performance issue

Fri Aug 11 13:46:18 CDT 2023

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 