performance issue

[Jim Edwards]

That example doesn't include record variables.  Do you have a similar one
with record vars?



On Mon, Aug 7, 2023 at 4:32 PM Wei-Keng Liao <wkliao at northwestern.edu>
wrote:

> Hi, Jim
>
> To eliminate the overheads of PIO, I suggest to use this PnetCDF example
> program
> and add a scalar variable to see if the same happens.
>
>
> https://github.com/Parallel-NetCDF/PnetCDF/blob/master/examples/C/nonblocking_write.c
>
> Wei-keng
>
> On Aug 7, 2023, at 4:28 PM, Jim Edwards <jedwards at ucar.edu> wrote:
>
> Hi Wei-Keng,
>
> The cb_nodes doesn't seem to be affected.
>
> Not using independent mode doesn't seem to have helped.  I have the
> pioperf program now writing two files.  One with only
> decomposed fields and one with one additional field, rundate, which is a
> string with the date in it.
>
> The performance is drastically different:
>                                                          IO tasks
> vars      Mb/s                           Time (s)
>  RESULT: write    SUBSET         1       256        64    12067.7548254854
>       25.1577347560    (without scalar)
>  RESULT: write    SUBSET         1       256        64      286.4615089145
>     1059.8190875640      (with scalar)
>
>
> On Mon, Aug 7, 2023 at 1:47 PM Wei-Keng Liao <wkliao at northwestern.edu>
> wrote:
>
>> Is that the reason for why cb_nodes is 1?
>> Strange, because cb_nodes is set at the file open time.
>>
>> Entering the independent data mode in PnetCDF can be completely avoided
>> if using the nonblocking APIs.
>>
>> I would suggest your codes to use the nonblocking APIs in the following
>> way.
>>
>> /* for non-partitioned variables */
>> if (rank == 0) {
>>     ncmpi_iput_var_int(fh, varid[0], data[0], &req[0]); /* write the
>> whole variable */
>>     ncmpi_iput_var_int(fh, varid[1], data[1], &req[1]);
>>     ...
>> }
>> /* for partitioned variables */
>> ncmpi_iput_vara_int(fh, varid[j], data[j], starts[j], counts[j], &req[j]);
>> ...
>>
>>
>> /* commit all posted nonblocking requests */
>> ncmpi_wait_all(ncid, NC_REQ_ALL, NC_REQ_NULL, NULL);
>>
>>
>> Wei-keng
>>
>> > On Aug 7, 2023, at 2:12 PM, Jim Edwards <jedwards at ucar.edu> wrote:
>> >
>> > Hi Wei-Keng,
>> >
>> > I think that I've found the problem.   In the model I am writing a
>> number of scalar variables to the file as well as the decomposed variables.
>> > for the scalar variables I use a code structure like:
>> >
>> > ncmpi_begin_indep_data(fh);
>> > ncmpi_put_vars_int(fh, varid, start, count, stride, data);
>> > ncmpi_end_indep_data(fh);
>> >
>> > In my pioperf test code I didn't write any scalars - this morning I
>> added one and the write performance for the decomposed variables got very
>> very
>> > bad.  What can I do about it?
>> >
>> > Jim
>> >
>> >
>> > --
>> > 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/parallel-netcdf/attachments/20230807/deb3fec7/attachment.html>