysmith/Src/petsc/src/sys/logging/xmllogevent.c > [0]PETSC ERROR: #2 PetscLogView_Nested() line 1399 in > /Users/barrysmith/Src/petsc/src/sys/logging/xmllogevent.c > > > > Possibly related issue: If you run an example that has nothing that is > actually logged but attempt to use the -log_view it crashes, there is some > implicit assumption in your generation of the xml that some values will be > non-empty. > > > > > > > On Sep 18, 2<image002.png>015, at 10:09 PM, Barry Smith <[email protected]> > wrote: > > > Thank you for contributing the nested logging. I have incorporated into the > PETSc branch barry/xml-nested-logging if you look at > https://bitbucket.org/petsc/petsc/commits/bb1d7374b64f295b2ed5ff23b89435d65e905a54?at=masteryou > can see exactly what I have incorporated into PETSc. I will merge it into > next for portability testing in the next couple of days. I expect over time > as I understand it better I will be able to improve its integration with > PETSc. Currently to generate the nested logging it is as simple to use as > -log_view :filename.xml:ascii_xml > > Thanks again, > > Barry > > > > > > > On Sep 14, 2015, at 7:45 AM, Koos Huijssen <[email protected]> wrote: > > Dear PETSc development team, > > We have developed an extension of the PETSc event logging facilities that has > the following advanced features: > > - It allows logging of events in the form of a nested tree. So if some > function is called from multiple locations in the code, these instances are > distinguished. This in contrast with the standard event logger, which only > logs the amount of total call time. > - It allows the output report to be formatted in XML format. This output can > then be viewed in a human-friendly form in a web browser > with the use of the XSL Transformation script performance_xml2html.xsl. The > html features an nested timings tree that can be expanded and collapsed as > desired. > > This tool has been very useful for us to analyze the code and pinpoint > performance bottle necks. We think that it can be useful for others as well, > and therefore we are providing the code here for integration in the open > source distribution of PETSc. > > For more information I refer to the included manual. We have also provided a > test program and a makefile for convenience. The test program can be run > using MPI with for instance 3-6 processes. > > I apologize for not using the git repo to submit the developed code. I also > apologize for not adhering to the PETSc coding standards (or at least not as > far as I know), but I hope that it is not too far off.. Apart from the whole > capital/underscore standardization stuff one issue may require special > attention, namely the (ab)use of the format PETSc_VIEWER_ASCII_IMPL for > signaling the XML format in XMLViewer.c. I couldn't find an already existing > and better fitting format, but it could be necessary to add a new format here > for this purpose. > > Can you take it up from here and realize the integration of the code in the > PETSc distribution? > > With kind regards, > > Koos Huijssen > > -- > ____________________________________________________________________ > > VORtech BV - Scientific software engineers > ____________________________________________________________________ > > Dr.ir. Koos Huijssen > > P.O. Box 260 > 2600 AG Delft > The Netherlands > > phone +31(0)15-285 0125 > mobile +31(0)6-3333 0803 > email [email protected] > web www.vortech.nl > ____________________________________________________________________ > > <timers.tar.gz> > >
