Which MPI are you using? OpenMPI is notorious for just *locking up* like
this...
On Mon, Mar 18, 2013 at 9:17 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
