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
