HTの効果が現れない場合

同じくポリエチレンの重合度466の鎖一本を伸び切った状態で真空中で分子動力学計算した．計算時間は5psと長くしてある．並列化の効率が低下しているが，これは相互作用が鎖に沿って２次元的であるためだろう．物理４コアまでは計算時間は短くなっているが，hyperthreadingのある５〜８では寧ろ物理４コアより計算時間が遅くなっている．相互作用が２次元的な場合には，スレッド数は物理コア数までとするのがよいようだ．こうした系では，物理８コアの方が，hypethreadingで論理８コアとするよりも遥かに計算時間は短縮出来る．

Core i7とAthlon X2との比較

core i7とHyperthreadingの効果(2)

ポリエチレン１本鎖，重合度466

他の計算条件はcore i7とHyperthreadingの効果(1)とほぼ同じ．

ほぼ同じ原子数，密度であるが，連結されたことにより，計算時間が約３倍掛かっている．スレッド数に対する計算速度の向上の度合いは，（１）の場合と同程度．物理コア４＋論理コア１の５スレッドでは一旦計算速度が低下するが，６～８スレッドで計算速度が向上するのも同じ現象．

８スレッドで，物理コア６個程度の計算速度になる．

Core i7とHyperthreadingの効果(1)

Core i7をMaterials Studio 4.3でベンチマークテストした．

【系】butane 100分子，密度〜0.8cm-3，Amorphous Cellで充填

【CPU】Core i7 940 2.93 GHz, 4 core

【計算法】MD,  NVT, 0.1ps, 298K

【力場】compass

スレッド数の逆数に対して，CPU timeをプロットした．

物理コア数と同じスレッド数４までは順調に伸びているが，スレッド５では４よりも速度が落ちる（グラフで跳ね上がっているところ）．複数回実行しても同じ結果になった．スレッド６〜８は，物理コア並みの速度アップである．スレッド８で論理コア数８と同じになる．この時の速度は実質物理コア６程度ではないかと思われる．無機物や分子集合系のシミュレーションでは，コア数の効果は大きく，hyperthreadingも効く様である．

物理４コアまでの直線を外挿すると，物理６コアで3.60 s，物理８コアで2.97 sとなった．

#BIOSYM btcl 3
#
# Input File For Discover Generated By Materials Studio
# Input Client Model Document: C:Documents and SettingssasakiMy DocumentsMaterials Studio ProjectsUntitled0109 FilesDocuments3D Atomistic.xsd
# Job: [MTG9C] - 3D Atomistic Disco Min
#
autoEcho off
#
# Begin Forcefield Section
begin forcefield = compass

# File setup
set file [open energy_table.out w]

# Nonbond section:
forcefield nonbond
-separate_coulomb
vdw
summation_method = atom_based
cutoff = 9.50
spline_width = 1.00
buffer_width = 0.50
coulomb
dielectric_value = 1.0

# End Forcefield Section
#

# Minimization Section: All-trans
minimize
method = newton
iteration_limit = 5000
sd
convergence = 1000.0000000
line_search_precision = 0.5000000
cg
convergence = 10.0000000
line_search_precision = 0.5000000
method = fletcher
newton
convergence = 0.1000000
line_search_precision = 0.5000000
max_atoms = 200
method = bfgs

set energyValue_all_trans [energy]

#set restraint
restraint create rst1 torsion cn

restraint scale rst1 1000

#increment
$k = 1

for {$i = 0} {$i < 360.1} {incr i $k} {

molGeom set torsion $i cn
restraint target rst1 $i

# Minimization Section:
minimize
method = newton
iteration_limit = 5000
sd
convergence = 1000.0000000
line_search_precision = 0.5000000
cg
convergence = 10.0000000
line_search_precision = 0.5000000
method = fletcher
newton
convergence = 0.1000000
line_search_precision = 0.5000000
max_atoms = 200
method = bfgs

set energyValue [energy]

molGeom get torsion phi cn

#cc

$delta_E = $energyValue - $energyValue_all_trans
puts $file "[format "%5i%12.5f" $i $delta_E] [object phi]"

