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Fixed nbnxn_4xN performance regression
2015-10-15
Berk Hess
Fi
x
ed nbnxn_4xN perf
o
rmance
regression
commit
|
commitdiff
|
tree
2015-10-07
Berk H
e
ss
Fix bu
g
s with intermol in
t
eraction
s
and DD
commit
|
commitdiff
|
tree
2015-09-15
Be
r
k
Hess
Det
e
ct incorrect cyc
l
e count
i
n
g
commit
|
commitdiff
|
tree
2015-08-14
B
e
rk Hess
Make
m
drun -nt work agai
n
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
F
i
x
t
o
o small GPU
pair coun
t
estimates
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix
b
ug in GPU
list balancin
g
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix D
D
DLB state i
s
sue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix bug in
GPU list balancin
g
commit
|
commitdiff
|
tree
2015-07-04
B
e
r
k Hess
Obey O
p
enMP threa
d
count
limit with
tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Fix two P
M
E DLB trigg
e
r
i
ssu
e
s
commit
|
commitdiff
|
tree
2015-07-03
B
e
rk Hess
Corr
e
ct grompp p
u
ll warning me
s
sage
commit
|
commitdiff
|
tree
2015-06-30
Be
r
k Hess
Fix inconsi
s
tent O
p
enMP aut
o
mation
commit
|
commitdiff
|
tree
2015-06-30
B
erk Hess
e
nabled 1 PP + 1 P
M
E node
commit
|
commitdiff
|
tree
2015-06-30
Berk H
e
s
s
Add
ch
e
cks f
o
r ine
f
ficient resou
r
ce u
s
age
commit
|
commitdiff
|
tree
2015-06-29
Berk Hess
Improve DLB
+
P
M
E tuni
n
g with GPUs
commit
|
commitdiff
|
tree
2015-06-27
Berk Hess
Improve pa
i
r se
a
r
c
h thread load
balance
commit
|
commitdiff
|
tree
2015-06-27
Berk
Hess
Improved
the intra-GPU load balan
c
ing
commit
|
commitdiff
|
tree
2015-06-27
B
e
rk Hess
Reduce the use of nb
n
xn_consts
.
h
commit
|
commitdiff
|
tree
2015-06-27
Ber
k
Hess
Corrected nstca
l
clr
/
nstfep/ns
t
_repl_
e
x checks
commit
|
commitdiff
|
tree
2015-06-26
Berk Hess
Fixed V
e
rlet buffe
r
i
s
sue wit
h
2-wide S
I
MD
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Int
e
r
m
o
l
ecu
l
a
r bond
e
d interaction suppo
r
t a
d
ded
commit
|
commitdiff
|
tree
2015-06-25
Berk Hess
Reenabled SIMD k
e
r
n
e
ls without cut
-
offs
commit
|
commitdiff
|
tree
2015-06-24
Berk He
s
s
GP
U
Ewald table kernel now
u
ses CPU spacing
commit
|
commitdiff
|
tree
2015-06-24
Berk
H
ess
Avoid GPU selection with GPU e
m
ulation
commit
|
commitdiff
|
tree
2015-06-24
Berk H
e
s
s
Minor reformatting of
S
I
MD
m
ismatch
m
e
ssage
commit
|
commitdiff
|
tree
2015-06-24
Berk Hess
Ad
d
sugar to print
e
mpty line i
n
printBinar
y
In
f
orm
a
tion
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Fix
g_ene
r
gy average/RMSD bug
commit
|
commitdiff
|
tree
2015-06-22
Berk Hess
Update
l
aunch configur
a
tion
f
or
p
hysical nodes
commit
|
commitdiff
|
tree
2015-06-22
B
e
rk Hess
Avoid fp exceptions in
p
air searc
h
d
ebug
commit
|
commitdiff
|
tree
2015-06-22
Be
r
k
H
ess
Replaced h
a
rdw
a
r
e
thr
e
ads by
l
o
g
i
c
al cores in ou
t
pu
t
commit
|
commitdiff
|
tree
2015-06-18
B
erk Hess
Reduced the c
o
st of the pul
l
c
o
mm
u
nication
commit
|
commitdiff
|
tree
2015-06-17
Berk H
e
ss
Refacto
r
ed pull data structure
s
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Added miss
i
ng DD cycle counting
commit
|
commitdiff
|
tree
