OpenMPI by any chance? If so, switch to mvapich...
On Mon, Jul 16, 2012 at 9:42 AM, Albert <mailmd2011.gmail.com> wrote:
> Dear all:
> I've got a workstation with two GTX590 GPU and I've installed Amber
> 12 on it with ICC. I've do the test for CPU MPI running and it goes
> well. Recently, I found that the GPU jobs always stack there, however
> when it run with CPU with the same parameters, it goes well.
>
>
> /mpiexec -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -p apo.prmtop -c m6.rst
> -ref m6.rst -i npt1.in <http://npt1.in> -o npt1.out -r npt1.rst -x
> npt1.mdcrd -inf npt1.info <http://npt1.info>/
> /
> /
> /equilibration/
> / &cntrl/
> / imin=0, irest=0, ntx=1,/
> / nstlim=500000, dt=0.002,/
> / ntc=2, ntf=2,/
> / cut=10.0, /
> / ntb=2, ntp=3, taup=2.0, pres0=1,/
> / ntpr=5000, ntwx=5000, ntwr=50000,/
> / ntt=3, gamma_ln=1.0, ig=-1,/
> / iwrap=1,/
> / temp0=310.0,/
> / csurften=3, ninterface=2, gamma_ten=17,/
> / restraintmask='1-396 &!.H',/
> / restraint_wt=20,/
> / //
>
>
>
>
> however, I found that the npt1.out and npt1.info <http://npt1.info>
> stacked there after several hours of running: (it stucked at 1000 step)
>
>
> /
> /
> / ---------------------------------------------------/
> / APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION/
> / using 5000.0 points per unit in tabled values/
> / TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff/
> /| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500/
> /| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960/
> / ---------------------------------------------------/
> /|---------------------------------------------------/
> /| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION/
> /| with 50.0 points per unit in tabled values/
> /| Relative Error Limit not exceeded for r .gt. 2.33/
> /| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION/
> /| with 50.0 points per unit in tabled values/
> /| Relative Error Limit not exceeded for r .gt. 2.80/
> /|---------------------------------------------------/
> /
> /
> / NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> -4453.3/
> / Etot = -148181.3735 EKtot = 0.0000 EPtot =
> -148181.3735/
> / BOND = 193.2917 ANGLE = 1516.4845 DIHED =
> 5083.5499/
> / 1-4 NB = 2024.1678 1-4 EEL = 2370.5920 VDWAALS =
> 13450.3264/
> / EELEC = -172819.7858 EHBOND = 0.0000 RESTRAINT =
> 0.0000/
> / EKCMT = 0.0000 VIRIAL = 42217.2697 VOLUME =
> 439069.1196/
> /SURFTEN = 0.0000/
> /Density = 1.0017/
> /
> ------------------------------------------------------------------------------
>
> /
>
> Does anybody have any idea what happen?
> THX
> Albert
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Received on Mon Jul 16 2012 - 11:00:02 PDT
