performance issue
Jim Edwards
jedwards at ucar.edu
Fri Aug 11 14:01:06 CDT 2023
I'm sorry - I thought that I had provided that, but I guess not.
repo: git at github.com:jedwards4b/ParallelIO.git
branch: bugtest/lustre
On Fri, Aug 11, 2023 at 12:46 PM Wei-Keng Liao <wkliao at northwestern.edu>
wrote:
> Any particular github branch I should use?
>
> I got an error during make.
> /global/homes/w/wkliao/PIO/Github/ParallelIO/src/clib/pio_nc4.c:1481:18:
> error: call to undeclared function 'nc_inq_var_filter_ids'; ISO C99 and
> later do not support implicit function declarations
> [-Wimplicit-function-declaration]
> ierr = nc_inq_var_filter_ids(file->fh, varid, nfiltersp, ids);
> ^
>
>
> Setting these 2 does not help.
> #undef NC_HAS_ZSTD
> #undef NC_HAS_BZ2
>
>
> Wei-keng
>
> > On Aug 11, 2023, at 12:44 PM, Jim Edwards <jedwards at ucar.edu> wrote:
> >
> > I see I missed answering one question - total 2048 tasks. (16 nodes)
> >
> > On Fri, Aug 11, 2023 at 11:35 AM Jim Edwards <jedwards at ucar.edu> wrote:
> > Here is my run script on perlmutter:
> >
> > #!/usr/bin/env python
> > #
> > #SBATCH -A mp9
> > #SBATCH -C cpu
> > #SBATCH --qos=regular
> > #SBATCH --time=15
> > #SBATCH --nodes=16
> > #SBATCH --ntasks-per-node=128
> >
> > import os
> > import glob
> >
> > with open("pioperf.nl","w") as fd:
> > fd.write("&pioperf\n")
> > fd.write(" decompfile='ROUNDROBIN'\n")
> > # for filename in decompfiles:
> > # fd.write(" '"+filename+"',\n")
> > fd.write(" varsize=18560\n");
> > fd.write(" pio_typenames = 'pnetcdf','pnetcdf'\n");
> > fd.write(" rearrangers = 2\n");
> > fd.write(" nframes = 1\n");
> > fd.write(" nvars = 64\n");
> > fd.write(" niotasks = 16\n");
> > fd.write(" /\n")
> >
> > os.system("srun -n 2048 ~/parallelio/bld/tests/performance/pioperf ")
> >
> >
> > Module environment:
> > Currently Loaded Modules:
> > 1) craype-x86-milan 6) cpe/23.03
> 11) craype-accel-nvidia80 16) craype/2.7.20 21) cmake/3.24.3
> > 2) libfabric/1.15.2.0 7) xalt/2.10.2
> 12) gpu/1.0 17) cray-dsmml/0.2.2 22)
> cray-parallel-netcdf/1.12.3.3
> > 3) craype-network-ofi 8) Nsight-Compute/2022.1.1
> 13) evp-patch 18) cray-mpich/8.1.25 23) cray-hdf5/
> 1.12.2.3
> > 4) xpmem/2.5.2-2.4_3.49__gd0f7936.shasta 9) Nsight-Systems/2022.2.1
> 14) python/3.9-anaconda-2021.11 19) cray-libsci/23.02.1.1 24)
> cray-netcdf/4.9.0.3
> > 5) perftools-base/23.03.0 10) cudatoolkit/11.7
> 15) intel/2023.1.0 20) PrgEnv-intel/8.3.3
> >
> > cmake command:
> > CC=mpicc FC=mpifort cmake
> -DPNETCDF_DIR=$CRAY_PARALLEL_NETCDF_DIR/intel/19.0
> -DNETCDF_DIR=$CRAY_NETCDF_PREFIX -DHAVE_PAR_FILTERS=OFF ../
> >
> > There are a couple of issues with the build that can be fixed by editing
> file config.h (created in the bld directory by cmake)
> >
> > Add the following to config.h:
> >
> > #undef NC_HAS_ZSTD
> > #undef NC_HAS_BZ2
> >
> > then:
> > make pioperf
> >
> > once it's built run the submit script from $SCRATCH
> >
> > On Fri, Aug 11, 2023 at 11:13 AM Wei-Keng Liao <wkliao at northwestern.edu>
> wrote:
> > OK. I will test it myself on Perlmutter.
> > Do you have a small test program to reproduce or is it still pioperf?
> > If pioperf, are the build instructions on Perlmutter the same?
> >
> > Please let me know how you run on Perlmutter, i.e. no. process, nodes,
> > Lustre striping, problem size, etc.
> >
> > Does "1 16 64" in your results mean 16 I/O tasks and 64 variables,
> > yes this is correct
> >
> > and only 16 MPI processes out of total ? processes call PnetCDF APIs?
> >
> > yes this is also correct.
> >
> > Wei-keng
> >
> >> On Aug 11, 2023, at 9:35 AM, Jim Edwards <jedwards at ucar.edu> wrote:
> >>
> >> I tried on perlmutter and am seeing the same issue only maybe even
> worse:
> >>
> >> RESULT: write SUBSET 1 16 64
> 1261.0737058071 14.7176171500
> >> RESULT: write SUBSET 1 16 64
> 90.3736534450 205.3695882870
> >>
> >>
> >> On Fri, Aug 11, 2023 at 8:17 AM Jim Edwards <jedwards at ucar.edu> wrote:
> >> Hi Wei-Keng,
> >>
> >> I released that the numbers in this table are all showing the slow
> performing file and the fast file
> >> (the one without the scalar variable) are not represented - I will
> rerun and present these numbers again.
> >>
> >> Here are corrected numbers for a few cases:
> >> GPFS (/glade/work on derecho):
> >> RESULT: write SUBSET 1 16 64
> 4570.2078677815 4.0610844270
> >> RESULT: write SUBSET 1 16 64
> 4470.3231494386 4.1518251320
> >>
> >> Lustre, default PFL's:
> >> RESULT: write SUBSET 1 16 64
> 2808.6570137094 6.6081404420
> >> RESULT: write SUBSET 1 16 64
> 1025.1671656858 18.1043644600
> >>
> >> LUSTRE, no PFL's and very wide stripe:
> >> RESULT: write SUBSET 1 16 64
> 4687.6852437580 3.9593102000
> >> RESULT: write SUBSET 1 16 64
> 3001.4741125579 6.1836282120
> >>
> >> On Thu, Aug 10, 2023 at 11:34 AM Jim Edwards <jedwards at ucar.edu> wrote:
> >> the stripe settings
> >> lfs setstripe -c 96 -S 128M
> >> logs/c96_S128M/
> >>
> >>
> >
> >
> >
> > --
> > Jim Edwards
> >
> > CESM Software Engineer
> > National Center for Atmospheric Research
> > Boulder, CO
> >
> >
> > --
> > Jim Edwards
> >
> > CESM Software Engineer
> > National Center for Atmospheric Research
> > Boulder, CO
>
>
--
Jim Edwards
CESM Software Engineer
National Center for Atmospheric Research
Boulder, CO
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