[Nek5000-users] Performance problem

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Fri Aug 6 08:19:17 CDT 2010


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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