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Update pair-list buffer manual
2016-01-28
Ber
k
Hess
Update pair-list buffer
m
a
nual
commit
|
commitdiff
|
tree
2016-01-24
Ber
k
H
ess
Fix ex
a
ct continuatio
n
from non-energy steps
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
Fix energy file contin
u
at
i
on with md-vv
commit
|
commitdiff
|
tree
2016-01-24
Berk Hess
F
ix energy
aver
a
g
e
w
ith
c
ontinuation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
Fix PME load balancing ski
p
p
i
ng a
s
et
u
p
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Cor
r
ect vector check of gmx c
h
ec
k
commit
|
commitdiff
|
tree
2015-12-19
B
erk Hess
Bring performance estimation
up to date
commit
|
commitdiff
|
tree
2015-12-11
B
e
rk Hess
Fix bug with pu
l
l group
w
eights
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
R
emoved mdrun fatal_er
r
or wi
t
h P3M-AD
commit
|
commitdiff
|
tree
2015-11-09
B
e
rk Hess
Correct LINCS d
H
dl contribution
commit
|
commitdiff
|
tree
2015-11-02
Ber
k
Hess
F
i
x int
e
rmolec
u
la
r
in
t
eractions wit
h
small
mols
commit
|
commitdiff
|
tree
2015-10-15
Berk
H
ess
Fixed nbnxn_4
x
N p
e
rfor
m
ance regression
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
F
ix bugs
wit
h
inte
r
mol inte
r
actions
and DD
commit
|
commitdiff
|
tree
2015-09-15
Berk H
e
ss
Detect incorrect cyc
l
e c
o
u
n
ting
commit
|
commitdiff
|
tree
2015-08-14
Berk Hess
Make mdru
n
-nt wo
r
k agai
n
commit
|
commitdiff
|
tree
2015-07-06
B
erk
Hess
Fix too small GPU pair
cou
n
t estimates
commit
|
commitdiff
|
tree
2015-07-06
B
e
rk Hess
Fix bug in GPU list balancing
commit
|
commitdiff
|
tree
2015-07-05
Be
r
k
H
e
ss
Fix
D
D DLB
stat
e
issue
commit
|
commitdiff
|
tree
2015-07-05
B
e
rk He
s
s
Fix bug in
G
P
U list
b
alancing
commit
|
commitdiff
|
tree
2015-07-04
Be
r
k
Hess
Obey O
p
enMP t
h
read
cou
n
t limit with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix two PME DL
B
t
r
igger issues
commit
|
commitdiff
|
tree
2015-07-03
Be
r
k
Hess
Correc
t
g
r
o
mpp pull warning messa
g
e
commit
|
commitdiff
|
tree
2015-06-30
B
erk Hess
Fix inco
n
sistent Ope
n
MP
a
utomation
commit
|
commitdiff
|
tree
2015-06-30
Berk
H
ess
en
a
ble
d
1 PP + 1
PME node
commit
|
commitdiff
|
tree
2015-06-30
Berk Hess
Add
c
hecks for inefficien
t
resource usage
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
Im
p
rove DLB+PME tuning
w
ith GPUs
commit
|
commitdiff
|
tree
2015-06-27
Ber
k
Hess
Improve
p
air s
e
arch thread load bala
n
ce
commit
|
commitdiff
|
tree
2015-06-27
B
erk
Hess
Improved the
i
ntra-GPU load balancing
commit
|
commitdiff
|
tree
2015-06-27
B
er
k
H
ess
Reduce the use of nbnxn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
C
orrected nstcalc
l
r/nstfep/nst_
r
epl_ex ch
e
cks
commit
|
commitdiff
|
tree
2015-06-26
Berk Hes
s
Fixed Verlet
buff
e
r
issue wi
t
h 2-w
i
de SIMD
commit
|
commitdiff
|
tree
2015-06-25
B
erk Hess
Int
e
rmolecu
l
a
r
b
onded interaction
s
upport ad
d
ed
commit
|
commitdiff
|
tree
2015-06-25
Ber
k
Hess
R
e
enab
l
e
d
S
IMD kernel
s
without cut-offs
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
GPU E
w
ald tabl
e
kerne
l
now
u
ses CPU spaci
n
g
commit
|
commitdiff
|
tree