2015-06-16
Berk Hess
Automated the -gpu_
i
d option
commit
|
commitdiff
|
tree
2015-06-14
Berk Hess
R
e
fac
t
ored mdrun r
e
sourc
e
d
i
vi
s
i
o
n
commit
|
commitdiff
|
tree
2015-06-13
Berk He
s
s
Hardware reportin
g
n
ow c
o
v
e
rs all nodes
commit
|
commitdiff
|
tree
2015-06-05
Berk Hess
Do
n
't
u
s
e PME r
a
nks w
i
th GPU
s
and
-npme=-1
commit
|
commitdiff
|
tree
2015-05-27
Berk Hess
Ref
a
ctoring of PME load b
a
lancin
g
commit
|
commitdiff
|
tree
2015-05-23
Berk Hes
s
R
emoved
static from variables in gmx_lapac
k
commit
|
commitdiff
|
tree
2015-05-16
B
erk Hess
LINC
S
thread task
s
can now be
i
ndependen
t
commit
|
commitdiff
|
tree
2015-05-13
Berk Hes
s
Fixe
d
CUDA error with empt
y
dom
a
i
n
s
commit
|
commitdiff
|
tree
2015-05-13
B
erk Hess
Fix
s
e
g
v in g_covar
commit
|
commitdiff
|
tree
2015-05-11
Berk Hess
Ch
a
nge
d
FFTW warning fr
o
m
AVX to no SSE
commit
|
commitdiff
|
tree
2015-05-07
Berk Hess
Remo
v
ed
n
on-ff at
o
mtypes fro
m
opls
a
a an
d
charmm27
commit
|
commitdiff
|
tree
2015-05-04
Berk Hess
Fix
e
d GPU
n
on-local F
c
opy local
c
onditional
commit
|
commitdiff
|
tree
2015-04-28
Berk Hess
Re-enabled FMA for AVX-1
2
8-
F
MA
commit
|
commitdiff
|
tree
2015-04-22
Berk Hess
M
erge branch 'release-5-0'
commit
|
commitdiff
|
tree
2015-04-17
Berk Hes
s
Add valu
e
_
ref an
d
value to pull_co
o
rd_t
commit
|
commitdiff
|
tree
2015-04-17
Berk Hess
C
orre
c
t -n
t
mpi auto for intel nehalem
a
n
d old
e
r
commit
|
commitdiff
|
tree
2015-04-08
Berk He
s
s
A
dde
d
pull geome
t
ry di
r
ectio
n
-
relative
commit
|
commitdiff
|
tree
2015-04-01
Berk He
s
s
Corrected
f
orce-switch manual section
commit
|
commitdiff
|
tree
2015-03-19
B
e
rk Hess
Removed redu
c
tion of dH/
d
l without FE
commit
|
commitdiff
|
tree
2015-03-12
Berk Hess
Fixed
m
drun fp
e
x
c
ep
t
ion with -debug
commit
|
commitdiff
|
tree
2015-03-11
Berk Hess
Added upda
t
e x copy-b
a
ck to update
t
imer
commit
|
commitdiff
|
tree
2015-03-11
Berk
H
ess
Reduced c
o
st
o
f Berendsen pressure coupling
commit
|
commitdiff
|
tree
2015-03-06
Be
r
k Hess
I
m
prove thread
i
n
g
o
f bondeds
commit
|
commitdiff
|
tree
2015-03-05
Be
r
k He
s
s
Made DD exclus
i
on
p
roces
s
ing mor
e
e
f
ficient
commit
|
commitdiff
|
tree
2015-03-05
Berk Hess
S
I
MD ac
c
eleration for LINCS
commit
|
commitdiff
|
tree
2015-03-04
Berk Hess
Allow
p
u
ll groups of 1 atom w
i
th mass 0
commit
|
commitdiff
|
tree
2015-03-04
Berk He
s
s
COM pullin
g
options
p
er coord,
impr
o
ve
d
cylinder
commit
|
commitdiff
|
tree
2015-03-03
Berk Hess
Fix div
b
y zero in
P
P/PME ratio
commit
|
commitdiff
|
tree
2015-03-02
Berk H
e
ss
Added paren
t
hese
s
for c
a
sts in
SIM
D
macros
commit
|
commitdiff
|
tree
2015-02-24
B
erk
Hess
Fixed p
a
rallel d
i
strib
u
tion a
n
d
thr
e
ad c
o
unt reportin
g
commit
|
commitdiff
|
tree
2015-02-12
Berk Hess
Re-fixe
d
PME b
u
g with hi
g
h
O
p
e
nMP thr
e
a
d
c
ount
commit
|
commitdiff
|
tree
2015-02-06
Berk Hess
Re-
e
nabled
SIMD f
o
r angles and
d
i
hedr
a
ls
commit
|
commitdiff
|
tree
2015-02-04
Berk Hess
Correct
C
UD
A
kernel energy flag
commit
|
commitdiff
|
tree
2015-01-21
Berk Hess
Corrected RDT
S
CP war
n
ing te
x
t
commit
|
commitdiff
|
tree
2015-01-15
