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Fixed bug with LJ pot-switch in 4xN kernels
2014-02-24
Berk Hess
Fixed bug with LJ pot-switch i
n
4xN
kernels
commit
|
commitdiff
|
tree
2014-02-19
B
er
k
Hess
Implemented nb
n
xn
L
J
swit
c
h
f
u
nctions
commit
|
commitdiff
|
tree
2014-01-30
Berk
H
ess
Made reference SIMD
wor
k
again
commit
|
commitdiff
|
tree
2014-01-29
Berk Hes
s
Au
t
omated Verl
e
t
r
list fo
r
N
V
E simulations
commit
|
commitdiff
|
tree
2013-12-03
Berk
H
e
ss
Remov
e
d r
e
st
r
ictio
n
o
f
one
r
e
f
erence
p
ul
l
group
commit
|
commitdiff
|
tree
2013-12-02
Be
r
k Hess
Made cutoff-scheme=Verlet the defau
l
t
commit
|
commitdiff
|
tree
2013-12-02
Berk Hess
Renamed verlet-buffer-drift to
v
erlet-buffer-to
l
erance
commit
|
commitdiff
|
tree
2013-12-01
Berk He
s
s
Fi
x
ed
z
ero hardw
a
re thread count
commit
|
commitdiff
|
tree
2013-11-29
B
e
rk He
s
s
Created SIM
D
module
commit
|
commitdiff
|
tree
2013-11-26
Ber
k
Hes
s
Fixed return v
a
lue of
gm
x
_mtop_bo
n
deds_
f
ree_ene
r
gy
commit
|
commitdiff
|
tree
2013-11-15
Berk
H
e
s
s
corr
e
c
ted potential nbn
x
n SIMD
m
e
mory issue
commit
|
commitdiff
|
tree
2013-11-08
Berk Hes
s
fix nbnxn atom so
r
t
ing with d
i
s
t
a
n
t bon
d
e
ds
commit
|
commitdiff
|
tree
2013-11-07
Berk Hess
corrected dy
n
a
m
i
c load balanci
n
g when sharing GPU
s
commit
|
commitdiff
|
tree
2013-11-05
B
e
r
k
Hess
G
P
U
d
etection
i
s done once
p
er physical node
commit
|
commitdiff
|
tree
2013-11-05
Berk H
e
ss
removed
(harmless) lef
t
-
o
ver in
nbnxn S
I
M
D kernels
commit
|
commitdiff
|
tree
2013-10-31
B
erk Hess
re
o
rgan
i
zed GPU detection and s
e
lection
commit
|
commitdiff
|
tree
2013-10-29
B
e
rk Hess
corrected v
o
lume with s
e
ria
l
NPT replica exchange
commit
|
commitdiff
|
tree
2013-10-28
B
e
rk He
s
s
improv
e
d
the nbn
x
n
buffer size estimate wit
h
GP
U
s
commit
|
commitdiff
|
tree
2013-10-22
Berk Hess
fixed re
c
ent
b
u
g with CU
D
A texture objects
commit
|
commitdiff
|
tree
2013-10-22
B
e
rk Hess
fixed OpenMP thr
e
ads being pinne
d
to the same cores
commit
|
commitdiff
|
tree
2013-10-16
Berk H
e
ss
a
v
oid division by
z
ero i
n
SIMD angles and dihedr
a
ls
commit
|
commitdiff
|
tree
2013-10-16
Berk Hess
fixed a
h
a
l
f bin mis
a
lignment in
gmx_vanhove
-
or
commit
|
commitdiff
|
tree
2013-10-11
Berk Hess
introduce
d
genera
l
4-wide SIMD support
commit
|
commitdiff
|
tree
2013-10-10
Be
r
k Hess
fixed nbnxn 4x8
p
air search without AV
X
commit
|
commitdiff
|
tree
2013-10-02
Be
