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Remove OpenMP overhead at high parallelization
2016-06-22
Berk Hess
Remove Open
M
P overhead at high p
a
rall
e
l
ization
commit
|
commitdiff
|
tree
2016-06-22
Berk Hess
C
orrect GPU pair estimate for
l
ist splitting
commit
|
commitdiff
|
tree
2016-06-19
Be
r
k
Hess
Re
m
ove warnings on
c
heckp
o
int misma
t
ch
commit
|
commitdiff
|
tree
2016-06-17
Berk Hess
Rem
o
ve std::thread::hardwa
r
e
_
concurrency()
commit
|
commitdiff
|
tree
2016-06-14
Berk He
s
s
Fi
x
Open
C
L error
with
empty domains
commit
|
commitdiff
|
tree
2016-06-13
Berk Hess
Handle con
s
t
r
aint errors
with EM
commit
|
commitdiff
|
tree
2016-06-07
Be
r
k Hess
Fix
d
ata race i
n
hwinfo with threa
d
-M
P
I
commit
|
commitdiff
|
tree
2016-06-03
Berk Hess
Handle partially frozen and
constrained atoms
commit
|
commitdiff
|
tree
2016-05-31
B
erk
Hess
Reposition
n
bnxn
f
iller pa
r
ti
c
les
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Avoid numer
i
cal
o
verflow wit
h
ov
e
rlapp
i
ng ato
m
s
commit
|
commitdiff
|
tree
2016-05-31
Berk Hess
Add check for fini
t
e energies
commit
|
commitdiff
|
tree
2016-05-30
B
erk Hes
s
Add grompp che
c
k
for unbound atoms
commit
|
commitdiff
|
tree
2016-05-23
Ber
k
H
e
ss
Fix bug
i
n
v
-re
s
cale thermost
a
t & replic
a
exchan
g
e
commit
|
commitdiff
|
tree
2016-05-10
Berk
H
ess
Optimized the vsit
e
threading
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
F
i
x CUDA shmem bug
commit
|
commitdiff
|
tree
2016-05-10
Berk Hess
Su
p
por
t
cmap
w
ith QMMM
commit
|
commitdiff
|
tree
2016-05-08
Berk Hess
U
pdate mdrun terminati
o
n
i
n
fo
commit
|
commitdiff
|
tree
2016-05-06
Berk Hess
OpenMP paralleliza
t
ion for pull
commit
|
commitdiff
|
tree
2016-04-20
Berk
H
e
s
s
Fix
pull l
e
ge
n
d
w
ith e
x
t
e
rnal pote
n
tia
l
commit
|
commitdiff
|
tree
2016-04-19
Be
r
k
Hes
s
A
l
l
ow
rcoulomb>rvd
w
with PME
commit
|
commitdiff
|
tree
2016-04-19
Berk Hess
Broadca
s
t pul
l
external potential provider string
commit
|
commitdiff
|
tree
2016-04-19
B
e
r
k Hess
Fix gm
x
hbon
d
group
o
verl
a
p
check
commit
|
commitdiff
|
tree
2016-04-14
Berk Hes
s
Add
Q
M
M
M checks
commit
|
commitdiff
|
tree
2016-04-03
Berk Hess
C
orrect nrdf for 1D/2D sy
s
t
ems
commit
|
commitdiff
|
tree
2016-03-31
Berk Hess
Fix includes in r
e
adpul
l
.
