Hi Albert,
Use the serial version (pmemd.cuda) and see if that runs ok. GTX590's and
690's lack the PCI-E bandwidth to run successfully in parallel. With 2
GTX590s in your node I suggest running 4 independent jobs.
All the best
Ross
On 3/18/13 8:51 AM, "Albert" <mailmd2011.gmail.com> wrote:
>Hello:
>
> I am running NVT with following .in file by GPU acceleration
>
>heating gradually over 600ps
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=600000,dt=0.001,
> ntc=2,ntf=2,
> cut=9.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> tempi=0.0, temp0=300.0,
> restraintmask=':1-291 &!.H,WAT &.O',
> restraint_wt=6.0,
> iwrap=1,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=600000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
>
>
>with command:
>
>mpirun -n 2 pmemd.cuda.MPI -O -p sys.prmtop -c mini-05.rst7 -ref
>mini-05.rst7 -i nvt.in -o nvt.out -x nvt.trj -inf nvt.info -r nvt.rst7
>
>my jobs always stacked with following nvt.out log file after hours of
>running:
>
>
>
> 4. RESULTS
>--------------------------------------------------------------------------
>------
>
> ---------------------------------------------------
> 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. 2.39
>| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>| with 50.0 points per unit in tabled values
>| Relative Error Limit not exceeded for r .gt. 2.84
>|---------------------------------------------------
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS
>= 0.0
> Etot = -154386.9735 EKtot = 0.0000 EPtot =
>-154386.9735
> BOND = 151.7050 ANGLE = 751.2505 DIHED =
>4836.7085
> 1-4 NB = 954.6833 1-4 EEL = 12018.0185 VDWAALS =
>26886.9444
> EELEC = -199986.2836 EHBOND = 0.0000 RESTRAINT =
>0.0000
>
>--------------------------------------------------------------------------
>----
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>==========================================================================
>=====
>
>
>I don't observe any complain or errors in the job running. Does anyone
>have any advices? My workstation have two GTX590.
>
>thank you very much
>best
>Albert
>
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Received on Mon Mar 18 2013 - 09:30:04 PDT
