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Some overview content for Doxygen documentation.
2013-10-22
Be
r
k He
s
s
fixed OpenMP thread
s
bei
n
g
pinned
t
o
the same cores
commit
|
commitdiff
|
tree
2013-10-16
Berk
H
es
s
avoid division by z
e
ro in SIM
D
angles a
n
d dihedrals
commit
|
commitdiff
|
tree
2013-10-16
B
e
r
k He
s
s
fixed a hal
f
b
i
n misalignment in
g
m
x_vanhove
-
or
commit
|
commitdiff
|
tree
2013-10-11
Berk Hess
i
n
tro
d
uced general
4
-wide SIMD
suppo
r
t
commit
|
commitdiff
|
tree
2013-10-10
Berk
H
e
s
s
fixed
n
b
nxn
4
x8 p
a
i
r search without AVX
commit
|
commitdiff
|
tree
2013-10-02
B
e
rk Hess
Fixes reaction fie
l
d
f
r
e
e energy bug
commit
|
commitdiff
|
tree
2013-09-24
Berk H
e
ss
optimized generic
S
IMD invs
q
rt
commit
|
commitdiff
|
tree
2013-09-21
B
erk Hess
fixed multiple
distance restraint
s
w
ith
O
pen
M
P
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
made free energy PM
E
k
e
rnel
4
0%
faster
commit
|
commitdiff
|
tree
2013-09-16
Berk Hess
mdru
n
witho
u
t OpenMP
w
i
t
h
t
h
rea
d
-MPI now u
s
es all c
o
res
commit
|
commitdiff
|
tree
2013-09-13
Be
r
k Hess
corrected grompp constraint/DOF
w
arning with vs
i
tes
commit
|
commitdiff
|
tree
2013-08-25
Berk Hess
introd
u
ce
d
nbnxn data str
u
cture
f
or
b
o
unding
boxes
commit
|
commitdiff
|
tree
2013-08-20
Ber
k
Hes
s
fi
x
ed parallel normal
m
o
des with P
M
E
commit
|
commitdiff
|
tree
2013-07-24
Berk
Hess
imp
l
emented pl
a
in-C SIMD
ma
c
ros for referenc
e
commit
|
commitdiff
|
tree
2013-06-20
Ber
k
H
e
s
s
fixed SD and
BD
i
nte
g
r
a
t
o
r O
p
enM
P
performanc
e
commit
|
commitdiff
|
tree
2013-06-20
Berk Hess
f
lop
s
ta
b
le now report
s
CUDA analytical Ewald
commit
|
commitdiff
|
tree
2013-06-14
B
erk He
s
s
fi
x
ed
minor g
_
bar output issues
commit
|
commitdiff
|
tree
2013-06-05
Berk Hess
fix
e
d DD
i
nternal state corruption with energy mi
n
imizati
o
n
commit
|
commitdiff
|
tree
2013-06-03
Berk Hess
fixed
d
ea
d
lock
w
ith rep
l
i
ca exchange
a
nd -maxh
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
f
i
xed
i
ncorre
c
t
scaling of cos-acce
l
eratio
n
viscosity
commit
|
commitdiff
|
tree
2013-04-29
B
e
rk Hess
ge
n
era
l
SIMD acceleration for angles+dih
e
drals
commit
|
commitdiff
|
tree
2013-04-26
Berk Hess
PME load b
a
lancing
now checks f
o
r PME grid restrict
i
on
s
commit
|
commitdiff
|
tree
2013-04-18
Berk He
s
s
changed md
r
un -nsteps to gmx_large_i
n
t
_t
commit
|
commitdiff
|
tree
2013-04-12
Berk Hes
s
improved
l
oad
b
a
lanci
n
g
with Verlet cut-of
f
scheme
commit
|
commitdiff
|
tree
2013-03-27
Be
r
k
H
e
ss
r
emoved x8
6
spec
i
f
ics fro
m
nbn
x
n SIM
D
k
e
rnels
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
corrected log file wal
l
time bre
a
k
down
commit
|
commitdiff
|
tree
2013-03-21
Berk Hess
ma
d
e
P
M
E work with a
mix of 1
