[AMBER] R: problem with pmemd.cuda

From: Giovanni Pavan <giovanni.pavan.supsi.ch>
Date: Thu, 10 Nov 2011 10:00:23 +0100

Dear Scott and Ross, dear all,

Regarding this problem, I want to inform you about a curious fact.
Before trying your suggestion I am presently running a test:

equil SAM
 &cntrl
  imin=0,
  irest=0,
  ntx=1,
  nstlim=2500000, #test: 5 ns MD simulation in
a row
  dt=0.002,
  ntc=2,
  ntf=2,
  cut=8.0,
  ntb=2, #trick to have pressure shown
  ntp=1,
  taup=999999999999999999999999999,
  ntpr=10000,
  ntwx=10000,
  ntt=3,
  gamma_ln=2.0,
  temp0=300,
  ntr=1,
  ig=-1,
  iwrap=1,
 /
fix surface
10.0

RES 1 5445
END
END

END

What is really curious...is that it seems that the problem occurs only at
the restart (so if I divide this run into 1 ns consecutive steps)
Just to remind you...before with the very same parameters I obtained an
error passing from step 1 to step 2 (so between the 1sn ns to the 2nd).
But if I launch like in this case a single 5 ns long run...no error is
encountered!

At the present time I am at the 3rd ns of this simulation, and the
trajectory looks perfectly reasonable.
However, before saying "problem solved!" I will wait and try to launch a 50
ns long MD run (which is a bit uncomfortable in terms of trajectory
size)...but if it works...

Another test I can do is this:
Since the run finish the 1st run, but evidently some problem occurs in the
restart...I could load .mdcrd into chimera or VMD --> save a pdb --> create
a new .inpcrd with leap --> start a new run from scratch

Which is also a bit uncomfortable ad a sort a not "elegant" brute
trick...but again...if it works...
Waiting for your opinions about that.
Bye
g


Dr. Giovanni Maria Pavan

SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
Centro Galleria 2, Manno 6928, Switzerland.
e-mail: giovanni.pavan.supsi.ch
skype: giovanni_pavan
phone: +41 58 666 65 60

-----Messaggio originale-----
Da: Scott Le Grand [mailto:varelse2005.gmail.com]
Inviato: giovedì, 10. novembre 2011 01:17
A: giovanni.pavan.supsi.ch; AMBER Mailing List
Oggetto: Re: [AMBER] problem with pmemd.cuda

Try setting iwrap=0 in all your input files...

I am suspicious that molecules are getting wrapped but their constraints
aren't...


On Wed, Nov 9, 2011 at 1:07 AM, Giovanni Pavan
<giovanni.pavan.supsi.ch>wrote:

> Dear all,
>
> I am running a simulation on a single C2050 GPU.
>
> The system is quite unconventional and composed by 9 single strand
> DNAs attached with a short tiol onto a surface of gold
>
> The system is created in order to have an equal spacing between each
> ssDNA (also in terms of periodic images).
>
> To do so the water box is created with 0 buffer in X and Y directions,
> and with opportune spacing along Z.
>
>
>
> The system seems to pass successfully the heating to 300K
>
> After that, I run NVT MD simulation in order to maintain the box
> dimensions constant.
>
> The simulation is divided into 1ns stages and here the gold surface is
> restrained with ntr=1 and a constant of 10.0.
>
> The 1st part of simulation (1ns - but this is true independently on
> the length of each stage) passes without problems , but when it goes
> to step 2
>
> Starting from RST1 I obtain the following message:
>
>
>
> Error: unspecified launch failure launching kernel kReduceForces
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
>
>
>
> My input file is below. (# indicates a comment just to make it clear).
>
>
>
> equil SAM
>
> &cntrl
>
> imin=0,
>
> irest=0,
>
> ntx=1,
>
> nstlim=5000,
>
> dt=0.002,
>
> ntc=2,
>
> ntf=2,
>
> cut=8.0,
>
> ntb=2, #the run is actually an NVT,
>
> ntp=1, #this trick is used to monitor
>
> taup=999999999999999999999999999, #pressure and density
>
> ntpr=1000,
>
> ntwx=1000,
>
> ntt=3,
>
> gamma_ln=2.0,
>
> temp0=300,
>
> ntr=1,
>
> ig=-1,
>
> iwrap=1,
>
> ioutfm=1,
>
> /
>
> fix surface
>
> 10.0
>
>
> RES 1 5445
>
> END
>
> END
>
>
> END
>
>
>
> I need your help, since I don't understand if the problem is related
> to the system or to some problem with the GPU.
>
> (it seems more the 2nd case as from
> http://dev-archive.ambermd.org/201103/0019.html ).
>
> Maybe a problem due to a too short cutoff?
>
> I eagerly look forward to receive any comment from you.
>
> Best,
>
> Giovanni
>
>
>
> Dr. Giovanni Maria Pavan
>
>
>
> SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)
>
> Centro Galleria 2, Manno 6928, Switzerland.
>
> e-mail: giovanni.pavan.supsi.ch
>
> skype: giovanni_pavan
>
> phone: +41 58 666 65 60
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Nov 10 2011 - 01:30:03 PST
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