cpp
commit
|
commitdiff
|
tree
2016-03-31
Berk
Hess
Add o
p
t
i
on fo
r
external
p
ull potential
commit
|
commitdiff
|
tree
2016-03-30
Berk Hess
Correct
mdr
u
n tMP
I
(non-
)
parallel error message
commit
|
commitdiff
|
tree
2016-03-26
B
e
rk He
s
s
Add
r
eal/SIMD
t
emp
l
ate for
L
J-14 pairs
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
Av
o
i
d assertion failure in pme_loadbal_d
o
commit
|
commitdiff
|
tree
2016-03-22
Berk Hes
s
Ma
k
e gmx van
h
ove wor
k
witho
u
t
PBC
commit
|
commitdiff
|
tree
2016-03-22
Berk Hess
LJ combi
n
ation rule kernels for
C
UDA
commit
|
commitdiff
|
tree
2016-03-21
Berk H
e
ss
Moved pu
l
l initialization back
to mdrunner
commit
|
commitdiff
|
tree
2016-03-18
Berk Hes
s
Fix n
o
n-normalization of FFT autocorr
commit
|
commitdiff
|
tree
2016-03-14
Berk Hess
Remove
r
e
str
i
ction
o
n d
i
hdra
l
types order
commit
|
commitdiff
|
tree
2016-03-12
Berk Hess
Split off Fermi kernel fr
o
m CU
D
A
k
ernel
commit
|
commitdiff
|
tree
2016-03-09
Berk H
e
ss
Fix
E
wal
d
3
D
C dipo
l
e with Verlet scheme
commit
|
commitdiff
|
tree
2016-03-04
Berk
Hess
Converted c
s
ettle(
)
to use real/S
i
m
d
R
eal template
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Use SIMD
t
r
a
nspose s
c
atter in b
o
ndeds
commit
|
commitdiff
|
tree
2016-03-03
Berk Hess
Us
e
rve
c
4 for listed f
o
rce buffer
commit
|
commitdiff
|
tree
2016-02-27
B
e
rk Hess
R
em
o
ve epsfac from GPU ker
n
el inner-loops
commit
|
commitdiff
|
tree
2016-02-27
Berk Hes
s
Mino
r
code r
e
ordering i
n
GP
U
kern
e
ls
commit
|
commitdiff
|
tree
2016-02-26
B
erk
H
ess
Fix compilation wit
h
Simd4
F
loat, without Simd4Double
commit
|
commitdiff
|
tree
2016-02-19
B
e
rk Hess
Fix excessive list splitti
n
g
commit
|
commitdiff
|
tree
2016-02-17
B
e
rk Hess
Re
n
amed nbnxn
static const
i
nts
commit
|
commitdiff
|
tree
2016-02-11
Berk Hess
Add SIMD v
e
r
s
i
o
n of pbc_dx_ai
u
c
commit
|
commitdiff
|
tree
2016-02-09
Berk
Hess
Replaced nbnxn search
+
grid simd
m
acro
s
commit
|
commitdiff
|
tree
2016-02-07
B
erk Hess
Fix i
n
correct cm
a
p parsing
commit
|
commitdiff
|
tree
2016-02-05
Berk H
e
ss
F
ix incorrect cmap pars
i
ng
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
Replac
e
d
l
iterals in nbnxn
l
ists
b
y
i
nts
commit
|
commitdiff
|
tree
2016-02-03
B
er
k
Hess
Fix
m
drun removing Verlet buffer with EM
commit
|
commitdiff
|
tree
2016-02-03
Berk Hess
F
ix SET
T
LE erro
r
handl
i
n
g
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k
Hes
s
Added documentation for pme grid indexing
commit
|
commitdiff
|
tree
2016-01-29
B
er
k
Hess
Fix T
P
I ignoring PME mes
h
contrib
u
ti
o
ns
.
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
U
p
d
ate -ntom
p
_pme
-
npm
e
c
heck
commit
|
commitdiff
|
tree
2016-01-29
Berk Hess
Add
c
he
c
k for
d
o
uble
perturba
t
i
o
n
commit
|
commitdiff
|
tree
2016-01-29
Be
r
k Hess
Fix LINCS tr
i
ang
l
e
c
o
nstr
a
int t
h
read
i
ssu
e
commit
|
commitdiff
|
tree
2016-01-28
Be
r
k Hess
Update pa
i
r-li
s
t
b
uffer
m
an
u
al
commit
|
commitdiff
|
tree
2016-01-24
Be
r
k Hess
F
i
x exact continuation fro
m
non-
e
nergy step
s
commit
|
commitdiff
|
tree
2016-01-24
B
e
r
k Hess
Fix en
e
rgy file
c
o
ntinu
a
tion wi
t
h md-vv
commit
|
commitdiff
|
tree
2016-01-24
Be
r
k He
s
s
Fix
energy ave
r
age with continuation
commit
|
commitdiff
|
tree
2016-01-08
B
erk Hess
Fix PME load bala
n
c
i
n
g skip
p
ing
a setup
commit
|
commitdiff
|
tree
2015-12-29
Berk Hess
Corr
e
ct vec
t
or
c
heck of
g
mx check
commit
|
commitdiff
|
tree
2015-12-27
Berk Hess
Reorga
n
iz
e
d d
o
mdec initialization
commit
|
commitdiff
|
tree
2015-12-20
Berk H
e
s
s
Merge
release-5
-
1 i
n
to
master
commit
|
commitdiff
|
tree
2015-12-19
Be
r
k
Hess
Bri
n
g perform
a
n
c
e esti
m
ation up
to date
commit
|
commitdiff
|
tree
2015-12-17
Be
r
k
H
e
s
s
Removed
topology point
e
r
s from D
D
struct
commit
|
commitdiff
|
tree
2015-12-16
Berk
H
e
s
s
A
dd one element to state rvec a
r
rays
commit
|
commitdiff
|
tree
2015-12-12
Berk
H
ess
Removed unu
s
ed mdru
n
o
p
tion
-
d
n
commit
|
commitdiff
|
tree
2015-12-11
Berk He
s
s
Fix
b
ug with pull grou
p
weights
commit
|
commitdiff
|
tree
2015-12-07
Berk
Hess
Moved pull par
a
ms to m
d
types/pu
l
l-params
.