a
nd
more thread
s
commit
|
commitdiff
|
tree
2013-03-14
Berk Hess
c
o
r
re
c
ted gr
o
m
pp rvd
w
charge-gr
o
up
r
a
dii check
commit
|
commitdiff
|
tree
2013-03-05
Berk
H
e
ss
f
i
xed bug with DD
c
ut-
o
ff check and PME DLB
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fixed recent
b
ug wit
h
sorti
n
g
a
t
oms
f
or GPUs
commit
|
commitdiff
|
tree
2013-02-26
B
e
rk Hess
fixed
PME t
i
me prin
t
w
ith
-ntom
p
_
p
me != -ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
a
d
d
ed md
r
un check for Verlet
+
perturbed at
o
m
s
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
fixed
i
ssu
e
s wi
t
h FEP s
o
f
t
-core and cut-off'
s
commit
|
commitdiff
|
tree
2013-02-18
Berk Hess
fix
e
d
G
PU p
a
r
ticl
e
gridding perform
a
n
ce issue
commit
|
commitdiff
|
tree
2013-02-15
Berk Hess
i
m
prove
d
PME load balancing re
p
o
r
t
i
n
g
commit
|
commitdiff
|
tree
2013-02-06
Berk Hess
fixe
d
b
u
g
w
ith sd integrator and OpenMP
t
hr
e
adin
g
commit
|
commitdiff
|
tree
2013-02-05
Berk Hess
i
mproved
lo
a
d bala
n
cin
g
o
n the GPU
commit
|
commitdiff
|
tree
2013-02-04
Berk
Hess
fixed segv in
i
n
i
t_forcerec w
i
th
f
r->hwinfo=NULL
commit
|
commitdiff
|
tree
2013-02-01
Berk Hess
PME-onl
y
cou
n
t
ers a
r
e now r
e
s
e
t with
-
maxh -resethway
commit
|
commitdiff
|
tree
2013-01-18
Berk Hess
thread affinity now
u
ses some to
p
ology inform
a
t
io
n
commit
|
commitdiff
|
tree
2013-01-17
Berk
H
ess
f
i
xed SD+BD int
e
gration
slowing d
o
wn with
Ope
n
MP
t
hreads
commit
|
commitdiff
|
tree
2013-01-17
Berk He
s
s
imp
r
oved CUDA kernel performance by p
r
e-
l
oadin
g
cj
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixed nbnxn hybrid mode
with
O
penMP
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
made PME lo
a
d balancing + D
D
D
L
B more
efficien
t
commit
|
commitdiff
|
tree
2013-01-16
Berk
H
ess
split of
f
pick_n
b
nx
n
_res
o
u
rce from nb
n
x
n
_pick_n
b
n
x
n
commit
|
commitdiff
|
tree
2013-01-13
Berk
Hess
fixed resettin
g
s
t
a
t
es wit
h
parallel Ver
l
et schem
e
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
p
r
epared the nbnxn code
f
or non-x86 SIMD
commit
|
commitdiff
|
tree
2013-01-11
Berk Hess
made SHAKE work
a
g
ain with
p
article dec
o
mpostion
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fixed nb
n
xn
n
o LJ co
m
b
.
rule AV
X
256 PME
k
ernel
commit
|
commitdiff
|
tree
2013-01-10
Berk Hess
fixed bug
w
it
h
Verlet
+ DD +
b
onded
atom comm
u
nication
commit
|
commitdiff
|
tree
2013-01-07
B
er
k
Hess
fixed
nbnxn AVX-
2
5
6 Ewald table pointe
r
alignm
e
nt
commit
|
commitdiff
|
tree
2013-01-02
Berk Hess
minor spee
d
-
u
p and code cl
e
an-up in nbnxn
kernel
s
commit
|
commitdiff
|
tree
2012-12-20
Berk Hess
fixed rece
n
t
b
ugs
i
n
L
I
NC
S
for derivatives
commit
|
commitdiff
|
tree
2012-12-18
Berk H
e
s
s
r
enamed
gmx_x86_simd_macros
.
