[Nek5000-users] [*] Re: Performance problem
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Aug 6 10:57:23 CDT 2010
This is weird. I have a 2D equivalent of this system, with the same
parameters, mesh structure and it is quite fast.
On 08/06/2010 06:49 PM, nek5000-users at lists.mcs.anl.gov wrote:
> I guess your system has a problem. The TEMP solve takes ~0.14 sec for step 6 and 22.2 sec for step 7. Overall step 6 takes 8.4 sec and step 7 51.1 sec although the iteration counts are very similar!
>
> Stefan
>
>
>
> Check this:
>
> 0: Step 6, t= 2.0307248E-01, DT= 3.0347043E-05, C= 2.043 4.8383E+01 3.0220E+00
> 0: Solving for heat
> 0: Solving for fluid
> 0: 0.000000000000000E+000 p22 6 2
> 0: 6 Hmholtz TEMP: 64 7.0899E-08 7.6377E+01 7.7888E-08
> 0: 6 2.0307E-01 1.3816E-01 Heat done
> 0: 0.000000000000000E+000 p22 6 1
> 0: 6 Hmholtz VELX: 57 1.0070E-05 5.8954E+04 1.2278E-05
> 0: 0.000000000000000E+000 p22 6 1
> 0: 6 Hmholtz VELY: 56 1.1755E-05 5.8020E+04 1.2278E-05
> 0: 0.000000000000000E+000 p22 6 1
> 0: 6 Hmholtz VELZ: 57 1.0011E-05 7.7873E+04 1.2278E-05
> 0: 6 U-Pres gmres: 48 1.6044E-09 2.3009E-09 2.3009E+00 4.5887E+00 6.8322E+00
> 0: 6 DNORM, DIVEX 1.604430720383758E-009 1.604426975107925E-009
> 0: 6 2.0307E-01 7.4035E+00 Fluid done
> 0: Step 7, t= 2.0310283E-01, DT= 3.0347043E-05, C= 2.052 5.6850E+01 8.4673E+00
> 0: Solving for heat
> 0: Solving for fluid
> 0: 0.000000000000000E+000 p22 7 2
> 0: 7 Hmholtz TEMP: 64 6.9851E-08 7.6526E+01 7.8021E-08
> 0: 7 2.0310E-01 2.2240E+01 Heat done
> 0: 0.000000000000000E+000 p22 7 1
> 0: 7 Hmholtz VELX: 57 1.0101E-05 5.8874E+04 1.2295E-05
> 0: 0.000000000000000E+000 p22 7 1
> 0: 7 Hmholtz VELY: 56 1.1723E-05 5.7947E+04 1.2295E-05
> 0: 0.000000000000000E+000 p22 7 1
> 0: 7 Hmholtz VELZ: 57 9.9682E-06 7.7881E+04 1.2295E-05
> 0: 7 U-Pres gmres: 48 1.6001E-09 2.2892E-09 2.2892E+00 1.9881E+00 3.3138E+00
> 0: 7 DNORM, DIVEX 1.600110264916237E-009 1.600109913837109E-009
> 0: 7 2.0310E-01 1.9966E+01 Fluid done
> 0: Step 8, t= 2.0313318E-01, DT= 3.0347043E-05, C= 2.060 1.0837E+02 5.1516E+01
>
> On Aug 6, 2010, at 3:08 PM,<nek5000-users at lists.mcs.anl.gov> wrote:
>
>> Mani,
>>
>> I think there must be something else wrong ... I'm seeing about
>> 5 sec/step on a 64 proc. linux cluster.
>>
>> If you'd like to send me a gzip'd file w/ the essentials, contact
>> me off-list (fischer at mcs.anl.gov) and I can take a closer look.
>>
>> Paul
>>
>>
>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>
>>> If you set p94& p95 to 5 (say), I recommend strongly to set p12 (dt) to
>>>
>>> -3e-5
>>>
>>> in your case. The reason for this is that the projection scheme is much
>>> more stable for fixed dt.
>>>
>>> On the whole, however, Stefan's earlier comments about using, say, lx1=8
>>> and fewer elements is a better strategy. It's also possible that we should switch your coarse-grid solve at this scale to AMG.
>>>
>>> Paul
>>>
>>>
>>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>>
>>>>> - set param(102) and param(103) to 5 (this will turn on the residual projection)
>>>> Should this be param 94& 95 ?
>>>>
>>>> - Paul
>>>> On Fri, 6 Aug 2010, nek5000-users at lists.mcs.anl.gov wrote:
>>>>> Ok here are some suggestions to improve the performance:
>>>>> - set timestep, param(12), to -3e-5
>>>>> - set param(102) and param(103) to 5 (this will turn on the residual projection)
>>>>> - increase lgmres (in SIZE) to 40
>>>>> - you have want to tune the Helmholtz (velocity) and pressure tolerance (e.g. 1e-8 and 1e-5)
>>>>> btw: what's the Reynolds number of this flow?
>>>>> Stefan
>>>>> On Aug 6, 2010, at 11:13 AM,<nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>> Dear Mani,
>>>>>> I haven't checked your logfile yet but there are my first thoughts:
>>>>>> N=4 is low
>>>>>> Your polynomial order (N=4) is low and the tensor-product formulation won't buy you much. The performance of all matrix-matrix multiplies (MxM) will limited by the memory access times. This is in particular a problem on multi-core and multi-socket machines. We have seen that the performance drop can be significant.
>>>>>> On top of that you carry around a large number of duplicate DOF and your surface to volume ratio is high (more communication). I
>>>>>> Parallel Performance
>>>>>> Your gridpoints per core (~4700) is quite small!
>>>>>> On Blue Gene (BG) systems we can scale well (e.g. 70-80% parallel efficiency) with around 10k gridpoints per core. On other system (e.g. Cray XT5) you need much more gridpoints per core (say 80k) because the network has a higher latency (NEK is sensitive to latency not bandwidth) and the processors are much faster.
>>>>>> Cheers,
>>>>>> Stefan
>>>>>> On Aug 6, 2010, at 10:51 AM,<nek5000-users at lists.mcs.anl.gov> wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I'm solving for Rayleigh-Benard convection in a 3D box of 37632, 4rth order elements. I fired the job on 512 processors on a machine with quad-core, quad socket configuration (32 nodes with 16 cores each ) with a 20 Gbps infiniband interconnect. In 12 hours it has run 163 time steps. Is this normal or is there maybe some way to improve performance? Attached is the SIZE file.
>>>>>>> Regards,
>>>>>>> Mani chandra
>>>>>>> <SIZE.txt>_______________________________________________
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