Hi,
The update to Amber12.21 does not work. I tried it in different ways but the errors are always the same (please find attached two examples of the scripts I tried and the error message I got).
I contacted the people in charge of the supercomputer we use, they did the update as follow:
"
# ./configure -cuda -mpi -intel
"
I even tried using:
module load cuda/5.5.22
module load intel/13.1
instead of:
module load cuda/4.2.9
module load intel/12.1 (as in the two scripts attached)
But it gives the same error.
Thanks in advance for your help.
Regards.
OZ
> Date: Thu, 14 Nov 2013 08:04:00 -0700
> Subject: Re: [AMBER] Temperature raises abnormally during accelerated MD
> From: daniel.r.roe.gmail.com
> To: roza2006.hotmail.fr
>
> Hi,
>
> On Wed, Nov 13, 2013 at 11:24 PM, O Z <roza2006.hotmail.fr> wrote:
> > The Amber update did not make any change. I decided to run my simulations
> > without using MPI (pmemd.cuda_SPDP instead of pmemd.cuda_SPDP.MPI), which
> > works the temperature is stable.
>
> Are you sure you are running with the updated code? This line:
>
> > module load amber/12.9
>
> Makes me think that you're running amber only up to bugfix 9. The
> current bugfix level is 21, and you need at least up to bugfix 19 to
> have the most recent CUDA code. Your code is not up to date unless you
> are seeing this in your MDOUT:
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 12.3.1
>
> -Dan
>
> >
> > mpirun -1sided -lsf -np 4 pmemd.cuda_SPDP -O -o MutPC_aMD_1-1_bis.out -i
> > mdrun_RandSeed.in -p Mut_Wat.parm7 -c MutPC_aMD_1-1.rst -ref
> > MutPC_aMD_1-1.rst -r MutPC_aMD_1-1_bis.rst -x MutPC_aMD_1-1_bis.mdcrd -amd
> > MutPC_aMD_1-1_bis.log
> >
> >
> >
> >
> >
> >
> >> Date: Tue, 5 Nov 2013 08:19:26 -0700
> >
> >> From: daniel.r.roe.gmail.com
> >> To: amber.ambermd.org
> >> Subject: Re: [AMBER] Temperature raises abnormally during accelerated MD
> >>
> >> Hi,
> >>
> >> I received your output files and I note that your problems appear to
> >> start when you start using pmemd.cuda.MPI with 2 nodes
> >> (WTPC_aMD_1-2.out), and that you are running an old version of the
> >> CUDA code (12.1), which is over a year out of date. There have been
> >> major improvements and fixes to the CUDA code since then; the current
> >> version is 12.3.1. Try updating your Amber installation by re-running
> >> configure and re-compiling, then restart the 'WTPC_aMD_1-2.out' run
> >> and see if the temperature jump still occurs.
> >>
> >> -Dan
> >>
> >>
> >> On Mon, Nov 4, 2013 at 12:41 AM, O Z <roza2006.hotmail.fr> wrote:
> >> > Dear Amber users,
> >> >
> >> > I have been running Accelerated MD on my system. I set up my aMD
> >> > parameters as explained on the Amber manual:
> >> >
> >> > from 10ns MD results (trajectory from 50 to 60 ns).
> >> >
> >> >
> >> >
> >> > ave Dihedral: 2095.80
> >> >
> >> >
> >> > ave EPtot: -194481.05
> >> >
> >> >
> >> > total atoms: 60616
> >> >
> >> >
> >> > protein residues: 199 (3.5*199=696.5)
> >> >
> >> >
> >> > AlphaD: 1/5 * 696.5 = 139.3
> >> >
> >> >
> >> > EthreshD: 696.5 + 2095 = 2791.5
> >> >
> >> >
> >> > alphaP: 60616 * (1/5) = 12123.2
> >> >
> >> >
> >> > EthresP: -194481.05 + 12123.2 = -191091.1
> >> >
> >> > I used these parameters as follow:
> >> >
> >> > &cntrl
> >> >
> >> >
> >> > imin=0,
> >> >
> >> >
> >> > ntx=5,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ntpr=25000, ntwx=25000, ntwe=25000, ntwprt=0,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ntf=2, ntb=2, cut=12.0, ntp=1, pres0=1.0, comp=44.6, taup=1.0,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > iwrap=1, nscm=250,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > nstlim=25000000, dt=0.002,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ntt=3, temp0=298.0, tautp=1.0, gamma_ln=3, ig=-1,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > ntc=2, irest=1,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > iamd=3,EthreshD=2791.5,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > alphaD=139.3,EthreshP=-191091.0549,
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > alphaP=12123.2
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > /
> >> >
> >> >
> >> > I am running aMD at 298K but in the output file I noticed
> >> > that the temperature raises a lot from 298K to about 320K (please see
> >> > file attached).
> >> >
> >> >
> >> > Is that due to the boost function? Or is it a normal behaviour, even if
> >> > I use the NPT ensemble?
> >> >
> >> > Many thanks for your help.
> >> > Regards.
> >> > OZ
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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Received on Thu Nov 21 2013 - 18:00:02 PST