h to gmx_s
i
md_macr
o
s
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
imp
l
em
e
nted n
b
nxn AVX-2
5
6 2x
(
N+N)
ke
r
nels
commit
|
commitdiff
|
tree
2012-12-11
Berk
Hess
reduced PLINCS comm
u
nication wit
h
H-bond constraints
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fixed GPU
pair-se
a
r
c
h
wit
h
GM
X
_CPU
_
ACCELE
R
A
T
IO
N
=Non
e
commit
|
commitdiff
|
tree
2012-12-06
Berk
H
ess
remove
d
last OpenMP O(nthreads)
bottleneck
commit
|
commitdiff
|
tree
2012-12-05
Be
r
k Hess
fixed inc
o
r
r
e
c
t vi
r
ial
with vi
r
tual sites
and O
p
enMP
commit
|
commitdiff
|
tree
2012-12-05
Be
r
k Hes
s
fixed
segv
in Verlet pair-search
w
ith trilini
c
D
D
commit
|
commitdiff
|
tree
2012-11-30
B
e
rk Hess
fix
e
d issue
w
ith -mu
l
t
i
and
GPUs
commit
|
commitdiff
|
tree
2012-11-28
B
e
rk Hess
f
i
x
ed thread p
i
nning
w
i
th mdrun -multi
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
e
xtended nbnxn x86 SI
M
D k
e
r
n
e
l
blendv support
commit
|
commitdiff
|
tree
2012-11-27
Berk Hess
f
i
x
ed bug in nbnxn OpenMP non-
b
onded for
c
e reduction
commit
|
commitdiff
|
tree
2012-11-26
Ber
k
H
e
ss
made nbn
x
n
a
n
aly
t
ical Ewald c
o
nsistent
commit
|
commitdiff
|
tree
2012-11-26
Ber
k
H
ess
add
e
d nbnxn analytic
a
l
E
w
ald co
r
re
c
tion ke
r
n
e
ls
commit
|
commitdiff
|
tree
2012-11-16
B
erk He
s
s
r
e
duced the c
o
st of the nbnxn OpenMP nb-force red
u
ction
commit
|
commitdiff
|
tree
2012-11-15
Berk Hess
fix
e
d incorrect
1-4 energies with
OpenMP + ener
g
y groups
commit
|
commitdiff
|
tree
2012-11-14
Berk Hess
f
ixed nbnxn x86 SIMD
n
o
n-bonded p
e
rfo
r
mance
r
egression
commit
|
commitdiff
|
tree
2012-11-12
B
e
rk Hess
nbnxn C
P
U fo
r
ce buffe
r
reduction now
u
se
s
S
I
M
D
commit
|
commitdiff
|
tree
2012-11-06
Berk Hes
s
Merge "Add option to
i
ns
t
a
ll libcudart" i
n
t
o release-4-6
commit
|
commitdiff
|
tree
2012-11-06
Ber
k
H
es
s
Merg
e
"don't execute any mpi
_
i
n
fo
/
mpin
a
me in t
h
e pat
h
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Ber
k
Hess
M
erge "updated several things related wit
h
OpenMP threa
d
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
updated
several things
r
elated
w
it
h
O
p
enMP th
r
e
a
d count
commit
|
commitdiff
|
tree
2012-10-26
B
er
k
H
e
s
s
fixed incorrect PME load balancin
g
limit
a
t
i
o
n
commit
|
commitdiff
|
tree
2012-10-26
B
e
r
k
He
s
s
set the
d
e
f
ault for nstdhdl to 1
0
0
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
f
ixed i
n
correct g
r
oup energ
i
es with nbnxn CPU kernels
commit
|
commitdiff
|
tree
2012-10-23
Berk Hess
f
ixed
b
ondfree
.