2015-06-24
B
er
k
Hess
Avoid
GPU s
e
lection with GPU emulation
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Mino
r
r
eformatting
of SIMD mis
m
at
c
h message
commit
|
commitdiff
|
tree
2015-06-24
Berk Hes
s
A
dd sug
a
r to print e
m
pty line in prin
t
BinaryInformation
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix g_ener
g
y averag
e
/R
M
SD bu
g
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
U
pda
t
e launc
h
configuration f
o
r physical node
s
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Avoid
f
p excep
t
ions in pair
sear
c
h
debu
g
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
R
e
pl
a
ced hardw
a
re threads by l
o
gical cores in outpu
t
commit
|
commitdiff
|
tree
2015-06-18
Berk Hess
Reduced the cost of t
h
e pull communication
commit
|
commitdiff
|
tree
2015-06-17
B
erk He
s
s
Refactor
e
d pull dat
a
structures
commit
|
commitdiff
|
tree
2015-06-16
B
e
rk
H
e
s
s
Added mis
s
ing
D
D cycl
e
countin
g
commit
|
commitdiff
|
tree
2015-06-16
B
e
r
k H
e
ss
Auto
m
ate
d
t
he
-
gpu_
i
d
option
commit
|
commitdiff
|
tree
2015-06-14
B
erk
He
s
s
Refac
t
ored mdrun reso
u
r
c
e div
i
sio
n
commit
|
commitdiff
|
tree
2015-06-13
Be
r
k Hess
Hardware rep
o
rting now cover
s
all nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk
Hess
Don
'
t
us
e
PME ranks
with
G
PUs an
d
-npm
e
=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Ref
a
ctoring of PME loa
d
balancing
commit
|
commitdiff
|
tree
2015-05-23
Be
r
k
H
ess
Removed
s
tatic from variables in gmx_la
p
ack
commit
|
commitdiff
|
tree
2015-05-16
B
e
rk Hess
LINCS th
r
e
a
d
tas
k
s can now
be independent
commit
|
commitdiff
|
tree
2015-05-13
B
erk Hess
Fixe
d
C
U
DA
e
rror with empty domains
commit
|
commitdiff
|
tree
2015-05-13
Ber
k
He
s
s
Fix segv in g_cova
r
commit
|
commitdiff
|
tree
2015-05-11
Berk Hes
s
C
h
a
n
g
ed
F
FTW warnin
g
f
rom
A
V
X
to no
SSE
commit
|
commitdiff
|
tree
2015-05-07
B
erk
H
ess
Remove
d
no
n
-ff atom
t
y
p
es from oplsaa
a
nd charmm27
commit
|
commitdiff
|
tree
2015-05-04
B
e
rk
Hess
Fix
e
d GPU non-l
o
ca
l
F cop
y
loc
a
l conditional
commit
|
commitdiff
|
tree
2015-04-28
Berk
H
ess
Re-enabled FMA for AVX-12
8
-
FMA
commit
|
commitdiff
|
tree
2015-04-22
B
e
rk Hess
Merge branch 're
l
eas
e
-5-
0
'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Add val
u
e_re
f
a
n
d
v
alue to pull_coord_t
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
Correct -nt
m
pi a
u
to for intel n
e
halem and older
commit
|
commitdiff
|
tree
2015-04-08
Berk Hess
Added pull geometry directi
o
n-
r
elati
v
e
commit
|
commitdiff
|
tree
2015-04-01
Berk Hess
Corrected force
-
switch manual se
c
ti
o
n
commit
|
commitdiff
|
tree
2015-03-19
Berk Hess
Rem
o
ved reduction of
d
H/d
l
without
F
E
commit
|
commitdiff
|
tree
2015-03-12
Berk Hess
Fi
x
ed mdrun fp exception
w
ith -de
b
ug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Added update x
copy-bac
k
to update timer
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Reduced cost
o
f Be
r
endsen pressur
e
coupling
commit
|
commitdiff
|
tree
2015-03-06
B
e
rk Hess
Improv
e
threadin
g
of
bondeds
commit
|
commitdiff
|
tree
2015-03-05
B
e
rk
H
e
ss
Ma
d
e
DD exclusion processing more e