h
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Increase p
d
b chain ids to 62 in out
p
u
t
commit
|
commitdiff
|
tree
2015-12-02
Berk Hes
s
Re
f
act
o
red
set_
p
bc_dd
commit
|
commitdiff
|
tree
2015-12-02
Berk Hess
Made t_inputr
e
c
c
onst in
P
M
E load balancin
g
commit
|
commitdiff
|
tree
2015-12-01
Berk Hess
P
u
ll group coun
t
fo
r
coords
s
tored in tpr
commit
|
commitdiff
|
tree
2015-11-19
Berk Hess
Removed mdrun fatal_
e
r
r
or with P3M-AD
commit
|
commitdiff
|
tree
2015-11-18
B
e
r
k Hes
s
Removed Rea
c
tion-F
i
el
d
-nec
commit
|
commitdiff
|
tree
2015-11-14
Berk
H
ess
Optimi
z
ed the
bon
d
ed t
h
rea
d
force reduc
t
i
o
n
commit
|
commitdiff
|
tree
2015-11-11
Ber
k
He
s
s
Fixed (ha
r
mless) fp except
i
on
in
w
allcycle_sum
commit
|
commitdiff
|
tree
2015-11-09
B
e
rk Hess
Cor
r
ect LIN
C
S dHdl c
o
ntribut
i
on
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Fix no wallcy
c
le support
commit
|
commitdiff
|
tree
2015-11-03
Berk Hess
Re
m
oved n
b
nxn ke
r
nel blendv optimiz
a
t
ion
commit
|
commitdiff
|
tree
2015-11-02
Berk
H
ess
F
i
x intermolecul
a
r
i
nteract
i
ons with small mols
commit
|
commitdiff
|
tree
2015-10-15
Berk Hess
Fixed nb
n
xn_4xN performance regr
e
ssion
commit
|
commitdiff
|
tree
2015-10-07
Berk Hess
F
ix bugs
w
ith intermol
i
n
t
eractions and DD
commit
|
commitdiff
|
tree
2015-10-01
Berk Hess
Remo
v
ed CU
D
A
polli
n
g wait
commit
|
commitdiff
|
tree
2015-09-27
Berk
Hess
Mo
v
e
gmx_domdec_comm_t definition
commit
|
commitdiff
|
tree
2015-09-22
Berk Hess
Remo
v
ed useless multiple shifts in
p
bc
.
cpp
commit
|
commitdiff
|
tree
2015-09-16
Berk Hess
Split n
b
nxn_grid
.
c off from nbnxn
_
search
.
c
commit
|
commitdiff
|
tree
2015-09-15
Berk Hess
Detect incorrect c
y
cl
e
counting
commit
|
commitdiff
|
tree
2015-08-25
Berk Hess
S
implify
c
hanging the
t
px_versio
n
commit
|
commitdiff
|
tree
2015-08-14
Berk H
e
ss
M
a
ke
m
d
run
-
nt
work
a
gain
commit
|
commitdiff
|
tree
2015-08-13
Berk Hess
A
dded set_
p
ull_coord_reference_value
commit
|
commitdiff
|
tree
2015-08-12
Berk Hess
A
d
ded const qualifiers t
o
c
ore
MD routines
commit
|
commitdiff
|
tree
2015-07-08
Ber
k
He
s
s
Sep
a
r
a
t
ed b
o
nded and Ewald correctio
n
threadin
g
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix too
small
G
PU
p
air count estimates
commit
|
commitdiff
|
tree
2015-07-06
Berk Hess
Fix bug in
G
PU li
s
t
bal
a
n
c
in
g
commit
|
commitdiff
|
tree
2015-07-05
B
e
rk
H
e
s
s
Fix
DD
D
LB state
i
ssue
commit
|
commitdiff
|
tree
2015-07-05
Berk H
e
ss
Fix bug in GPU list
b
a
lancing
commit
|
commitdiff
|
tree
2015-07-04
Berk Hess
Ob
e
y
OpenMP thread count
l
i
mit with tMPI
commit
|
commitdiff
|
tree
2015-07-04
Berk H
e
ss
Fix two PME DLB trigger issu
e
s
commit
|
commitdiff
|
tree
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