#
# Write coordinate file:
}

#BIOSYM btcl 3
#
#  Input File For Discover Generated By Materials Studio
#  Input Client Model Document: C:Documents and SettingssasakiMy DocumentsMaterials Studio ProjectsUntitled0109 FilesDocuments3D Atomistic.xsd
#  Job: [MTG9C] - 3D Atomistic Disco Min
#
  autoEcho off
#
# Begin Forcefield Section
  begin forcefield = compass

# File setup
      set file [open energy_table.out w]

# Nonbond section:
  forcefield nonbond
      -separate_coulomb
    vdw
    summation_method = atom_based
      cutoff = 9.50
      spline_width = 1.00
      buffer_width = 0.50
    coulomb
    dielectric_value = 1.0

# End Forcefield Section
#

# Minimization Section: All-trans
  minimize
    method = newton
    iteration_limit = 5000
         sd
            convergence = 1000.0000000
            line_search_precision = 0.5000000
         cg
            convergence = 10.0000000
            line_search_precision = 0.5000000
            method = fletcher
         newton
            convergence = 0.1000000
            line_search_precision = 0.5000000
            max_atoms = 200
            method = bfgs

        set energyValue_all_trans [energy]

#set restraint
   restraint create rst1 torsion cn
   restraint create rst2 torsion cc
 restraint scale rst1 1000
 restraint scale rst2 1000

#increment
$k = 5

       for {$i = 0+$k} {$i < 361-$k} {incr i $k} {
 for  {$j = 0+$k } {$j < 361-$k} {incr j $k}  {

   molGeom set torsion $i cn
     molGeom set torsion $j cc

   restraint target rst1 $i
   restraint target rst2 $j

# Minimization Section:
  minimize
    method = newton
    iteration_limit = 5000
         sd
            convergence = 1000.0000000
            line_search_precision = 0.5000000
         cg
            convergence = 10.0000000
            line_search_precision = 0.5000000
            method = fletcher
         newton
            convergence = 0.1000000
            line_search_precision = 0.5000000
            max_atoms = 200
            method = bfgs

        set energyValue [energy]

    molGeom get torsion phi cn
 molGeom get torsion psi cc
#cc

 $delta_E = $energyValue - $energyValue_all_trans
        puts $file "[format "%5i%5i%12.5f" $i $j  $delta_E]   [object phi]   [object psi]"