r
k Hess
Fixes reaction field free
e
ne
r
gy bug
commit
|
commitdiff
|
tree
2013-09-24
B
erk Hess
opt
i
mized generic
S
IMD invsqrt
commit
|
commitdiff
|
tree
2013-09-21
Berk Hess
f
ixed multiple distance res
t
rai
n
ts w
i
th OpenMP
commit
|
commitdiff
|
tree
2013-09-18
Berk Hess
m
a
d
e free energy PME kernel
4
0
% fa
s
te
r
commit
|
commitdiff
|
tree
2013-09-16
B
e
rk Hess
mdrun
wi
t
hout OpenMP wit
h
thread-MPI now
u
s
es
all cores
commit
|
commitdiff
|
tree
2013-09-13
Berk Hess
co
r
rec
t
ed grompp con
s
traint/DOF w
a
r
n
ing with
v
s
ites
commit
|
commitdiff
|
tree
2013-08-25
B
e
rk Hess
i
ntroduced nbn
x
n data structur
e
for bou
n
d
i
ng boxes
commit
|
commitdiff
|
tree
2013-08-20
Berk Hess
fixed parallel normal modes
w
it
h
PM
E
commit
|
commitdiff
|
tree
2013-07-24
Berk Hess
implemented plain-C SIMD macros
f
or reference
commit
|
commitdiff
|
tree
2013-06-20
Be
r
k
Hess
fixed SD and BD
i
ntegrat
o
r OpenMP performance
commit
|
commitdiff
|
tree
2013-06-20
B
erk Hess
flops
tabl
e
now reports C
U
D
A
anal
y
t
ical Ewald
commit
|
commitdiff
|
tree
2013-06-14
Berk Hes
s
fixed minor
g
_bar output
issues
commit
|
commitdiff
|
tree
2013-06-05
Berk
H
e
ss
f
ixed DD i
n
ternal
s
tate
c
orru
p
t
ion
with en
e
r
gy minimization
commit
|
commitdiff
|
tree
2013-06-03
B
e
rk Hess
fixe
d
deadlock w
i
t
h replica e
x
chang
e
and -maxh
commit
|
commitdiff
|
tree
2013-05-08
Berk Hess
fixed
i
ncorre
c
t
scaling of cos-accele
r
ation visc
o
sity
commit
|
commitdiff
|
tree
2013-04-29
B
e
rk Hes
s
general SIMD acceleration
f
or angle
s
+dihedrals
commit
|
commitdiff
|
tree
2013-04-26
Berk Hes
s
PME load b
a
lancing now
check
s
f
o
r PME grid restrictions
commit
|
commitdiff
|
tree
2013-04-18
B
e
r
k Hess
changed mdrun -nstep
s
to
g
m
x_large_
i
nt_t
commit
|
commitdiff
|
tree
2013-04-12
Berk Hess
improve
d
load
balancing with
V
erl
e
t cut-off scheme
commit
|
commitdiff
|
tree
2013-03-27
Berk Hess
r
e
moved x86 s
p
ecifics from nbnxn
SIMD kernels
commit
|
commitdiff
|
tree
2013-03-27
B
e
rk Hess
corrected
lo
g
file wall
t
im
e
breakdown
commit
|
commitdiff
|
tree
2013-03-21
Ber
k
Hess
ma
d
e PME w
o
rk with a mix
of
1
and more t
h
r
e
ads
commit
|
commitdiff
|
tree
2013-03-14
Berk H
e
ss
co
r
r
e
c
t
ed grompp rvdw charge-gro
u
p r
a
dii chec
k
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
fixed bug wi
t
h DD cut-off check
a
nd P
M
E DLB
commit
|
commitdiff
|
tree
2013-03-05
Berk Hess
f
ixed
recen
t
bug w
i
th s
o
rting atom
s
for
GPU
s
commit
