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Add nbnxn pair-list rebalancing
2016-06-22
Berk
H
e
ss
A
dd nbnxn
pai
r
-l
i
st reb
a
lancing
commit
|
commitdiff
|
tree
2016-06-22
Berk He
s
s
Remove OpenMP
overhead at hi
g
h p
a
ralleli
z
a
t
ion
commit
|
commitdiff
|
tree
2016-06-22
Berk Hes
s
C
o
rrect GPU
p
air estimate fo
r
list splitting
commit
|
commitdiff
|
tree
2016-06-19
B
e
rk Hess
Remov
e
war
n
ings on che
c
kpoint m
i
s
m
atch
commit
|
commitdiff
|
tree
2016-06-17
Berk
H
e
s
s
Remove std::th
r
e
a
d:
:
hardware_concurrency(
)
commit
|
commitdiff
|
tree
2016-06-14
B
erk
H
es
s
F
i
x
O
penCL e
r
ror with empty
domains
commit
|
commitdiff
|
tree
2016-06-13
B
erk Hess
H
andle constraint
errors w
i
th EM
commit
|
commitdiff
|
tree
2016-06-07
Ber
k
Hess
Fix data race in hwinfo with thread-MPI
commit
|
commitdiff
|
tree
2016-06-03
B
e
rk
Hess
Handle partial
l
y fr
o
ze
n
and cons
t
ra
i
ned atoms
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Re
p
o
s
i
t
ion nbnxn filler particles
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Avoid numerical
o
ver
f
low wit
h
overlapping atom
s
commit
|
commitdiff
|
tree
2016-05-31
Berk Hes
s
A
dd ch
e
ck for fini
t
e energies
commit
|
commitdiff
|
tree
2016-05-30
Berk Hess
A
d
d
grompp che
c
k
f
or
unb
o
und atom
s
commit
|
commitdiff
|
tree
2016-05-23
Ber
k
Hess
Fix
b
u
g
in v-rescale the
r
m
o
sta
t
&
repl
i
ca exchange
commit
|
commitdiff
|
tree
2016-05-10
B
e
r
k
Hess
O
p
tim
i
zed
t
h
e
vsite threading
commit
|
commitdiff
|
tree
2016-05-10
Berk He
s
s
Fix CUD
A
shmem
b
ug
commit
|
commitdiff
|
tree
2016-05-10
Be
r
k Hess
Support cmap
with QMMM
commit
|
commitdiff
|
tree
2016-05-08
Be
r
k
Hess
Update mdrun te
r
mination
i
nfo
commit
|
commitdiff
|
tree
2016-05-06
Berk He
s
s
OpenMP pa
r
al
l
elizatio
n
for pul
l
commit
|
commitdiff
|
tree
2016-04-20
Berk Hess
Fix pull
l
e
gend with external potential
commit
|
commitdiff
|
tree
2016-04-19
Berk He
s
s
A
l
low
r
c
oul
o
mb>r
v
dw with P
M
E
commit
|
commitdiff
|
tree
2016-04-19
B
erk He
s
s
Broa
d
cast pull
external pote
n
t
ial
p
rovider s
t
ring
commit
|
commitdiff
|
tree
2016-04-19
B
e
r
k
H
ess
Fix gmx hb
o
nd grou
p
overlap check
commit
|
commitdiff
|
tree
2016-04-14
B
erk
H
es
s
Add QMMM che
c
ks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
C
orrect nrdf for 1D/2
D
syste
m
s
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix
i
ncludes in readp
u
l
l
.
