Hi Himanshu,
Does this work with the CPU code? - Your mdin file is VERY complicated with lots of redundant settings in it. nsnb for example should NOT be set, although it should be ignored by pmemd.
I'd start by checking if the CPU code works fine. Then go through every option in your mdin file and remove those that are defaults to simplify things. E.g. remove all the minimization related stuff if you have imin=0. Also why are you setting a,b,c in the mdin file and overriding what's in the inpcrd/restrt file?
With regards to your message title you say binary restart but it appears what you mean here is binary trajectory since amber 11 does not support binary restart files - well I think it might support the very old method (as opposed to netcdf) and I doubt that is ever tested anymore.
The NANs are likely because your simulation is blowing up. Can you confirm that setting ioutfm=0 and changing nothing else means it runs fine but setting ioutfm=1 and rerunning causes the problem?
All the best
Ross
> -----Original Message-----
> From: HIMANSHU JOSHI [mailto:himanshuphy87.gmail.com]
> Sent: Thursday, July 12, 2012 10:47 PM
> To: AMBER Mailing List
> Subject: [AMBER] AMBER11_CUDA issue with binary restart
>
> Dear friends,
> I am running a simulation of DNA with amber11 pmemd.cuda (MPI).
> As I started saving trajectories in binary format with ioutfm = 1, the
> job ran well for 1 ns but its
> not able to restart the job in next step.
> Job is getting killed with the message
>
> " *forrtl: severe (174): SIGSEGV, segmentation fault occurred* "
>
> when I tail the restart file I got
>
> NaN NaN NaN NaN NaN NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN NaN NaN
> NaN
> NaN NaN NaN
> 226.7152699 226.7152699 226.7152699 109.4712175 109.4712175
> 109.4712175
>
>
>
> Here is the input file.
>
> NVT dynamics for DNA, 9.0 cut
> &cntrl
> nmropt = 0,
> ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
> ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
> ntwprt = 0, ntwr = 500,
>
> ntf = 2, ntb = 1, dielc = 1.0,
> cut = 9.0, nsnb = 10,
>
> ipol = 0,
>
> ibelly = 0, ntr = 0,
>
> imin = 0,
> maxcyc = 5000,
> ncyc = 2000,
> ntmin = 1, dx0 = 0.1, dxm = 0.5, drms =
> 0.0001,
>
> nstlim = 500000
> nscm = 1000,
> t = 0.0, dt = 0.002,
>
> temp0 = 300.0, tempi = 10.0,
> ig = 71277, heat = 0.0,
> ntt = 1, dtemp = 0.0,
> ioutfm = 1
> ioutfm = 1
> tautp = 1.0,
>
>
> ntp = 0, pres0 = 1.0, comp = 44.6,
> taup = 0.5,
>
> ntc = 2, tol = 0.0005,
>
> &end
> &ewald
> a = 62.9065214, b = 46.8818659, c = 192.6251811,
> &end
>
> Have anyone faced the same problem before, if yes please share your
> solution.
> *
> *
> --
> *With Regards,
> HIMANSHU JOSHI
> Graduate Scholar, Center for Condense Matter Theory
> Department of Physics IISc.,Bangalore India 560012*
> ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
> सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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Received on Fri Jul 13 2012 - 07:00:03 PDT