|
commitdiff
|
tree
2013-02-26
Berk Hess
fixed PME t
i
me print with -nt
o
m
p
_pme != -ntomp
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
ad
d
ed
mdrun check for
V
erlet
+
perturbed atoms
commit
|
commitdiff
|
tree
2013-02-20
Berk Hess
fixe
d
i
s
sues with FEP soft-core and
c
u
t-off's
commit
|
commitdiff
|
tree
2013-02-18
Berk
Hess
fixed GPU particle gr
i
dding
p
er
f
ormance issue
commit
|
commitdiff
|
tree
2013-02-15
Berk Hess
improv
e
d P
M
E
load balancing reporting
commit
|
commitdiff
|
tree
2013-02-06
Be
r
k
H
ess
f
i
xed bug with sd i
n
tegrato
r
and Op
e
n
MP th
r
eading
commit
|
commitdiff
|
tree
2013-02-05
Berk Hess
imp
r
oved
l
oad balancing
o
n
the GPU
commit
|
commitdiff
|
tree
2013-02-04
Berk
Hess
fixed segv in init
_
forcerec wit
h
f
r
->hwi
n
fo=NULL
commit
|
commitdiff
|
tree
2013-02-01
Berk He
s
s
PME
-
onl
y
counte
r
s
a
re now re
s
et with -m
a
xh -rese
t
hway
commit
|
commitdiff
|
tree
2013-01-18
Berk Hess
thread aff
i
nity n
o
w uses
s
ome top
o
logy information
commit
|
commitdiff
|
tree
2013-01-17
Berk H
e
s
s
fixed SD+BD in
t
egra
t
ion slowing
d
o
wn with OpenM
P
th
r
e
a
ds
commit
|
commitdiff
|
tree
2013-01-17
Berk
Hess
i
m
proved CUDA kernel pe
r
formance by pre-loading cj
commit
|
commitdiff
|
tree
2013-01-17
B
e
r
k
H
ess
f
ixed nb
n
x
n hybrid mode with
Ope
n
MP
commit
|
commitdiff
|
tree
2013-01-17
Berk
Hess
made
PME loa
d
balancing + DD
DLB more e
f
ficient
commit
|
commitdiff
|
tree
2013-01-16
Berk
H
es
s
split off p
i
c
k
_nbnxn_r
e
source from n
b
nxn_pick_nbnxn
commit
|
commitdiff
|
tree
2013-01-13
Berk Hes
s
fixed resetting states with parallel Ve
r
let scheme
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
pre
p
ared the nbnxn code
f
o
r non-x86 SI
M
D
commit
|
commitdiff
|
tree
2013-01-11
Be
r
k Hess
made SHA
K
E
w
ork again with particle decompostion
commit
|
commitdiff
|
tree
2013-01-10
Berk
H
ess
fixed n
b
nxn
no LJ comb
.
rule AVX256 PME kern
e
l
commit
|
commitdiff
|
tree
2013-01-10
Berk H
e
ss
f
ixed b
u
g
w
ith
V
erlet + DD +
b
onded atom comm
u
nic
a
tion
commit
|
commitdiff
|
tree
2013-01-07
Berk
Hess
fixed nbnx
n
AVX-256 Ewal
d
table
pointer alignment
commit
|
commitdiff
|
tree
2013-01-02
Berk Hess
minor
s
p
eed-up an
d
code cle
a
n-up in n
b
nxn kernels
commit
|
commitdiff
|
tree
2012-12-20
Berk Hess
fixed recent bu
g
s in LINCS f
o
r derivativ
e
s
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
renamed g
m
x
_
x86_
s
i
md_macro
s
.
h to g
m
x
_
simd_m
a
c
r
os
.