c th
r
ead safety wit
h
free energy
commit
|
commitdiff
|
tree
2012-10-23
Ber
k
Hess
m
o
ve
d
p
a
rt of n
b
nxn_search
.
c
t
o nbnxn_atomdata
.
c
commit
|
commitdiff
|
tree
2012-10-23
Berk Hess
fix
e
d incorrect LJ en
e
rgy with GPU and
PME load balancin
g
commit
|
commitdiff
|
tree
2012-10-22
Berk Hess
added OpenMP para
l
lel
i
za
t
i
o
n
for virtual sites
commit
|
commitdiff
|
tree
2012-10-18
Ber
k
Hess
re
n
amed
c
o
nstra
i
nt
variables rm
d
r to vir_r_m_dr
commit
|
commitdiff
|
tree
2012-10-18
Berk Hess
added OpenM
P
parallelizati
o
n to
L
IN
C
S
projection
commit
|
commitdiff
|
tree
2012-10-17
Berk H
e
ss
renamed pme_switch
.
.
.
to pme_loadba
l
.
.
.
commit
|
commitdiff
|
tree
2012-10-16
Berk Hess
m
a
de p
a
ir-search
wit
h
G
P
U
2
0% fa
s
te
r
commit
|
commitdiff
|
tree
2012-10-12
Berk Hess
Merge
"Fix illeg
a
l
b
arrier in worksharing" into r
e
lease-4-6
commit
|
commitdiff
|
tree
2012-10-08
B
e
rk Hess
made
n
on-bonded potential shifts mdp options
commit
|
commitdiff
|
tree
2012-10-04
Berk Hess
fixed
b
ackwa
r
d compa
t
ibility of tpr
f
iles
with
d
ihres
commit
|
commitdiff
|
tree
2012-10-03
Ber
k
He
s
s
imp
r
oved t
h
e energy conservation with SETTLE
commit
|
commitdiff
|
tree
2012-09-13
Berk H
e
s
s
fix
e
d recent bug with grompp check
for
P-R P
-
coupling
commit
|
commitdiff
|
tree
2012-08-29
Berk
H
ess
bug fix for pme
.
c
M
PI_CO
M
M_NU
L
L fi
x
dcf
8
b67e
commit
|
commitdiff
|
tree
2012-08-09
Berk
H
ess
fi
x
ed
t
rjcon
v
not
w
r
i
ting velocities with cpt input
commit
|
commitdiff
|
tree
2012-08-06
Berk
H
ess
fixed incorrect TPI results w
i
th dynamic box
commit
|
commitdiff
|
tree
2012-07-18
Ber
k
Hes
s
fixed DD c
h
arg
e
gro
u
p
displ
a
c
e
ment
e
rror check
commit
|
commitdiff
|
tree
2012-07-17
Berk Hess
fix a
segfau
l
t in sse_mask_
i
n
it
commit
|
commitdiff
|
tree
2012-07-04
Berk Hess
set default f
o
r rcoulomb, rvdw and rlist to -1
commit
|
commitdiff
|
tree
2012-06-25
B
erk Hes
s
fix
e
d segv
/
hang with EM and foreign lambda
v
alues
commit
|
commitdiff
|
tree
2012-06-25
B
erk Hes
s
ad
d
ed chec
k
for l
o
g
f
p!=NULL
wh
e
n
d
isabl
i
ng ac
c
eleratio
n
commit
|
commitdiff
|
tree
2012-05-24
Berk Hess
n
ow mdr
u
n alway
s
ini
t
ia
l
ize
s
MPI
commit
|
commitdiff
|
tree
2012-05-21
B
erk H
e
ss
grompp now retai
n
s the order of bon
d
s converted
to
.
.
.
commit
|
commitdiff
|
tree
next