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Use same matrix for Parrinello-Rahman and Berendsen coordinates scaling
2019-11-13
Artem Zhmurov
U
s
e sam
e
m
a
trix for Parrinello-Rahman and Be
r
endsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
A
rte
m
Zhmurov
R
e
m
ove ex
c
ess
i
ve
H2D and
D2H copie
s
of for
c
es
when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zh
m
urov
Disa
b
le GPU upda
t
e when
c
oordi
n
a
t
es swap
p
ing
is
e
nabled
commit
|
commitdiff
|
tree
2019-10-29
Artem Zh
m
urov
Switch the GP
U
buffer ops on when
updat
e
is o
n
G
P
U
commit
|
commitdiff
|
tree
2019-10-28
Artem Zh
m
ur
o
v
Fix missing
c
oor
d
inate
D
2H
c
opy with GPU u
p
d
ate and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmu
r
ov
Add ha
v
eCpuLocalFo
r
ces flag to DomainLifetimeWork
l
oad
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem Zhmur
o
v
Allow using upda
t
e flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmuro
v
Slight
impro
v
ements to decide
W
hetherT
o
U
s
eGpuF
o
rUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Remove un
n
ece
s
sary CUDA stream synchronization calls
commit
|
commitdiff
|
tree
2019-10-22
Ar
t
em Zhm
u
rov
R
e
nam
e
havePositionR
e
straints(
.
.
.
)
to haveRes
t
raints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmur
o
v
Update the cop
y
right message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Ar
t
em
Z
hmurov
Add environment variable
tha
t
changes
the
meaning
of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Arte
m
Z
h
murov
R
emov
e
excessive H2D
and D2H co
o
rdin
a
t
e
s copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
Rem
o
ve exce
s
siv
e
H2D and D2H co
p
ies of veloc
i
t
i
es whe
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
A
r
t
em Zhmurov
Li
n
k GP
U
force produ
c
er and consumer tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmurov
Fix the single-GPU update-constraints
commit
|
commitdiff
|
tree
2019-10-14
Artem Zhmurov
Add sep
a
r
a
te
constructor to StatePro
p
agat
o
rData
G
pu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
Centralize management of forces rea
d
y
on GPU event
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
C
h
ange copy mo
d
e to Async in PM
E
only rank
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Zhm
u
rov
C
e
ntralize manage
m
ent o
f
coordinates
ready on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Artem Zhmurov
Wrong local
i
ty
w
as us
e
d
when ignoring the PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmurov
Add management for velocities and forces copy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Art
e
m Zhmurov
F
i
x for the recent nightly failure
commit
|
commitdiff
|
tree
2019-10-07
Art
e
m Zhmurov
Pass the GPU str
e
ams to StatePropagator
D
ata
G
pu constructor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Cle
a
n
u
p the commen
t
s
s
e
c
tions in Update-Con
s
train
commit
|
commitdiff
|
tree
2019-10-07
Art
e
m Zhmu
r
ov
Fix a bug in G
P
U hal
o
ex
c
h
ange initialization
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix
the bug with of
f
loading
the
P
ME-only ranks
t
o
GPU
commit
|
commitdiff
|
tree
2019-10-02
Artem Zhmurov
Eli
m
inate
D2D copy in update cons
t
raints
commit
|
commitdiff
|
tree
2019-10-01
A
r
tem Zhmurov
Sta
t
eP
r
o
pagatorDataGpu
o
b
j
ect to manage GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Art
e
m Zhmurov
S
l
i
ght i
m
provements t
o
GPU upd
a
te/con
s
traints initializat
i
on
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmu
r
ov
Introduce stream managemen
t
to GPU Update-Constraints
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmu
r
ov
D
isable GPU update/constraints when neithe
r
PME
nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Arte
m
Zhmurov
C
hange Padd
e
d
V
ecto
r
to Padded
H
o
s
tVector
f
or force CP
U
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Z
h
mu
r
ov
F
ix
for the post-submit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmur
o
v
Decouple GPU forc
e
buffer management from b
u
ffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Decouple coo
r
dinates buffer management from
b
uffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zh
m
urov
Re
o
r
g
anize PME code:
commit
|
commitdiff
|
tree
2019-09-10
A
r
tem Zhmurov
Making
D
e
viceBuffer
a
vailible
in no
n
-G
P
U
b
uilds
commit
|
commitdiff
|
tree
2019-09-03
Artem Z
h
mu
r
o
v
A
d
d Parrinello-Rahman pressur
e
coupling to
CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhm
u
r
o
v
Add
t
e
m
pe
r
ature co
u
p
l
ing to CUDA Leap-Frog integr
a
tor
commit
|
commitdiff
|
tree
2019-08-25
Ar
t
em Zhm
u
rov
Mak
e
use of recent
c
h
anges to prepar
e
KernelArgu
m
ents
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Mis
c
eleneo
u
s
i
mprovements
t
o
the Lea
p
Frog tests
commit
|
commitdiff
|
tree
2019-08-14
Artem Zhmurov
B
u
gF
i
x: Z
e
roing
t
he padded
a
rea
o
f coordinates
v
ec
t
ors
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
A
r
tem Zhm
u
r
ov
Make use
o
f
refe
r
ence d
a
t
a
in
int
e
gr
a
tor t
e
sts
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmurov
Make
u
se of
r
eference data in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Art
e
m Zhmu
r
ov
Prepare Upd
a
t
e
and Constr
a
int
s
for Domai
n
Deco
m
position
commit
|
commitdiff
|
tree
2019-08-09
Artem
Zhm
u
rov
Re
f
actor
i
n
g
of the SETTL
E
tests
commit
|
commitdiff
|
tree
2019-08-08
A
r
tem Zh
m
uro
v
Refactor Le
a
p-Frog
t
ests
a
nd co
n
nect th
e
m
to CPU v
e
rs
i
on
commit
|
commitdiff
|
tree
2019-08-06
Artem Z
h
m
u
r
ov
Fix
for cmake l
i
sts
i
n mdlib test
s
commit
|
commitdiff
|
tree
2019-08-06
A
rtem Zhmurov
Remove
PIm
p
l
s
caffolding
from CUDA version
of
L
eap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem
Z
h
mur
o
v
Change the file struct
u
re
in
c
onstraints t
e
sts
commit
|
commitdiff
|
tree
2019-07-31
A
r
tem Zh
m
u
r
o
v
Introduce
f
u
nctio
n
t
h
a
t
che
c
k
s if the computa
t
ions
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmurov
Remove PImpl
scaffoldi
n
g
f
r
o
m CUDA
version of
SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmurov
Remove PImpl
s
c
affolding
from
C
UDA v
e
rsion of
L
IN
C
S
commit
|
commitdiff
|
tree
2019-07-04
A
rtem Zhmurov
Us
e
reallocateDeviceB
u
ffer(
.
