I don't think so, because it works well before....
On 07/16/2012 07:56 PM, Scott Le Grand wrote:
> 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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>>
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Received on Mon Jul 16 2012 - 11:30:02 PDT
