Dear Ross,
Thank you for your advices. They re-installed the updates and now I am running my simulations using only "module load amber/12.21" instead of:
"module load cuda/5.5.22
module load intel/13.1
module load amber/12.21"
and it works perfectly fine.
Thanks again,
All the best
OZ
> Date: Thu, 21 Nov 2013 18:05:08 -0800
> From: ross.rosswalker.co.uk
> To: amber.ambermd.org
> Subject: Re: [AMBER] Temperature raises abnormally during accelerated MD
>
> Hi Oz,
>
> Can you verify that it did indeed update properly - as in you now see
> version 12.3.1 in your mdout file.
>
> Also can you try the GNU compilers please. We are investigating issues
> with a potential race condition triggered by the intel compilers right now
> and they make no difference to the performance of the GPU code anyway. I'd
> also suggest trying just the single GPU (if you've got 4 GPUs in a node
> it's better to run 4 runs from different random seeds and get more
> sampling) than it is to run a single 4 GPU job.
>
> All the best
> Ross
>
>
> On 11/21/13 5:29 PM, "O Z" <roza2006.hotmail.fr> wrote:
>
> >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
> >
> >
> >
> >
> >
> ># make install
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >With intel/13.1 and cuda/5.5.22 loaded. And it installs just fine.
> >"
> >
> >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)
> > _______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Dec 04 2013 - 17:30:02 PST
