Thanks for your message Hai,
I'm running on a cluster, but directly from its bash shell, as we have not
yet installed a queuing system. Shouldn't I see any error directly in the
shell?
-----Original Message-----
From: Hai Nguyen [mailto:nhai.qn.gmail.com]
Sent: Friday, December 16, 2016 8:32 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] pmemd.cuda incomplete output file
are you running on a cluster? You might want to check the error log
specified by your script.
(e.g :
http://stackoverflow.com/questions/9096959/how-to-specify-error-log-file-and
-output-file-in-qsub
)
Hai
On Thu, Dec 15, 2016 at 11:15 PM, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
> Dear Niel,
>
> Thanks for your reply. For both, pmemd and pmemd.cuda, Volume went
> from
> ~730000 to ~640000 in 200 ps during equilibration. Pmemd continues
> working up to 500 ps as specified, pmemd.cuda does not. No error
> message to be found. I also tried pmemd.cuda with an additional 50ps
> NVT equilibration before the NPT eq., but no luck there. I also tried
> the default barostat instead of Monte Carlo.
>
> Is there anything else I could try?
>
> This is my GPU:
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA_VISIBLE_DEVICES: 1
> | CUDA Capable Devices Detected: 1
> | CUDA Device ID in use: 0
> | CUDA Device Name: GeForce GTX TITAN X
> | CUDA Device Global Mem Size: 12206 MB
> | CUDA Device Num Multiprocessors: 24
> | CUDA Device Core Freq: 1.22 GHz
> |
> |--------------------------------------------------------
>
> -----Original Message-----
> From: Niel Henriksen [mailto:shireham.gmail.com]
> Sent: Friday, December 16, 2016 1:40 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] pmemd.cuda incomplete output file
>
> On Thu, Dec 15, 2016 at 1:31 PM, Andreas Tosstorff <
> andreas.tosstorff.cup.uni-muenchen.de> wrote:
>
> > Hi all,
> >
> > I ran the same job with pmemd instead of pmemd.CUDA and it worked
> > just fine. Any suggestions how I could make it run on pmemd.CUDA?
> >
> >
> Hi Andreas,
>
> Just a guess here, but is there any chance the volume is changing
> significantly during equilibration? If that is the case, you might
> see the error message I've copied below. Sometimes I've missed that
> message if stdout/stderr is redirected in a non-standard way (ie,
batch/queue system).
>
> Best,
> --Niel
>
> ERROR: Calculation halted. Periodic box dimensions have changed too
> much
> > from their initial values.
> > Your system density has likely changed by a large amount, probably
from
> > starting the simulation from a structure a long way from equilibrium.
> > [Although this error can also occur if the simulation has blown up
> > for some reason]
> > The GPU code does not automatically reorganize grid cells and thus you
> > will need to restart the calculation from the previous restart file.
> > This will generate new grid cells and allow the calculation to
> continue.
> > It may be necessary to repeat this restarting multiple times if
> > your system
> > is a long way from an equilibrated density.
> > Alternatively you can run with the CPU code until the density has
> > converged
> > and then switch back to the GPU code.
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Received on Fri Dec 16 2016 - 00:00:03 PST