cp
p
commit
|
commitdiff
|
tree
2016-03-31
B
erk H
e
ss
A
d
d
o
ption for external pull
p
ot
e
ntial
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
C
o
rrect mdrun
t
MPI
(
n
on-)
p
arallel er
r
or messa
g
e
commit
|
commitdiff
|
tree
2016-03-26
B
e
r
k
Hess
Add real/SIMD template for LJ
-
14
pair
s
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Avoi
d
assert
i
on failure
i
n
pme_loadbal_do
commit
|
commitdiff
|
tree
2016-03-22
Ber
k
He
s
s
M
a
k
e gmx vanhove work w
i
th
o
ut P
B
C
commit
|
commitdiff
|
tree
2016-03-22
Berk Hes
s
LJ combi
n
ation r
u
le kernels f
o
r CUDA
commit
|
commitdiff
|
tree
2016-03-21
B
e
rk
H
ess
Moved pull initialization b
a
ck
to
m
drunner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hess
Fi
x
non-normalization of FF
T
auto
c
orr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove restriction on dihd
r
altypes orde
r
commit
|
commitdiff
|
tree
2016-03-12
Berk Hes
s
Sp
l
it
o
ff Fermi kernel from CUDA
ke
r
nel
commit
|
commitdiff
|
tree
2016-03-09
Berk Hes
s
Fi
x
Ewald
3DC dipole with Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk Hess
Con
v
erted cse
t
tle() to use real/S
i
mdReal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
se SIMD transpose scatter in bondeds
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
U
se rvec
4
for listed force buffer
commit
|
commitdiff
|
tree
2016-02-27
B
erk Hess
Remove epsfac from GPU kern
e
l inner-loops
commit
|
commitdiff
|
tree
2016-02-27
B
e
rk Hess
Minor code re
o
rdering in GPU k
e
rnels
commit
|
commitdiff
|
tree
2016-02-26
Berk
He
s
s
Fix compilation
w
ith Simd4
F
loat, without S
i
md4Doub
l
e
commit
|
commitdiff
|
tree
2016-02-19
B
e
r
k
H
es
s
F
i
x
excessive lis
t
splitting
commit
|
commitdiff
|
tree
2016-02-17
Berk Hess
Renamed n
b
nxn static co
n
st
ints
commit
|
commitdiff
|
tree
2016-02-11
B
erk
Hess
Add SIMD version of pbc_dx_aiuc
commit
|
commitdiff
|
tree
2016-02-09
B
erk Hess
Replace
d
nbnxn
s
earch+gri
d
simd macro
s
commit
|
commitdiff
|
tree
2016-02-07
Berk Hess
Fix incorrect cmap
p
arsi
n
g
commit
|
commitdiff
|
tree
2016-02-05
Berk Hess
Fix incorrect
c
m
a
p parsin
g
commit
|
commitdiff
|
tree
2016-02-03
Ber
k
Hess
Re
p
laced literals in nbnxn l
i
sts by ints
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Fix m
d
run re
m
oving Verlet bu
f
fer with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk H
e
ss
Fix SETTLE error handli
n
g
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Added doc
u
mentation fo
r
pme grid in
d
exing
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Fix TPI ign
o
ring PME me
s
h
contributions
.
commit
|
commitdiff
|
tree
2016-01-29
Berk H
e
ss
U
p
date -ntomp_pme -npme
c
heck
commit
|
commitdiff
|
tree
2016-01-29
Berk Hes
s
Add check for do
u
bl
e
p
er
t
u
r
ba
t
ion
commit
|
commitdiff
|
tree
2016-01-29
B
e
rk Hess
F
i
x LINCS
t
r
i
a
n
gle
c
onstraint thread i
s
sue
commit
|
commitdiff
|
tree
2016-01-28
Berk Hess
Up
d
ate pair-list b
u
ffer manual
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
s
s
F
ix exact
c
on
t
i
nu
a
tio
n
from no
n
-ener
g
y steps
commit
|
commitdiff
|
tree
2016-01-24
Berk H
e
ss
Fix energy
file continu
a
t
ion w
i
t
h md-
v
v
commit
|
commitdiff
|
tree
2016-01-24
Berk He
s
s
Fix
en
e
rgy
average with co
n
tinuation
commit
|
commitdiff
|
tree
2016-01-08
Berk Hess
Fi
x
PME lo
a
d b
a
lancing
skipping a setup
commit
|
commitdiff
|
tree
2015-12-29
Ber
k
Hess
Correct ve
c
tor check o
f
