performance issue

Thu Aug 10 12:22:28 CDT 2023

Here is our sweep of the parameter space:

./logs/c02_S001M/pioperf-c02_S001M.o1254947:dec2083 : RESULT:
91.2568175876      203.3820649310
./logs/c02_S001M/pioperf-c02_S001M.o1254947:dec2083 : RESULT:
92.1182210732      201.4802259940
./logs/c02_S004M/pioperf-c02_S004M.o1254940:dec0577 : RESULT:
329.6537701115       56.3014947280
./logs/c02_S004M/pioperf-c02_S004M.o1254940:dec0577 : RESULT:
331.4727932376       55.9925290360
./logs/c02_S016M/pioperf-c02_S016M.o1254933:dec0161 : RESULT:
769.7340678648       24.1122236560
./logs/c02_S016M/pioperf-c02_S016M.o1254933:dec0161 : RESULT:
783.5713927539       23.6864185850
./logs/c02_S032M/pioperf-c02_S032M.o1254926:dec0577 : RESULT:
1035.1709708580       17.9294054050
./logs/c02_S032M/pioperf-c02_S032M.o1254926:dec0577 : RESULT:
1047.1429289828       17.7244189750
./logs/c02_S064M/pioperf-c02_S064M.o1254919:dec0161 : RESULT:
1148.3652258918       16.1621055580
./logs/c02_S064M/pioperf-c02_S064M.o1254919:dec0161 : RESULT:
1151.0578818115       16.1242977380
./logs/c02_S128M/pioperf-c02_S128M.o1254912:dec0577 : RESULT:
1274.3409716484       14.5643908600
./logs/c02_S128M/pioperf-c02_S128M.o1254912:dec0577 : RESULT:
1317.0599727821       14.0919930630
./logs/c04_S004M/pioperf-c04_S004M.o1254941:dec0161 : RESULT:
343.0181778797       54.1079196290
./logs/c04_S004M/pioperf-c04_S004M.o1254941:dec0161 : RESULT:
354.2258712407       52.3959470690
./logs/c04_S016M/pioperf-c04_S016M.o1254934:dec0577 : RESULT:
942.6368460375       19.6894488880
./logs/c04_S016M/pioperf-c04_S016M.o1254934:dec0577 : RESULT:
944.2729162573       19.6553344700
./logs/c04_S032M/pioperf-c04_S032M.o1254927:dec0161 : RESULT:
1313.3396548286       14.1319116740
./logs/c04_S032M/pioperf-c04_S032M.o1254927:dec0161 : RESULT:
1335.6182195583       13.8961865960
./logs/c04_S064M/pioperf-c04_S064M.o1254920:dec0577 : RESULT:
1609.7018723157       11.5300853650
./logs/c04_S064M/pioperf-c04_S064M.o1254920:dec0577 : RESULT:
1664.6891018193       11.1492289940
./logs/c04_S128M/pioperf-c04_S128M.o1254913:dec0161 : RESULT:
1921.4885407968        9.6591780830
./logs/c04_S128M/pioperf-c04_S128M.o1254913:dec0161 : RESULT:
1950.4420873454        9.5157913790
./logs/c06_S004M/pioperf-c06_S004M.o1254942:dec0577 : RESULT:
362.3356698753       51.2232207400
./logs/c06_S004M/pioperf-c06_S004M.o1254942:dec0577 : RESULT:
363.0765787757       51.1186925430
./logs/c06_S016M/pioperf-c06_S016M.o1254935:dec0161 : RESULT:
952.6217959754       19.4830730080
./logs/c06_S016M/pioperf-c06_S016M.o1254935:dec0161 : RESULT:
972.3610628258       19.0875598680
./logs/c06_S032M/pioperf-c06_S032M.o1254928:dec0577 : RESULT:
1440.7021713493       12.8826070850
./logs/c06_S032M/pioperf-c06_S032M.o1254928:dec0577 : RESULT:
1453.8729235808       12.7659025070
./logs/c06_S064M/pioperf-c06_S064M.o1254921:dec0161 : RESULT:
1822.0246479036       10.1864703210
./logs/c06_S064M/pioperf-c06_S064M.o1254921:dec0161 : RESULT:
1863.8737349725        9.9577560710
./logs/c06_S128M/pioperf-c06_S128M.o1254914:dec0577 : RESULT:
2277.4926061236        8.1493129550
./logs/c06_S128M/pioperf-c06_S128M.o1254914:dec0577 : RESULT:
2325.8628081953        7.9798343800
./logs/c12_S004M/pioperf-c12_S004M.o1254943:dec2083 : RESULT:
349.2503347567       53.1423971660
./logs/c12_S004M/pioperf-c12_S004M.o1254943:dec2083 : RESULT:
375.3362671288       49.4489918120
./logs/c12_S016M/pioperf-c12_S016M.o1254936:dec0577 : RESULT:
1034.4932215248       17.9411518740
./logs/c12_S016M/pioperf-c12_S016M.o1254936:dec0577 : RESULT:
1078.9753283698       17.2015054580
./logs/c12_S032M/pioperf-c12_S032M.o1254929:dec0161 : RESULT:
1564.2446068140       11.8651519840
./logs/c12_S032M/pioperf-c12_S032M.o1254929:dec0161 : RESULT:
1615.7171524077       11.4871591060
./logs/c12_S064M/pioperf-c12_S064M.o1254922:dec0577 : RESULT:
2240.1838384079        8.2850343270
./logs/c12_S064M/pioperf-c12_S064M.o1254922:dec0577 : RESULT:
2245.5085567722        8.2653882320
./logs/c12_S128M/pioperf-c12_S128M.o1254915:dec0161 : RESULT:
2798.8898011180        6.6312006970
./logs/c12_S128M/pioperf-c12_S128M.o1254915:dec0161 : RESULT:
2877.7394474960        6.4495067530
./logs/c24_S004M/pioperf-c24_S004M.o1254944:dec0577 : RESULT:
345.1242519527       53.7777333670
./logs/c24_S004M/pioperf-c24_S004M.o1254944:dec0577 : RESULT:
351.4297493271       52.8128311150
./logs/c24_S016M/pioperf-c24_S016M.o1254937:dec0161 : RESULT:
925.2242106049       20.0600025240
./logs/c24_S016M/pioperf-c24_S016M.o1254937:dec0161 : RESULT:
954.0638835219       19.4536239350
./logs/c24_S032M/pioperf-c24_S032M.o1254930:dec0577 : RESULT:
1452.2920020184       12.7797990860
./logs/c24_S032M/pioperf-c24_S032M.o1254930:dec0577 : RESULT:
1471.4735322672       12.6132068250
./logs/c24_S064M/pioperf-c24_S064M.o1254923:dec0161 : RESULT:
2050.9979556500        9.0492532910
./logs/c24_S064M/pioperf-c24_S064M.o1254923:dec0161 : RESULT:
2114.0203423275        8.7794803240
./logs/c24_S128M/pioperf-c24_S128M.o1254916:dec0577 : RESULT:
2675.1011803584        6.9380553290
./logs/c24_S128M/pioperf-c24_S128M.o1254916:dec0577 : RESULT:
2693.2253543755        6.8913653920
./logs/c48_S004M/pioperf-c48_S004M.o1254945:dec2083 : RESULT:
340.1527179740       54.5637268770
./logs/c48_S004M/pioperf-c48_S004M.o1254945:dec2083 : RESULT:
371.8511430332       49.9124457400
./logs/c48_S016M/pioperf-c48_S016M.o1254938:dec0577 : RESULT:
1093.3036084645       16.9760712910
./logs/c48_S016M/pioperf-c48_S016M.o1254938:dec0577 : RESULT:
1110.7761821018       16.7090367070
./logs/c48_S032M/pioperf-c48_S032M.o1254931:dec0161 : RESULT:
1542.1770323116       12.0349347780
./logs/c48_S032M/pioperf-c48_S032M.o1254931:dec0161 : RESULT:
1546.3824217323       12.0022057540
./logs/c48_S064M/pioperf-c48_S064M.o1254924:dec0577 : RESULT:
2217.8654888939        8.3684065120
./logs/c48_S064M/pioperf-c48_S064M.o1254924:dec0577 : RESULT:
2257.5814223090        8.2211874250
./logs/c48_S128M/pioperf-c48_S128M.o1254917:dec0161 : RESULT:
2944.0786904926        6.3041793210
./logs/c48_S128M/pioperf-c48_S128M.o1254917:dec0161 : RESULT:
3011.5947346521        6.1628478050
./logs/c96_S004M/pioperf-c96_S004M.o1254946:dec0577 : RESULT:
339.0226605915       54.7456030450
./logs/c96_S004M/pioperf-c96_S004M.o1254946:dec0577 : RESULT:
340.8120077996       54.4581751090
./logs/c96_S016M/pioperf-c96_S016M.o1254939:dec0161 : RESULT:
1081.0376152838       17.1686902820
./logs/c96_S016M/pioperf-c96_S016M.o1254939:dec0161 : RESULT:
786.6881169129       23.5925770340
./logs/c96_S032M/pioperf-c96_S032M.o1254932:dec0577 : RESULT:
1485.9194264343       12.4905830490
./logs/c96_S032M/pioperf-c96_S032M.o1254932:dec0577 : RESULT:
1550.1228426459       11.9732446290
./logs/c96_S064M/pioperf-c96_S064M.o1254925:dec0161 : RESULT:
2264.4052929602        8.1964125670
./logs/c96_S064M/pioperf-c96_S064M.o1254925:dec0161 : RESULT:
2295.6724959924        8.0847769150
./logs/c96_S128M/pioperf-c96_S128M.o1254918:dec0577 : RESULT:
2762.3676993794        6.7188738140
./logs/c96_S128M/pioperf-c96_S128M.o1254918:dec0577 : RESULT:
2813.8936765002        6.5958426770