Berk Hess
F
i
x allocation issue with VV integrator
commit
|
commitdiff
|
tree
2014-12-22
B
er
k
Hess
Fixed p
b
c=xy + 2
w
a
l
l
s
+
Verlet sche
m
e
commit
|
commitdiff
|
tree
2014-12-22
Berk Hess
Fix bug FE +
G
PU + 2/3
D
domain decomposition
commit
|
commitdiff
|
tree
2014-12-11
Berk Hess
A
d
ded grompp er
r
or for pulling to ne
g
ative
d
istance
commit
|
commitdiff
|
tree
2014-12-09
Berk Hess
Fi
x
recent bug
with trilinic 1D DD
commit
|
commitdiff
|
tree
2014-12-08
Ber
k
Hess
Fixed pull
coord init wi
t
h r
a
te!=0,
t_s
t
art!=0
commit
|
commitdiff
|
tree
2014-12-08
Berk Hess
Added PBC n
o
te to comm-mo
d
e=angular warning
commit
|
commitdiff
|
tree
2014-12-05
Berk He
s
s
Make
d
omd
e
c
a
prop
e
r
modul
e
commit
|
commitdiff
|
tree
2014-12-05
Be
r
k Hess
Clarif
i
ed grompp pull erro
r
messag
e
s
commit
|
commitdiff
|
tree
2014-12-05
Berk Hess
A
v
oid rac
e
on
d
vdl
with Verlet+
O
penMP+LINCS
+
FE+VV
commit
|
commitdiff
|
tree
2014-12-01
Berk Hess
Added warning for un
n
ecess
a
ry soft-core
commit
|
commitdiff
|
tree
2014-11-26
Berk Hes
s
Fix
e
d triclinic 1xNx1 domain decompos
i
tion
commit
|
commitdiff
|
tree
2014-11-25
Berk
H
ess
Fixed twin
-
range +
freeze
+
const
r
a
ints
commit
|
commitdiff
|
tree
2014-11-24
Berk Hess
Av
o
id NaN in
r
l
ist buffer calculation
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Co
r
rec
t
e
d parameter for sorting on search g
r
id
commit
|
commitdiff
|
tree
2014-11-12
Berk Hess
Fix D
D
bonded
i
nteraction range print
commit
|
commitdiff
|
tree
2014-10-20
Berk Hess
Remove
d
f_no
v
irsum reduction in Verlet schem
e
commit
|
commitdiff
|
tree
2014-10-07
Berk
Hess
F
ixes is
s
u
e
w
ith vsiten
a
nd Verl
e
t
buffe
r
s
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Avoid DLB with
o
verlo
a
ded PME ra
n
ks
commit
|
commitdiff
|
tree
2014-09-30
Berk Hess
Added GPU local wai
t
to load balan
c
ing
commit
|
commitdiff
|
tree
2014-09-29
B
erk Hess
Domai
n
de
c
ompo
s
ition no
w
checks the
r
list bu
f
fer
commit
|
commitdiff
|
tree
2014-09-29
Be
r
k
Hess
SIM
D
a
cc
e
l
erat
i
on for
RB dihedr
a
ls
commit
|
commitdiff
|
tree
2014-09-29
Be
r
k Hess
Av
o
id
P
ME tuning decreas
i
ng rcoulomb
commit
|
commitdiff
|
tree
2014-09-29
Berk
H
es
s
Fix calc_grid avoiding
P
ME g
r
id fac
t
or 84
commit
|
commitdiff
|
tree
2014-09-09
Berk
Hess
Fixe
d
DD state collec
t
ion is
s
u
e
commit
|
commitdiff
|
tree
2014-09-08
Berk
H
e
s
s
C
heck for implicit solvent
+
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-28
Berk Hess
Fix
e
d two
P
ME
issues with MPI+OpenMP
commit
|
commitdiff
|
tree
2014-08-25
Berk Hess
Fixed
b
ugs in vsiteN with OpenMP
commit
|
commitdiff
|
tree
2014-08-24
Berk
Hess
Initialize unused velocity cons
t
raint components
commit
|
commitdiff
|
tree
2014-08-17
Berk Hess
Hal
v
ed th
e
cost
o
f the
p
ull comm
u
nic
a
t
i
on
commit
|
commitdiff
|
tree
2014-08-14
Berk Hess
Corrected SIMD ma
t
h
o
ve
r
flow doc
u
m
ent
a
ti
o
n
commit
|
commitdiff
|
tree
2014-08-10
B
erk Hess
Added check
s
fo
r
TPI
+
Verlet scheme
commit
|
commitdiff
|
tree
2014-08-05
Berk He
s
s
F
ix
h
ang with LJ-PME and
empty domain
s
commit
|
commitdiff
|
tree
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