Re: [AMBER] How to read mdinfo file without crashing the simulation?

From: Karolina Markowska <markowska.kar.gmail.com>
Date: Thu, 21 Apr 2016 12:43:18 +0200

Hi,

I'm using a simple command like:

pmemd.cuda -O -i prod1.in -o prod1.out -p *.prmtop -c emd2.crd -x prod1.nc
-r prod1.crd

I'm running my jobs on a cluster with 4GPUs and the queueing system I use
is Torque.

And in the prod.in file looks like that:

50 ns accelerated MD (aMD) Langevin dynamics
 &cntrl
  imin=0,
  irest=1,
  ntx=5,
  nstlim=25000000,
  dt=0.002,
  ntc=2,
  ntf=2,
  nscm=0,
  ig=-1,
  cut=8.0,
  ntb=2,
  ntp=1,
  ntpr=1000,
  ntwx=1000,
  ntt=3,
  gamma_ln=1.0,
  temp0=300.0,
  ioutfm=1,
  iwrap=1,
  iamd=3,
  ethreshd=5545, alphad=239,
  ethreshp=-174476, alphap=12195,
 /

Is it OK?

Best regards.


2016-04-21 12:13 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:

> On Thu, 21 Apr 2016 11:01:03 +0200
> Karolina Markowska <markowska.kar.gmail.com> wrote:
>
> > At line 810 of file runfiles.F90 (unit = 7, file = 'mdinfo')
> > Fortran runtime error: Resource temporarily unavailable
>
> This error message tells you that the data has not been finished
> writing yet. So you obviously can't access it until it has. The pmemd
> code does no guard against errors here and terminates.
>
> The interesting question is now why the file is not ready yet. This
> may be related to the setup of your system. How are you running your
> jobs?
>
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Received on Thu Apr 21 2016 - 04:00:03 PDT
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