Yes, one should rely on MKL (or Cray LibSci, if using the Cray toolchain) on Cori. But I'm guessing that this will make no noticeable difference for what Justin is doing.
--Richard On Mon, Apr 3, 2017 at 12:57 PM, murat keçeli <[email protected]> wrote: > How about replacing --download-fblaslapack with vendor specific > BLAS/LAPACK? > > Murat > > On Mon, Apr 3, 2017 at 2:45 PM, Richard Mills <[email protected]> > wrote: > >> On Mon, Apr 3, 2017 at 12:24 PM, Zhang, Hong <[email protected]> wrote: >> >>> >>> On Apr 3, 2017, at 1:44 PM, Justin Chang <[email protected]> wrote: >>> >>> Richard, >>> >>> This is what my job script looks like: >>> >>> #!/bin/bash >>> #SBATCH -N 16 >>> #SBATCH -C knl,quad,flat >>> #SBATCH -p regular >>> #SBATCH -J knlflat1024 >>> #SBATCH -L SCRATCH >>> #SBATCH -o knlflat1024.o%j >>> #SBATCH --mail-type=ALL >>> #SBATCH [email protected] >>> #SBATCH -t 00:20:00 >>> >>> #run the application: >>> cd $SCRATCH/Icesheet >>> sbcast --compress=lz4 ./ex48cori /tmp/ex48cori >>> srun -n 1024 -c 4 --cpu_bind=cores numactl -p 1 /tmp/ex48cori -M 128 -N >>> 128 -P 16 -thi_mat_type baij -pc_type mg -mg_coarse_pc_type gamg -da_refine >>> 1 >>> >>> >>> Maybe it is a typo. It should be numactl -m 1. >>> >> >> "-p 1" will also work. "-p" means to "prefer" NUMA node 1 (the MCDRAM), >> whereas "-m" means to use only NUMA node 1. In the former case, MCDRAM >> will be used for allocations until the available memory there has been >> exhausted, and then things will spill over into the DRAM. One would think >> that "-m" would be better for doing performance studies, but on systems >> where the nodes have swap space enabled, you can get terrible performance >> if your code's working set exceeds the size of the MCDRAM, as the system >> will obediently obey your wishes to not use the DRAM and go straight to the >> swap disk! I assume the Cori nodes don't have swap space, though I could >> be wrong. >> >> >>> According to the NERSC info pages, they say to add the "numactl" if >>> using flat mode. Previously I tried cache mode but the performance seems to >>> be unaffected. >>> >>> >>> Using cache mode should give similar performance as using flat mode with >>> the numactl option. But both approaches should be significant faster than >>> using flat mode without the numactl option. I usually see over 3X speedup. >>> You can also do such comparison to see if the high-bandwidth memory is >>> working properly. >>> >>> I also comparerd 256 haswell nodes vs 256 KNL nodes and haswell is >>> nearly 4-5x faster. Though I suspect this drastic change has much to do >>> with the initial coarse grid size now being extremely small. >>> >>> I think you may be right about why you see such a big difference. The >> KNL nodes need enough work to be able to use the SIMD lanes effectively. >> Also, if your problem gets small enough, then it's going to be able to fit >> in the Haswell's L3 cache. Although KNL has MCDRAM and this delivers *a >> lot* more memory bandwidth than the DDR4 memory, it will deliver a lot less >> bandwidth than the Haswell's L3. >> >>> I'll give the COPTFLAGS a try and see what happens >>> >>> >>> Make sure to use --with-memalign=64 for data alignment when configuring >>> PETSc. >>> >> >> Ah, yes, I forgot that. Thanks for mentioning it, Hong! >> >> >>> The option -xMIC-AVX512 would improve the vectorization performance. But >>> it may cause problems for the MPIBAIJ format for some unknown reason. >>> MPIAIJ should work fine with this option. >>> >> >> Hmm. Try both, and, if you see worse performance with MPIBAIJ, let us >> know and I'll try to figure this out. >> >> --Richard >> >> >>> >>> Hong (Mr.) >>> >>> Thanks, >>> Justin >>> >>> On Mon, Apr 3, 2017 at 1:36 PM, Richard Mills <[email protected]> >>> wrote: >>> >>>> Hi Justin, >>>> >>>> How is the MCDRAM (on-package "high-bandwidth memory") configured for >>>> your KNL runs? And if it is in "flat" mode, what are you doing to ensure >>>> that you use the MCDRAM? Doing this wrong seems to be one of the most >>>> common reasons for unexpected poor performance on KNL. >>>> >>>> I'm not that familiar with the environment on Cori, but I think that if >>>> you are building for KNL, you should add "-xMIC-AVX512" to your compiler >>>> flags to explicitly instruct the compiler to use the AVX512 instruction >>>> set. I usually use something along the lines of >>>> >>>> 'COPTFLAGS=-g -O3 -fp-model fast -xMIC-AVX512' >>>> >>>> (The "-g" just adds symbols, which make the output from performance >>>> profiling tools much more useful.) >>>> >>>> That said, I think that if you are comparing 1024 Haswell cores vs. >>>> 1024 KNL cores (so double the number of Haswell nodes), I'm not surprised >>>> that the simulations are almost twice as fast using the Haswell nodes. >>>> Keep in mind that individual KNL cores are much less powerful than an >>>> individual Haswell node. You are also using roughly twice the power >>>> footprint (dual socket Haswell node should be roughly equivalent to a KNL >>>> node, I believe). How do things look on when you compare equal nodes? >>>> >>>> Cheers, >>>> Richard >>>> >>>> On Mon, Apr 3, 2017 at 11:13 AM, Justin Chang <[email protected]> >>>> wrote: >>>> >>>>> Hi all, >>>>> >>>>> On NERSC's Cori I have the following configure options for PETSc: >>>>> >>>>> ./configure --download-fblaslapack --with-cc=cc >>>>> --with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0 >>>>> --with-debugging=0 --with-fc=ftn --with-fortranlib-autodetect=0 >>>>> --with-mpiexec=srun --with-64-bit-indices=1 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>> FOPTFLAGS=-O3 PETSC_ARCH=arch-cori-opt >>>>> >>>>> Where I swapped out the default Intel programming environment with >>>>> that of Cray (e.g., 'module switch PrgEnv-intel/6.0.3 PrgEnv-cray/6.0.3'). >>>>> I want to document the performance difference between Cori's Haswell and >>>>> KNL processors. >>>>> >>>>> When I run a PETSc example like SNES ex48 on 1024 cores (32 Haswell >>>>> and 16 KNL nodes), the simulations are almost twice as fast on Haswell >>>>> nodes. Which leads me to suspect that I am not doing something right for >>>>> KNL. Does anyone know what are some "optimal" configure options for >>>>> running >>>>> PETSc on KNL? >>>>> >>>>> Thanks, >>>>> Justin >>>>> >>>> >>>> >>> >>> >> >