f
f
icient
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
SIMD acce
l
eration for L
I
N
C
S
commit
|
commitdiff
|
tree
2015-03-04
Berk
H
ess
Al
l
o
w
pu
l
l groups of 1 at
o
m
with mas
s
0
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
COM pulling opt
i
ons per coord, imp
r
oved cylinder
commit
|
commitdiff
|
tree
2015-03-03
Berk Hess
Fix div
b
y zero in PP/PM
E
rat
i
o
commit
|
commitdiff
|
tree
2015-03-02
Berk
H
ess
Added parentheses for c
a
sts in SIMD macros
commit
|
commitdiff
|
tree
2015-02-24
Be
r
k
H
e
s
s
F
ixed parall
e
l
d
istributio
n
a
nd
t
h
r
ead cou
n
t reporting
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-fixed PME b
u
g
w
ith h
i
gh OpenMP
thread count
commit
|
commitdiff
|
tree
2015-02-06
Berk
H
e
ss
Re-ena
b
led SIMD f
o
r ang
l
es and di
h
edrals
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Correc
t
C
U
D
A kernel energy flag
commit
|
commitdiff
|
tree
2015-01-21
B
erk
Hess
Corrected RDTSCP warning text
commit
|
commitdiff
|
tree
2015-01-15
B
erk Hess
Fix allocat
i
on is
s
u
e
w
i
th VV
i
nt
e
g
rat
o
r
commit
|
commitdiff
|
tree
2014-12-22
B
e
rk H
e
ss
Fixe
d
pbc=x
y
+
2 wa
l
ls + Verlet scheme
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fix
bug F
E
+
G
PU + 2
/
3D dom
a
in decomposition
commit
|
commitdiff
|
tree
2014-12-11
Berk Hess
Added
g
ro
m
pp error
for
p
ulling
t
o negative
distance
commit
|
commitdiff
|
tree
2014-12-09
Berk H
e
ss
Fix r
e
cent bug with t
r
ilinic 1D D
D
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Fixed p
u
ll
c
oord init
w
ith rate!=0, t_star
t
!
=
0
commit
|
commitdiff
|
tree
2014-12-08
Ber
k
Hess
Added
P
B
C note to comm-m
o
de=angul
a
r warning
commit
|
commitdiff
|
tree
2014-12-05
B
e
rk Hess
Make dom
d
ec
a
proper mo
d
ule
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
Clarified grom
p
p pul
l
err
o
r messa
g
e
s
commit
|
commitdiff
|
tree
2014-12-05
Be
r
k Hes
s
Avoi
d
race on dvdl with
Verlet+OpenMP
+
LINC
S
+
FE+VV
commit
|
commitdiff
|
tree
2014-12-01
B
e
rk Hess
Added warning for unnecessa
r
y soft-core
commit
|
commitdiff
|
tree
2014-11-26
B
erk H
e
ss
Fix
e
d triclinic 1xNx1 d
o
main deco
m
position
commit
|
commitdiff
|
tree
2014-11-25
Berk Hess
Fixed twin-rang
e
+ freeze + const
r
a
ints
commit
|
commitdiff
|
tree
2014-11-24
Berk H
e
ss
Avoi
d
NaN
i
n
rlist
buf
f
e
r
calc
u
lation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Correcte
d
p
a
rameter f
o
r
s
o
r
t
i
ng on search
grid
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
F
i
x
DD bon
d
ed
i
nteraction range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Remove
d
f_
n
ovirsum red
u
ct
i
on in V
e
rle
t
scheme
commit
|
commitdiff
|
tree
2014-10-07
Berk Hess
Fixes is
s
ue
with vsi
t
en and V
e
rlet bu
f
fers
commit
|
commitdiff
|
tree
2014-09-30
Berk
Hess
Avoid
D
LB with ove
r
loaded PM
E
ranks
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Ad
d
ed G
P
U local w
a
it to load b
a
lanci
n
g
commit
|
commitdiff
|
tree
2014-09-29
Be
r
k Hess
Do
m
ain decompo
s
ition no
w
chec
k
s the rlis
t
b
uffe
r
commit
|
commitdiff
|
tree
2014-09-29
Ber
k
Hess
S
I
MD acc
e
ler
a
t
i
o
n for R
B
dihed
r
als
commit
|
commitdiff
|
tree
next