gmx c
h
eck
commit
|
commitdiff
|
tree
2015-12-27
B
erk Hess
Re
o
rganized domdec initialization
commit
|
commitdiff
|
tree
2015-12-20
Berk Hes
s
Merge
r
elease-5-1
i
n
t
o
master
commit
|
commitdiff
|
tree
2015-12-19
Berk
Hess
Bring per
f
o
r
mance estimati
o
n up to date
commit
|
commitdiff
|
tree
2015-12-17
Berk Hess
R
e
moved topology pointers from DD stru
c
t
commit
|
commitdiff
|
tree
2015-12-16
Ber
k
Hess
Add
one ele
m
ent to state rvec arrays
commit
|
commitdiff
|
tree
2015-12-12
Berk Hess
R
emo
v
ed unused mdrun optio
n
-dn
commit
|
commitdiff
|
tree
2015-12-11
Berk H
e
ss
Fix bug with pu
l
l grou
p
weights
commit
|
commitdiff
|
tree
2015-12-07
Berk
Hess
Moved pull params to m
d
t
y
pe
s
/pull-params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk
Hess
Increase pdb
cha
i
n ids to 62 in outp
u
t
commit
|
commitdiff
|
tree
2015-12-02
B
erk
Hess
Refac
t
ored
s
et_
p
bc_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Made t_inp
u
trec
c
onst in P
M
E l
o
ad ba
l
ancing
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
Pull
grou
p
cou
n
t for co
o
rds stored i
n
tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk
H
ess
Removed
m
dru
n
f
a
t
a
l
_err
o
r with
P
3
M-AD
commit
|
commitdiff
|
tree
2015-11-18
Berk Hess
Removed Reaction-Field-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk He
s
s
Optimize
d
the bonded thr
e
ad
f
orc
e
reducti
o
n
commit
|
commitdiff
|
tree
2015-11-11
Berk Hess
F
i
xed (harmless) fp except
i
on in
wa
l
l
c
ycle_sum
commit
|
commitdiff
|
tree
2015-11-09
Berk He
s
s
Cor
r
ect LINCS dHdl contributi
o
n
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Fix no w
a
llcy
c
l
e
suppo
r
t
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Re
m
oved nbnxn kernel ble
n
dv optimizat
i
on
commit
|
commitdiff
|
tree
2015-11-02
B
e
rk Hess
F
i
x intermolecular intera
c
t
i
ons with small mols
commit
|
commitdiff
|
tree
2015-10-15
Ber
k
Hes
s
Fixed nbnxn_4x
N
perfor
m
ance r
e
gressio
n
commit
|
commitdiff
|
tree
2015-10-07
Ber
k
Hess
Fi
x
bugs wi
t
h inte
r
m
ol intera
c
tions and
D
D
commit
|
commitdiff
|
tree
2015-10-01
B
erk Hess
Remov
e
d CUDA poll
i
ng
w
ait
commit
|
commitdiff
|
tree
2015-09-27
Ber
k
Hess
M
o
ve gm
x
_domdec_comm_t de
f
i
nition
commit
|
commitdiff
|
tree
2015-09-22
B
erk Hess
Removed
us
e
less multiple shifts in pbc
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hes
s
Split n
b
nxn_
g
rid
.
c off from nbnxn_search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk H
e
ss
D
e
te
c
t incorrec
t
c
y
c
l
e counting
commit
|
commitdiff
|
tree
2015-08-25
Berk H
e
ss
Simplify
changing the tpx
_
version
commit
|
commitdiff
|
tree
2015-08-14
Berk
H
ess
Make mdrun -n
t
work a
g
ain
commit
|
commitdiff
|
tree
2015-08-13
Berk H
e
ss
Added
set_pul
l
_coord_reference_value
commit
|
commitdiff
|
tree
2015-08-12
Berk Hess
Adde
d
const qualifiers to core MD routines
commit
|
commitdiff
|
tree
2015-07-08
Ber
k
H
e
ss
Sepa
r
ated bonde
d
and Ewald correction threa
d
in
g
commit
|
commitdiff
|
tree
2015-07-06
Berk Hes
s
Fix too small
GPU pair c
o
un
t
e
stimat
e
s
commit
|
commitdiff
|
tree
2015-07-06
Be
r
k H
e
ss
Fix
bug
in GPU list bala
n
cing
commit
|
commitdiff
|
tree
2015-07-05
Be
r
k Hess
Fix DD DLB
state issue
commit
|
commitdiff
|
tree
2015-07-05
Berk Hess
Fix bug in G
P
U list balancing
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Obe
y
OpenMP
th
r
ead count limit with t
M
PI
commit
|
commitdiff
|
tree
next