Ross,
Still getting the same output as before. I am going to pull down Amber11
and
recompile with the new code. The new release looks great! Going to put
both
of my gpu's to work in my GTX295. Still trying to find a 470 or 480 online
but
they are all sold out.
Cheers,
~Levi
On Mon, Apr 26, 2010 at 12:36 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Levi,
>
> This is fixed in AMBER 11 now. For your copy try locating the following
> loop
> in cuda/gpu.cpp:
>
> for (int i = gpu->sim.atoms; i < gpu->sim.stride; i++)
> {
> gpu->pbAtom->_pSysData[i] = 99999999000.0
> + i * 1000.0;
> gpu->pbAtom->_pSysData[i + gpu->sim.stride] = 99999999000.0
> + i * 1000.0;
> gpu->pbAtom->_pSysData[i + gpu->sim.stride2] = 99999999000.0
> + i * 1000.0;
> gpu->pbAtomXYSP->_pSysData[i].x = 99999999000.0f
> + i * 1000.0;
> gpu->pbAtomXYSP->_pSysData[i].y = 99999999000.0f
> + i * 1000.0;
> gpu->pbAtomZSP->_pSysData[i] = 99999999000.0f
> + i * 1000.0;
> }
>
> and change it to:
>
> for (int i = gpu->sim.atoms; i < gpu->sim.stride; i++)
> {
> gpu->pbAtom->_pSysData[i] = 999999000.0 +
> i * 200.0;
> gpu->pbAtom->_pSysData[i + gpu->sim.stride] = 999999000.0 +
> i * 200.0;
> gpu->pbAtom->_pSysData[i + gpu->sim.stride2] = 999999000.0 +
> i * 200.0;
> gpu->pbAtomXYSP->_pSysData[i].x = 999999000.0f +
> i * 200.0;
> gpu->pbAtomXYSP->_pSysData[i].y = 999999000.0f +
> i * 200.0;
> gpu->pbAtomZSP->_pSysData[i] = 999999000.0f +
> i * 200.0;
> }
>
> See if that works.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Levi Pierce
> > Sent: Saturday, April 24, 2010 7:05 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] pmemd.cuda problem
> >
> > Ross,
> >
> > I gave nscm=0 a try and same result.
> >
> > NSTEP = 1000 TIME(PS) = 419.000 TEMP(K) = 312.76 PRESS =
> > 0.0
> > Etot = ************** EKtot = 300.8112 EPtot =
> > **************
> > BOND = 80.7068 ANGLE = 182.6906 DIHED =
> > 292.4277
> > 1-4 NB = 85.6465 1-4 EEL = 1165.3455 VDWAALS =
> > **************
> > EELEC = ************** EGB = -448.5671 RESTRAINT =
> > 0.0000
> >
> > Attached are my prmtop and the rst file. This was my input
> >
> > > CYC MD
> > > &cntrl
> > > imin=0,irest=1,ntx=5,
> > > nstlim=25000000,dt=0.002,ntb=0,
> > > tempi=300, temp0=300,
> > > ntf=2,ntc=2,tol=0.000001,
> > > ntpr=1000, ntwx=1000, ntwr=1000,
> > > cut=9999.0, rgbmax=15.0,gbsa=0,
> > > igb=5,ntt=3,nscm=1000,gamma_ln = 1.0
> > > /
> >
> >
> > Thanks
> > ~Levi
> >
> > On Sat, Apr 24, 2010 at 6:43 PM, Ross Walker <ross.rosswalker.co.uk>
> > wrote:
> >
> > > Hi Levi,
> > >
> > > > I have been running pmemd.cuda on several different
> > > > small peptide systems. After minimization and equilibration
> > > > with sander I run md with pmemd.cuda which produces the
> > > > following output in the mdinfo file:
> > > >
> > > > NSTEP = 1000 TIME(PS) = 419.000 TEMP(K) = 312.76
> > PRESS =
> > > > 0.0
> > > > Etot = ************** EKtot = 300.8112 EPtot =
> > > > **************
> > > > BOND = 80.7068 ANGLE = 182.6906 DIHED =
> > > > 292.4277
> > > > 1-4 NB = 85.6465 1-4 EEL = 1165.3455 VDWAALS =
> > > > **************
> > > > EELEC = ************** EGB = -448.5671 RESTRAINT =
> > > > 0.0000
> > >
> > > > CYC MD
> > > > &cntrl
> > > > imin=0,irest=1,ntx=5,
> > > > nstlim=25000000,dt=0.002,ntb=0,
> > > > tempi=300, temp0=300,
> > > > ntf=2,ntc=2,tol=0.000001,
> > > > ntpr=1000, ntwx=1000, ntwr=1000,
> > > > cut=9999.0, rgbmax=15.0,gbsa=0,
> > > > igb=5,ntt=3,nscm=1000,gamma_ln = 1.0
> > > > /
> > >
> > > Can you try this with nscm=0 and see if that works?
> > >
> > > Additionally can you send me your input files so I can try this with
> > the
> > > AMBER 11 code.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery,
> > may not
> > > be read every day, and should not be used for urgent or sensitive
> > issues.
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
>
>
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Received on Mon Apr 26 2010 - 09:30:03 PDT
