Hi Neha,
There should be no difference in the density - or any of the properties - using a single or multiple GPUs. Can you confirm that if you restart the calculation from the restart file at the 40.65ns stage you show below on a single GPU then the simulation continues at a density of approximately 0.99?
The key being to isolate that the problem is just from using more than 1 GPU and not from some other issue such as an incorrect setting in the mdin file for example.
It would also help if you can provide some more details about your setup, GPU model, AMBER version etc.
Note, as an aside running a single simulation on multiple GPUs is not always faster so you might want to check that you actually get a speed improvement from using more than 1 GPU at once. Although that's separate from the issue you are reporting since even if it runs slower on multiple GPUs it shouldn't give incorrect answers.
All the best
Ross
> On Nov 8, 2017, at 1:15 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
>
> Dear List,
>
> I am running NPT simulation using parallel gpus. Upon using pmemd.cuda, the
> density is 0.99.
>
>
> A V E R A G E S O V E R 2000 S T E P S
>
>
> NSTEP = 10000000 TIME(PS) = 40650.000 TEMP(K) = 309.99 PRESS =
> 1.8
> Etot = -461754.3426 EKtot = 120156.4717 EPtot =
> -581910.8142
> BOND = 2213.1206 ANGLE = 2543.5550 DIHED =
> 5043.7658
> 1-4 NB = 5223.7909 1-4 EEL = 9977.1082 VDWAALS =
> 81530.0154
> EELEC = -688536.8366 EHBOND = 0.0000 RESTRAINT =
> 94.6664
> EAMBER (non-restraint) = -582005.4806
> EKCMT = 57615.1448 VIRIAL = 57540.2827 VOLUME =
> 1978006.8374
> Density =
> 0.9904
> -----------------------------------------------------------
> -------------------
>
>
> When I use parallel gpus, (the jobs are still onging), the density is 0.87.
> I was wondering if this is the expected behaviour when using
> pmemd.cuda.MPI.
>
>
>
>
> NSTEP = 70000 TIME(PS) = 40790.000 TEMP(K) = 310.56 PRESS =
> -7.3
> Etot = -203302.7551 EKtot = 113220.4141 EPtot =
> -316523.1692
> BOND = 2874.4111 ANGLE = 3392.6226 DIHED =
> 5522.4047
> 1-4 NB = 5274.6312 1-4 EEL = 9963.2258 VDWAALS =
> 54760.1196
> EELEC = -534081.2338 EHBOND = 0.0000 RESTRAINT =
> 117.8627
> EAMBER (non-restraint) = -316641.0319
> EKCMT = 53755.0242 VIRIAL = 54084.9861 VOLUME =
> 2107014.1166
> Density =
> 0.8749
> ------------------------------------------------------------------------------
>
>
> NSTEP = 75000 TIME(PS) = 40800.000 TEMP(K) = 309.02 PRESS =
> 12.8
> Etot = -204018.1082 EKtot = 112657.9297 EPtot =
> -316676.0379
> BOND = 2955.5325 ANGLE = 3323.3666 DIHED =
> 5514.8454
> 1-4 NB = 5328.7581 1-4 EEL = 9964.6209 VDWAALS =
> 55136.4175
> EELEC = -534740.1213 EHBOND = 0.0000 RESTRAINT =
> 122.2405
> EAMBER (non-restraint) = -316798.2784
> EKCMT = 53530.0160 VIRIAL = 52950.1399 VOLUME =
> 2104363.9330
> Density =
> 0.8760
> ------------------------------------------------------------------------------
>
> I am happy to provide more information on job script and input files if
> required.
>
> Regards,
> Neha
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Received on Wed Nov 08 2017 - 06:30:02 PST
