Dear developers,
I have compared the GPU performance of two different umbrella sampling methods in amber using AMBER18, fully updated. I observed low performance when turning on US via infe=1 and the &pmd - the output decreased form 20 ns/day to 6 ns/day (compared to infe=0). When applying the same restraint using nmropt=1, no decrease in performance was observed. Is this behavior correct/to be expected?
Cheers,
Åsmund
###### pmd #####
&cntrl
ig=-1
iwrap =1
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=10, ntb=1, ntp=0, tautp=10.0,
ntpr=500, ntwx=500, ntwr=1000,
ntt=1,
temp0=300.0,
tol=1.0e-8,jfastw=0,
infe=1,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
&pmd
output_file='pmd.dat'
output_freq=50
cv_file='cv.in'
/
NSTEP = 25500 TIME(PS) = 591.000 TEMP(K) = 300.71 PRESS = 0.0
Etot = -657462.4218 EKtot = 116350.1172 EPtot = -773812.5389
BOND = 1010.6757 ANGLE = 2714.6333 DIHED = 1961.8964
UB = 0.0000 IMP = 0.0000 CMAP = 263.6470
1-4 NB = 1232.4826 1-4 EEL = 15833.8706 VDWAALS = 113422.0802
EELEC = -910251.8367 EHBOND = 0.0000 RESTRAINT = 0.0119
EAMBER (non-restraint) = -773812.5509
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 250000 | Completed : 25500 | Remaining : 224500
|
| Average timings for last 2500 steps:
| Elapsed(s) = 66.90 Per Step(ms) = 26.76
| ns/day = 6.46 seconds/ns = 13379.64
|
| Average timings for all steps:
| Elapsed(s) = 681.80 Per Step(ms) = 26.74
| ns/day = 6.46 seconds/ns = 13368.59
##### nmropt ####
&cntrl
ig=-1
iwrap =1
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=10, ntb=1, ntp=0, tautp=10.0,
ntpr=500, ntwx=500, ntwr=1000,
ntt=1,
temp0=300.0,
tol=1.0e-8,jfastw=0,
nmropt=1,
/
&ewald
dsum_tol=1.0e-6,
order=4, skinnb=2.0, vdwmeth=1,
/
&wt
type='DUMPFREQ', istep1=50,
/
&wt type='END',
/
DISANG=disang.dat
DUMPAVE=distance.dat
NSTEP = 219000 TIME(PS) = 978.000 TEMP(K) = 299.62 PRESS = 0.0
Etot = -657369.7698 EKtot = 115927.8359 EPtot = -773297.6057
BOND = 1036.2415 ANGLE = 2707.2816 DIHED = 1990.8650
UB = 0.0000 IMP = 0.0000 CMAP = 255.2401
1-4 NB = 1235.2865 1-4 EEL = 15804.5869 VDWAALS = 112549.9441
EELEC = -908877.2922 EHBOND = 0.0000 RESTRAINT = 0.2408
EAMBER (non-restraint) = -773297.8465
NMR restraints: Bond = 0.241 Angle = 0.000 Torsion = 0.000
===============================================================================
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 250000 | Completed : 219000 | Remaining : 31000
|
| Average timings for last 9000 steps:
| Elapsed(s) = 60.40 Per Step(ms) = 6.71
| ns/day = 25.75 seconds/ns = 3355.59
|
| Average timings for all steps:
| Elapsed(s) = 1463.42 Per Step(ms) = 6.68
| ns/day = 25.86 seconds/ns = 3341.14
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Received on Tue Nov 05 2019 - 01:30:02 PST
