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 - 10:00:03 PDT
