The load balance is definitely out of whack.
BuildTwoSidedF 1 1.0 1.6722e-0241.0 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 MatMult 138 1.0 2.6604e+02 7.4 3.19e+10 2.1 8.2e+07 7.8e+06 0.0e+00 2 4 13 13 0 15 25100100 0 2935476 MatAssemblyBegin 1 1.0 1.6807e-0236.1 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 MatAssemblyEnd 1 1.0 3.5680e-01 3.9 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 VecNorm 2 1.0 4.4252e+0174.8 1.73e+07 1.0 0.0e+00 0.0e+00 2.0e+00 1 0 0 0 0 5 0 0 0 1 12780 VecCopy 6 1.0 6.5655e-02 2.6 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 VecAXPY 2 1.0 1.3793e-02 2.7 1.73e+07 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 41000838 VecScatterBegin 138 1.0 1.1653e+0285.8 0.00e+00 0.0 8.2e+07 7.8e+06 0.0e+00 1 0 13 13 0 4 0100100 0 0 VecScatterEnd 138 1.0 1.3653e+0222.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 4 0 0 0 0 0 VecSetRandom 1 1.0 9.6668e-01 2.2 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 Note that VecCopy/AXPY/SetRandom which are all embarrassingly parallel have a balance ratio above 2 which means some processes have more than twice the work of others. Meanwhile the ratio for anything with communication is extremely in balanced, some processes get to the synchronization point well before other processes. The first thing I would do is worry about the load imbalance, what is its cause? is it one process with much less work than others (not great but not terrible) or is it one process with much more work then the others (terrible) or something in between. I think once you get a handle on the load balance the rest may fall into place, otherwise we still have some exploring to do. This is not expected behavior for a good machine with a good network and a well balanced job. After you understand the load balancing you may need to use one of the parallel performance visualization tools to see why the synchronization is out of whack. Good luck Barry > On Jun 21, 2019, at 9:27 AM, Ale Foggia <amfog...@gmail.com> wrote: > > I'm sending one with a bit less time. > I'm timing the functions also with std::chronos and for the case of 180 > seconds the program runs out of memory (and crushes) before the PETSc log > gets to be printed, so I know the time only from my function. Anyway, in > every case, the times between std::chronos and the PETSc log match. > > (The large times are in part "4b- Building offdiagonal part" or "Event Stage > 5: Offdiag"). > > El vie., 21 jun. 2019 a las 16:09, Zhang, Junchao (<jczh...@mcs.anl.gov>) > escribió: > > > On Fri, Jun 21, 2019 at 8:07 AM Ale Foggia <amfog...@gmail.com> wrote: > Thanks both of you for your answers, > > El jue., 20 jun. 2019 a las 22:20, Smith, Barry F. (<bsm...@mcs.anl.gov>) > escribió: > > Note that this is a one time cost if the nonzero structure of the matrix > stays the same. It will not happen in future MatAssemblies. > > > On Jun 20, 2019, at 3:16 PM, Zhang, Junchao via petsc-users > > <petsc-users@mcs.anl.gov> wrote: > > > > Those messages were used to build MatMult communication pattern for the > > matrix. They were not part of the matrix entries-passing you imagined, but > > indeed happened in MatAssemblyEnd. If you want to make sure processors do > > not set remote entries, you can use > > MatSetOption(A,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE), which will generate an > > error when an off-proc entry is set. > > I started being concerned about this when I saw that the assembly was taking > a few hundreds of seconds in my code, like 180 seconds, which for me it's a > considerable time. Do you think (or maybe you need more information to answer > this) that this time is "reasonable" for communicating the pattern for the > matrix? I already checked that I'm not setting any remote entries. > It is not reasonable. Could you send log view of that test with 180 seconds > MatAssembly? > > Also I see (in my code) that even if there are no messages being passed > during MatAssemblyBegin, it is taking time and the "ratio" is very big. > > > > > > > --Junchao Zhang > > > > > > On Thu, Jun 20, 2019 at 4:13 AM Ale Foggia via petsc-users > > <petsc-users@mcs.anl.gov> wrote: > > Hello all! > > > > During the conference I showed you a problem happening during > > MatAssemblyEnd in a particular code that I have. Now, I tried the same with > > a simple code (a symmetric problem corresponding to the Laplacian operator > > in 1D, from the SLEPc Hands-On exercises). As I understand (and please, > > correct me if I'm wrong), in this case the elements of the matrix are > > computed locally by each process so there should not be any communication > > during the assembly. However, in the log I get that there are messages > > being passed. Also, the number of messages changes with the number of > > processes used and the size of the matrix. Could you please help me > > understand this? > > > > I attach the code I used and the log I get for a small problem. > > > > Cheers, > > Ale > > > > <log.txt>