#
# Write coordinate file:
}
puts $file ""
}

#!/gnuplot
#
#
# G N U P L O T
# Version 4.2 patchlevel 2
# last modified 31 Aug 2007
# System: MS-Windows 32 bit
#
# Copyright (C) 1986 - 1993, 1998, 2004, 2007
# Thomas Williams, Colin Kelley and many others
#
# Type `help` to access the on-line reference manual.
# The gnuplot FAQ is available from http://www.gnuplot.info/faq/
#
# Send bug reports and suggestions to <http://sourceforge.net/projects/gnuplot>
#
# set terminal windows color noenhanced font "Arial, 10"
# set output 'PAA35map'
unset clip points
set clip one
unset clip two
set bar 1.000000
set border 31 front linetype -1 linewidth 1.000
set xdata
set ydata
set zdata
set x2data
set y2data
set timefmt x "%d/%m/%y,%H:%M"
set timefmt y "%d/%m/%y,%H:%M"
set timefmt z "%d/%m/%y,%H:%M"
set timefmt x2 "%d/%m/%y,%H:%M"
set timefmt y2 "%d/%m/%y,%H:%M"
set timefmt cb "%d/%m/%y,%H:%M"
set boxwidth
set style fill empty border
set style rectangle back fc lt -3 fillstyle solid 1.00 border -1
set dgrid3d 10,10, 1
set dummy x,y
set format x "% g"
set format y ""
set format x2 "% g"
set format y2 "% g"
set format z ""
set format cb "% g"
set angles radians
set grid nopolar
set grid xtics nomxtics ytics nomytics noztics nomztics
nox2tics nomx2tics noy2tics nomy2tics nocbtics nomcbtics
set grid layerdefault linetype 0 linewidth 1.000, linetype 0 linewidth 1.000
set key title "energy map"
unset key
unset label
unset arrow
set style increment default
unset style line
unset style arrow
set style histogram clustered gap 2 title offset character 0, 0, 0
unset logscale
set offsets 0, 0, 0, 0
set pointsize 1
set encoding default
unset polar
unset parametric
unset decimalsign
set view map
set samples 100, 100
set isosamples 10, 10
unset surface
set contour base
set clabel '%8.3g'
set mapping cartesian
set datafile separator whitespace
unset hidden3d
set cntrparam order 4
set cntrparam bspline
set cntrparam levels incremental 0.5,0.5,2.5
set cntrparam points 30
set size ratio 0 1,1
set origin 0,0
set style data points
set style function lines
set xzeroaxis linetype -2 linewidth 1.000
set yzeroaxis linetype -2 linewidth 1.000
set zzeroaxis linetype -2 linewidth 1.000
set x2zeroaxis linetype -2 linewidth 1.000
set y2zeroaxis linetype -2 linewidth 1.000
set ticslevel 0.5
set mxtics default
set mytics default
set mztics default
set mx2tics default
set my2tics default
set mcbtics default
set xtics border in scale 1,0.5 mirror norotate offset character 0, 0, 0
set xtics 0.000000,60,360.000
set ytics border in scale 1,0.5 mirror norotate offset character 0, 0, 0
set ytics 0.000000,60,360.000
set ztics border in scale 1,0.5 nomirror norotate offset character 0, 0, 0
set ztics autofreq
set nox2tics
set noy2tics
set cbtics border in scale 1,0.5 mirror norotate offset character 0, 0, 0
set cbtics autofreq
set title ""
set title offset character 0, 0, 0 font "" norotate
set timestamp bottom
set timestamp ""
set timestamp offset character 0, 0, 0 font "" norotate
set rrange [ * : * ] noreverse nowriteback # (currently [0.000000:10.0000] )
set trange [ * : * ] noreverse nowriteback # (currently [-5.00000:5.00000] )
set urange [ * : * ] noreverse nowriteback # (currently [-5.00000:5.00000] )
set vrange [ * : * ] noreverse nowriteback # (currently [-5.00000:5.00000] )
set xlabel "psi"
set xlabel offset character 0, 0, 0 font "" textcolor lt -1 norotate
set x2label ""
set x2label offset character 0, 0, 0 font "" textcolor lt -1 norotate
set xrange [ * : * ] noreverse nowriteback # (currently [1.00000:10.0000] )
set x2range [ * : * ] noreverse nowriteback # (currently [-10.0000:10.0000] )
set ylabel "phi"
set ylabel offset character 0, 0, 0 font "" textcolor lt -1 rotate by 90
set y2label ""
set y2label offset character 0, 0, 0 font "" textcolor lt -1 rotate by 90
set yrange [ * : * ] noreverse nowriteback # (currently [-10.0000:10.0000] )
set y2range [ * : * ] noreverse nowriteback # (currently [-10.0000:10.0000] )
set zlabel ""
set zlabel offset character 0, 0, 0 font "" textcolor lt -1 norotate
set zrange [ * : * ] noreverse nowriteback # (currently [-10.0000:10.0000] )
set cblabel ""
set cblabel offset character 0, 0, 0 font "" textcolor lt -1 norotate
set cbrange [ * : * ] noreverse nowriteback # (currently [-10.0000:10.0000] )
set zero 1e-008
set lmargin -1
set bmargin -1
set rmargin -1
set tmargin -1
set locale "C"
set pm3d explicit at b
set pm3d scansautomatic
set pm3d interpolate 1,1 flush begin noftriangles nohidden3d corners2color mean
set palette positive nops_allcF maxcolors 0 gamma 1.5 color model RGB
set palette rgbformulae 7, 5, 15
set colorbox default
set colorbox vertical origin screen 0.9, 0.2, 0 size screen 0.05, 0.6, 0 bdefault
set loadpath
set fontpath
set fit noerrorvariables
GNUTERM = "win"
splot 'C:Documents and SettingsnkimuraMy DocumentsダウンロードPAA35.txt' using 1:2:3 with lines
# EOF