On Thu, Aug 10, 2023 at 11:09 AM Wei-Keng Liao <wkliao at northwestern.edu>
wrote:

> File striping size of 128 MB seems too big to me.
> I have never tried anything larger than 16 MB and
> learned that large sizes often performed worse.
>
> striping_unit=134217728
>
>
> Have you tried just 1 MB?
>
> Wei-keng
>
> On Aug 10, 2023, at 12:01 PM, Jim Edwards <jedwards at ucar.edu> wrote:
>
>
>
> On Thu, Aug 10, 2023 at 10:53 AM Wei-Keng Liao <wkliao at northwestern.edu>
> wrote:
>
>> From the file header dump you sent earlier, no PnetCDF hint is necessary.
>>
>> What MPI-IO hints are you using?
>>
> I am now using:
>
> MPICH_MPIIO_HINTS=*:romio_cb_read=enable:romio_cb_write=enable:striping_factor=48:striping_unit=134217728
>
> we explored the parameter space and this seems to be about the best for
> this particular file.   But I think that there is still something
> wrong at a low level and am working on trying to figure that out.
>
>
>> One question. Did you delete the output file before each run?
>>
>> Yes
>
>
>
>
>> Wei-keng
>>
>> On Aug 10, 2023, at 11:35 AM, Jim Edwards <jedwards at ucar.edu> wrote:
>>
>> We are having a lot of problems with darshan on our system - I'm working
>> with the darshan developers to resolve.
>>
>> I am setting MPIIO hints - but I see that there are some hints specific
>> to pnetcdf - do you have any recommendations?
>>
>> On Thu, Aug 10, 2023 at 10:15 AM Wei-Keng Liao <wkliao at northwestern.edu>
>> wrote:
>>
>>> Hi, Jim
>>>
>>> FYI. Darshan now can capture the I/O activities of PnetCDF,
>>> in addition to the already MPI-IO and POSIX-IO.
>>>
>>> Wei-keng
>>>
>>> On Aug 9, 2023, at 6:22 PM, Wei-Keng Liao <wkliao at northwestern.edu>
>>> wrote:
>>>
>>> In that case, I have the E3SM-IO benchmark that has a fairly complicate
>>> I/O
>>> partitioning pattern. It used the decomposition maps generated from PIO.
>>> https://github.com/Parallel-NetCDF/E3SM-IO
>>> <https://urldefense.com/v3/__https://github.com/Parallel-NetCDF/E3SM-IO__;!!Dq0X2DkFhyF93HkjWTBQKhk!UJAnknjDPQWY43szbAutlokjDrSHyBOcTlhEOChqYtThxnr812hxwvb8aSmHcEPiNOxNdOUHZi9Z2fyXbg2j6JH1HTo$>
>>>
>>> Wei-keng
>>>
>>> On Aug 9, 2023, at 6:17 PM, Jim Edwards <jedwards at ucar.edu> wrote:
>>>
>>> I think that your example case is too simple - it's doing a simple block
>>> decomposition.
>>> In order to get the performance difference I am observing I need to do a
>>> more complicated
>>> mapping.   I will work on a program that reproduces the problem without
>>> pio but it may take a
>>> while.
>>>
>>>
>>>
>>>
>>
>> --
>> 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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