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<div dir="ltr">Ale,
<div> I successfully built your code and submitted a job to the NERSC Cori machine requiring 32768 KNL cores and one and a half hours. It is estimated to run in 3 days. If you also observed the same problem with less cores, what is your input arguments? Currently,
I use what in your log file, ./main.x 38 -nn -j1 1.0 -d1 1.0 -eps_type krylovschur -eps_tol 1e-9 -log_view</div>
<div> The smaller the better. Thanks.<br clear="all">
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<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">--Junchao Zhang</div>
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<div dir="ltr" class="gmail_attr">On Mon, Jun 24, 2019 at 6:20 AM Ale Foggia <<a href="mailto:amfoggia@gmail.com">amfoggia@gmail.com</a>> wrote:<br>
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<div>Yes, I used KNL nodes. I you can perform the test would be great. Could it be that I'm not using the correct configuration of the KNL nodes? These are the environment variables I set:<br>
MKL_NUM_THREADS=1<br>
OMP_NUM_THREADS=1<br>
KMP_HW_SUBSET=1t<br>
KMP_AFFINITY=compact<br>
I_MPI_PIN_DOMAIN=socket<br>
I_MPI_PIN_PROCESSOR_LIST=0-63<br>
MKL_DYNAMIC=0</div>
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<div>The code is in <a href="https://github.com/amfoggia/LSQuantumED" target="_blank">
https://github.com/amfoggia/LSQuantumED</a> and it has a readme to compile it and run it. When I run the test I used only 32 processors per node, and I used 1024 nodes in total, and it's for nspins=38.</div>
<div>Thank you<br>
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<div dir="ltr" class="gmail_attr">El vie., 21 jun. 2019 a las 20:03, Zhang, Junchao (<<a href="mailto:jczhang@mcs.anl.gov" target="_blank">jczhang@mcs.anl.gov</a>>) escribió:<br>
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<div dir="ltr">Ale,
<div> Did you use Intel KNL nodes? Mr. Hong (cc'ed) did experiments on KNL nodes one year ago. He used 32768 processors and called MatAssemblyEnd 118 times and it used only 1.5 seconds in total. So I guess something was wrong with your test. If you can
share your code, I can have a test on our machine to see how it goes.</div>
<div> Thanks.<br clear="all">
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<div dir="ltr" class="gmail-m_-4834888061970788376gmail-m_-2608733206774855066m_-3757742888527942969gmail_signature">
<div dir="ltr">--Junchao Zhang</div>
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<div dir="ltr" class="gmail_attr">On Fri, Jun 21, 2019 at 11:00 AM Junchao Zhang <<a href="mailto:jczhang@mcs.anl.gov" target="_blank">jczhang@mcs.anl.gov</a>> wrote:<br>
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<div dir="ltr">MatAssembly was called once (in stage 5) and cost 2.5% of the total time. Look at stage 5. It says MatAssemblyBegin calls BuildTwoSidedF, which does global synchronization. The high max/min ratio means load imbalance. What I do not understand
is MatAssemblyEnd. The ratio is 1.0. It means processors are already synchronized. With 32768 processors, there are 1.2e+06 messages with average length 1.9e+06 bytes. So each processor sends 36 (1.2e+06/32768) ~2MB messages and it takes 54 seconds. Another
chance is the reduction at MatAssemblyEnd. I don't know why it needs 8 reductions. In my mind, one is enough. I need to look at the code.
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<div><font face="courier new, monospace">Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions --<br>
Avg %Total Avg %Total Count %Total Avg %Total Count %Total
<br>
0: Main Stage: 8.5045e+02 13.0% 3.0633e+15 14.0% 8.196e+07 13.1% 7.768e+06 13.1% 2.530e+02 13.0%
<br>
1: Create Basis: 7.9234e-02 0.0% 0.0000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
<br>
2: Create Lattice: 8.3944e-05 0.0% 0.0000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
<br>
3: Create Hamilt: 1.0694e+02 1.6% 0.0000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% 2.000e+00 0.1%
<br>
5: Offdiag: 1.6525e+02 2.5% 0.0000e+00 0.0% 1.188e+06 0.2% 1.942e+06 0.0% 8.000e+00 0.4%
<br>
6: Phys quantities: 5.4045e+03 82.8% 1.8866e+16 86.0% 5.417e+08 86.7% 7.768e+06 86.8% 1.674e+03 86.1% </font><br>
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<div>--- Event Stage 5: Offdiag<br>
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<div><span style="font-family:"courier new",monospace">BuildTwoSidedF 1 1.0 7.1565e+01 148448.9 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 28 0 0 0 0 0</span><br>
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<div><font face="courier new, monospace">MatAssemblyBegin 1 1.0 7.1565e+01 127783.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 28 0 0 0 0 0<br>
MatAssemblyEnd 1 1.0 5.3762e+01 1.0 0.00e+00 0.0 1.2e+06 1.9e+06 8.0e+00 1 0 0 0 0 33 0100100100 0<br>
VecSet 1 1.0 7.5533e-02 9.0 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</font><br>
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<div dir="ltr" class="gmail-m_-4834888061970788376gmail-m_-2608733206774855066gmail-m_-3757742888527942969gmail-m_1676599161167762965m_3414052773721223084gmail_signature">
<div dir="ltr">--Junchao Zhang</div>
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<div dir="ltr" class="gmail_attr">On Fri, Jun 21, 2019 at 10:34 AM Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>> wrote:<br>
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The load balance is definitely out of whack. <br>
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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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
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<br>
<br>
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. <br>
<br>
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.<br>
<br>
Good luck<br>
<br>
Barry<br>
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<br>
> On Jun 21, 2019, at 9:27 AM, Ale Foggia <<a href="mailto:amfoggia@gmail.com" target="_blank">amfoggia@gmail.com</a>> wrote:<br>
> <br>
> I'm sending one with a bit less time.<br>
> 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.<br>
> <br>
> (The large times are in part "4b- Building offdiagonal part" or "Event Stage 5: Offdiag").<br>
> <br>
> El vie., 21 jun. 2019 a las 16:09, Zhang, Junchao (<<a href="mailto:jczhang@mcs.anl.gov" target="_blank">jczhang@mcs.anl.gov</a>>) escribió:<br>
> <br>
> <br>
> On Fri, Jun 21, 2019 at 8:07 AM Ale Foggia <<a href="mailto:amfoggia@gmail.com" target="_blank">amfoggia@gmail.com</a>> wrote:<br>
> Thanks both of you for your answers,<br>
> <br>
> El jue., 20 jun. 2019 a las 22:20, Smith, Barry F. (<<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>>) escribió:<br>
> <br>
> 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.<br>
> <br>
> > On Jun 20, 2019, at 3:16 PM, Zhang, Junchao via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
> > <br>
> > 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.<br>
> <br>
> 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.
<br>
> It is not reasonable. Could you send log view of that test with 180 seconds MatAssembly?<br>
> <br>
> 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.<br>
> <br>
> > <br>
> > <br>
> > --Junchao Zhang<br>
> > <br>
> > <br>
> > On Thu, Jun 20, 2019 at 4:13 AM Ale Foggia via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
> > Hello all!<br>
> > <br>
> > 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?<br>
> > <br>
> > I attach the code I used and the log I get for a small problem.<br>
> > <br>
> > Cheers,<br>
> > Ale<br>
> > <br>
> <br>
> <log.txt><br>
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