.
.
) in CUDA v
e
rsion of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Early exit for CUDA
v
e
r
sions
o
f
S
ETT
L
E and L
I
N
C
S
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmuro
v
M
emory management fixes in CUDA versi
o
n of LINCS
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zhmurov
Com
b
i
n
e CU
D
A Le
a
p-
F
rog,
LINCS and SETT
L
E
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
Ar
t
em Zhmu
r
o
v
Combine CUDA L
e
a
p-Frog, LIN
C
S and SETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Art
e
m Zhmurov
Bug fix: Constraints tes
t
s
a
re not instant
i
ated wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Ar
t
em Zhmur
o
v
C
l
arify which of
the m
a
in
e
ne
r
gy terms are printed
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
C
larify the Ene
r
gyOutput III
commit
|
commitdiff
|
tree
2019-05-24
Artem
Zhmu
r
ov
Clarify
the EnergyOut
p
ut II
commit
|
commitdiff
|
tree
2019-05-13
Arte
m
Zhmurov
Clarify t
h
e EnergyOutput I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmu
r
ov
CUDA ver
s
ion of L
e
a
p
-F
r
og integ
r
a
t
or with basic tests
commit
|
commitdiff
|
tree
2019-05-06
Artem Z
h
mu
r
ov
Fix
i
n
g
minor
m
emory is
s
ue
s
in M
D
Lib
commit
|
commitdiff
|
tree
2019-05-02
Art
e
m Zh
m
urov
Use test with parameters for En
e
r
g
yOu
t
pu
t
commit
|
commitdiff
|
tree
2019-04-30
Artem
Z
hmuro
v
C
U
D
A versi
o
n of SETT
L
E algorithm with basic tests
commit
|
commitdiff
|
tree
2019-04-29
A
rtem Zhmurov
Fix for t
h
e
C
UDA v
e
rsion of LINCS
commit
|
commitdiff
|
tree
2019-04-28
Artem
Z
h
m
uro
v
CU
D
A vers
i
on of L
I
NCS
c
o
n
straints
.
commit
|
commitdiff
|
tree
2019-04-25
Ar
t
em Zhmur
o
v
Im
p
r
ovement
s
for energy ou
t
put tes
t
.
commit
|
commitdiff
|
tree
2019-04-16
A
r
tem Zhmuro
v
Fix
for the memory access
e
r
ror
in
constrain
t
s test
.
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
Remove isPressureCouplingStep(
.
.
.
)
commit
|
commitdiff
|
tree
2019-04-04
Artem
Zhmurov
Remove isTemperatureCo
u
pli
n
gStep(
.
.
.
)
commit
|
commitdiff
|
tree
2019-03-28
Artem Zhmurov
GPU naming conventions
commit
|
commitdiff
|
tree
2019-03-25
Artem
Z
hmurov
Remove
u
n
used headers
commit
|
commitdiff
|
tree
2019-03-13
Artem
Z
hmurov
Basic rou
t
ines to h
a
n
d
le per
i
odic
b
ou
n
d
a
ry
.
commit
|
commitdiff
|
tree
2019-02-21
Artem
Z
hmurov
Tes
t
f
o
r LINCS a
n
d SHAKE constraints
.
commit
|
commitdiff
|
tree
2019-02-19
Artem Zhmur
o
v
PBC se
t
u
p for GPU
i
s
mov
e
d
into p
b
cutils
.
commit
|
commitdiff
|
tree
2019-02-13
Arte
m
Zhmurov
Ignore Visual Stu
d
io Cod
e
m
e
t
a
data
.
commit
|
commitdiff
|
tree
2018-12-27
Art
e
m
Z
h
m
u
r
o
v
The te
s
ts
f
or LINCS and S
H
A
K
E
c
onstraints
.
commit
|
commitdiff
|
tree