h
commit
|
commitdiff
|
tree
2012-12-18
Berk Hess
implemen
t
ed nbnxn AVX-256 2x(N+N) kernels
commit
|
commitdiff
|
tree
2012-12-11
Ber
k
Hess
re
d
uce
d
PLINCS communication with H-bond con
s
tra
i
nts
commit
|
commitdiff
|
tree
2012-12-07
Berk Hess
fixed
G
P
U
pair-sear
c
h w
i
t
h GMX_CP
U
_ACCELERATION=None
commit
|
commitdiff
|
tree
2012-12-06
Berk Hess
removed
last OpenMP
O
(nth
r
eads) bo
t
tleneck
commit
|
commitdiff
|
tree
2012-12-05
Ber
k
Hess
fixed incorrect v
i
rial with
virtual
s
ites
a
nd
O
p
e
nMP
commit
|
commitdiff
|
tree
2012-12-05
Berk Hess
f
i
xe
d
segv in Ver
l
et
pair-s
e
arch
w
ith
t
rilini
c
DD
commit
|
commitdiff
|
tree
2012-11-30
Berk Hess
fixed issue wi
t
h -
m
ul
t
i and GPUs
commit
|
commitdiff
|
tree
2012-11-28
Berk Hess
fixed threa
d
pinning
w
ith mdr
u
n
-
m
ulti
commit
|
commitdiff
|
tree
2012-11-28
Berk
H
e
ss
extended nbnxn
x
86
S
I
MD
kernel blendv s
u
ppo
r
t
commit
|
commitdiff
|
tree
2012-11-27
Berk Hess
fixe
d
bug
in
n
b
n
xn OpenMP non-bonde
d
force
reduct
i
on
commit
|
commitdiff
|
tree
2012-11-26
Berk Hes
s
made nbnxn analytical Ewa
l
d
consist
e
n
t
commit
|
commitdiff
|
tree
2012-11-26
Berk
Hess
added
nbnxn
an
a
lytical Ewald co
r
re
c
ti
o
n kernels
commit
|
commitdiff
|
tree
2012-11-16
Be
r
k
Hess
r
e
duced t
h
e cost
of
the nbnxn Ope
n
MP nb-fo
r
ce
r
educ
t
ion
commit
|
commitdiff
|
tree
2012-11-15
Be
r
k
Hess
fix
e
d incorre
c
t 1-4 energies with Op
e
nMP + e
n
ergy groups
commit
|
commitdiff
|
tree
2012-11-14
Be
r
k
H
ess
fi
x
ed
nbnxn x86 SIMD non-bonded perf
o
rma
n
c
e
regression
commit
|
commitdiff
|
tree
2012-11-12
Ber
k
He
s
s
nbnxn CPU
fo
r
ce buffer
r
eduction now us
e
s
SIMD
commit
|
commitdiff
|
tree
2012-11-06
B
e
rk Hess
Merge "A
d
d
opt
i
o
n to instal
l
l
i
bcudart
"
in
t
o releas
e
-4-6
commit
|
commitdiff
|
tree
2012-11-06
Berk
Hess
Merg
e
"don't execute any mpi_info/mpiname in the path
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk
Hes
s
Mer
g
e "updated
several things related with OpenMP
t
hread
.
.
.
commit
|
commitdiff
|
tree
2012-11-05
Berk Hess
updated several th
i
ng
s
related with Ope
n
MP
t
hread
count
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
fixed incorr
e
ct PM
E
load bal
a
ncing limitation
commit
|
commitdiff
|
tree
2012-10-26
Berk Hess
set the def
a
ult for nstd
h
dl to 1
0
0
commit
|
commitdiff
|
tree
2012-10-26
B
e
rk H
e
ss
f
i
xed
i
n
c
orrect g
r
oup energies wi
t
h nbnxn CPU kernels
commit
|
commitdiff
|
tree
2012-10-23
Berk Hess
fixed
bondfree
.
c thread
safety with free energy
commit
|
commitdiff
|
tree
2012-10-23
B
erk
H
ess
mo
v
ed part of nbnx
n
_
s
earch
.
c to nbnxn_atomdata
.
c
commit
|
commitdiff
|
tree
2012-10-23
B
erk He
s
s
fixed incorrect LJ energy w
i
th GPU
a
n
d
P
M
E
l
oad bala
n
cing
commit
|
commitdiff
|
tree
2012-10-22
Berk Hess
added
O
penMP parallelization fo
r
virtual
si
t
es
commit
|
commitdiff
|
tree
next