Hi Ross,
Thanks for your help! Ok, I run the tests again all between 3-4 min:
TRPCage = 830.72 ns/day (I tested this several times and both mdifo and .out files are in agreement, please look below )
Myoglobin = 231.77 ns/day
DHFR NVE = 126.08 ns/day
DHFR NPT = 96.84 ns/day
Factor IX NVE = 35.30 ns/day
Factor IX NPT = 28.43 ns/day
Regards,
Filip
TRPCage
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 34000 steps:
| Elapsed(s) = 7.04 Per Step(ms) = 0.21
| ns/day = 834.48 seconds/ns = 103.54
|
| Average timings for all steps:
| Elapsed(s) = 187.21 Per Step(ms) = 0.21
| ns/day = 830.72 seconds/ns = 104.01
| -----------------------------------------------------
| Setup CPU time: 0.08 seconds
| NonSetup CPU time: 187.00 seconds
| Total CPU time: 187.08 seconds 0.05 hours
| Setup wall time: 0 seconds
| NonSetup wall time: 187 seconds
| Total wall time: 187 seconds 0.05 hours
NSTEP = 866000 TIME(PS) = 1782.000 TEMP(K) = 324.73 PRESS = 0.0
Etot = -240.2001 EKtot = 243.9234 EPtot = -484.1235
BOND = 68.9465 ANGLE = 171.5527 DIHED = 154.9060
1-4 NB = 60.8412 1-4 EEL = 897.5257 VDWAALS = -95.3436
EELEC = -1339.5914 EGB = -402.9605 RESTRAINT = 0.0000
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 900000 | Completed : 866000 | Remaining : 34000
|
| Average timings for last 288000 steps:
| Elapsed(s) = 59.96 Per Step(ms) = 0.21
| ns/day = 830.01 seconds/ns = 104.10
|
| Average timings for all steps:
| Elapsed(s) = 180.17 Per Step(ms) = 0.21
| ns/day = 830.57 seconds/ns = 104.02
|
|
| Estimated time remaining: 7.1 seconds.
------------------------------------------------------------------------------
JAC:
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 24000 steps:
| Elapsed(s) = 32.82 Per Step(ms) = 1.37
| ns/day = 126.37 seconds/ns = 683.68
|
| Average timings for all steps:
| Elapsed(s) = 274.11 Per Step(ms) = 1.37
| ns/day = 126.08 seconds/ns = 685.28
| -----------------------------------------------------
| Setup CPU time: 0.21 seconds
| NonSetup CPU time: 273.80 seconds
| Total CPU time: 274.01 seconds 0.08 hours
| Setup wall time: 0 seconds
| NonSetup wall time: 275 seconds
| Total wall time: 275 seconds 0.08 hours
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 200000 | Completed : 176000 | Remaining : 24000
|
| Average timings for last 44000 steps:
| Elapsed(s) = 60.09 Per Step(ms) = 1.37
| ns/day = 126.54 seconds/ns = 682.79
|
| Average timings for all steps:
| Elapsed(s) = 241.30 Per Step(ms) = 1.37
| ns/day = 126.04 seconds/ns = 685.50
|
|
| Estimated time remaining: 32.9 seconds.
------------------------------------------------------------------------------
On Sunday, November 24, 2013 12:17 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
Hi Filip,
The timings are only accurate for runs longer than 60 seconds. Ideally
benchmark runs should be between 2.5 and 5 minutes to get reliable
timings, especially on the new GPUs that adjust the clock speed based on
temperature - those tend to start out fast and then throttle back unless
you have decent cooling. Can you adjust the value of nstlim so it runs for
at least 2.5 mins and try again for trpcage and myoglobin please. The same
is true for DHFR and FactorIX if those took less than 60 seconds.
All the best
Ross
On 11/22/13 8:50 PM, "filip fratev" <filipfratev.yahoo.com> wrote:
>Hi Ross and Scott,
>
>
>>Nice! - Now just wait for the next version of AMBER running on two of
>>those cards with peer to peer. :-)
>
>I really wait for the new version ! :) Hope that there will be a great
>GPU scale! :)
>
>>If you could possibly run the GB tests as well - TRPCage, Myoglobin and
>>Nucleosome it would be really helpful - then I can put them on the
>>website.
>
>Ok, I have never tested GB and observed a significant difference between
>the numbers in mdinfo and output files for the first two tests. I provide
>info for both of them (mdinfo is the second one):
>
>
>TRPCage = 833.11/ 745.41 ns/day
>
>Myoglobin = 231.62 /222.63 ns/day
>
>
>Nucleosome =3.99 / 3.99 ns /day
>
>
> output file:
>| Final Performance Info:
>| -----------------------------------------------------
>| Average timings for last 249000 steps:
>| Elapsed(s) = 51.62 Per Step(ms) = 0.21
>| ns/day = 833.48 seconds/ns = 103.66
>|
>| Average timings for all steps:
>| Elapsed(s) = 51.85 Per Step(ms) = 0.21
>| ns/day = 833.11 seconds/ns = 103.71
>| -----------------------------------------------------
>
>mdinfo:
>
>--------------------------------------------------------------------------
>----
>| Current Timing Info
>| -------------------
>| Total steps : 250000 | Completed : 1000 | Remaining : 249000
>|
>| Average timings for last 1000 steps:
>| Elapsed(s) = 0.23 Per Step(ms) = 0.23
>| ns/day = 745.41 seconds/ns = 115.91
>|
>| Average timings for all steps:
>| Elapsed(s) = 0.23 Per Step(ms) = 0.23
>| ns/day = 745.41 seconds/ns = 115.91
>|
>|
>| Estimated time remaining: 57.7 seconds.
>
>--------------------------------------------------------------------------
>----
>
>
>
>
>On Friday, November 22, 2013 7:56 PM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>Nice! - Now just wait for the next version of AMBER running on two of
>those cards with peer to peer. :-)
>
>
>If you could possibly run the GB tests as well - TRPCage, Myoglobin and
>Nucleosome it would be really helpful - then I can put them on the
>website.
>
>Thanks for the info.
>
>All the best
>Ross
>
>On 11/22/13 12:03 AM, "filip fratev" <filipfratev.yahoo.com> wrote:
>
>>Hi all,
>>Some benchmarks of EVGA GTX 780 Ti SC. PCI2.0, CPU 2600K, Cuda 5.0:
>>
>>DHFR NVE = 126.02 ns/day
>>DHFR NPT = 97.24 ns/day
>>
>>Factor IX NVE =35.76 ns/day
>>Factor IX NPT =28.62 ns/day
>>
>>Cellulose NVE = 8.43 ns/day
>>Cellulose NPT = 6.85 ns/day
>>
>>Regards,
>>Filip
>>_______________________________________________
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>>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Sun Nov 24 2013 - 00:30:02 PST
