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Rename SettleCuda to SettleGpu
2020-01-20
A
r
tem
Zhmurov
Rename SettleCuda to S
e
ttle
G
pu
commit
|
commitdiff
|
tree
2020-01-20
Art
e
m Zhmurov
Rename LincsCuda into
L
incsGpu
commit
|
commitdiff
|
tree
2020-01-20
A
r
te
m
Z
h
murov
Rena
m
e Leap
F
rogCud
a
to LeapFrogGp
u
commit
|
commitdiff
|
tree
2020-01-09
Arte
m
Zh
m
uro
v
Change
s
ignature
o
f the setPbc(
.
.
.
) method in update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Ar
t
em Zhmuro
v
Make PBC type enumeration into Pb
c
Type enu
m
c
lass
commit
|
commitdiff
|
tree
2019-12-31
Artem Zh
m
urov
Inform user
why
f
orc
i
n
g GP
U
update is n
o
t poss
i
ble
commit
|
commitdiff
|
tree
2019-12-31
Art
e
m Zhmurov
Add descr
i
pt
i
on of
G
M
X_FORCE_UPD
A
TE_DEFAULT_G
P
U dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Fix gpuupdate
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
Arte
m
Zhmurov
Chan
g
e the be
h
avior of the GP
U
up
d
ate UI
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zh
m
ur
o
v
Add a not
e
to the log
f
ile
w
hen -update gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m Zhmu
r
ov
C
lean bad auto-f
o
rmat
i
n decidegpuusage dox
y
gen comments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zh
m
u
rov
Clean-up buffer-ops CUDA k
e
rnels
commit
|
commitdiff
|
tree
2019-12-13
Ar
t
e
m
Zhmur
o
v
Cl
e
an up outdated
c
omment
s
in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allow using GPU u
p
dat
e
with D
D
a
n
d updat
e
groups
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem
Z
h
murov
Enable m
o
st o
f
the pul
l
ing flav
o
rs with GPU update
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Cla
r
ify what
setting zero to some output mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zh
m
u
rov
Avoid unn
e
cessar
y
re
i
nterpret_c
a
st of c
o
ordinates buffer
commit
|
commitdiff
|
tree
2019-12-10
Art
e
m
Z
hmu
r
o
v
Set
GPU
update to fals
e
i
n
ca
s
e of
a
rerun
commit
|
commitdiff
|
tree
2019-12-06
Artem Zhmurov
Pass array re
f
i
nstead of
c
asting to bas
i
c a
r
ray in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
t
e
m Zhmurov
Pr
i
nt
OpenCL error info in case of
f
ailed a
s
sertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Z
h
murov
M
a
ke Leap-Frog C
U
DA kernel selection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zhm
u
rov
Rename
s
ome var
i
ables in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Art
e
m
Zhmurov
Cl
e
ar device fo
r
ce buffe
r
if it was real
l
ocated
commit
|
commitdiff
|
tree
2019-11-28
Artem
Zhmur
o
v
Fi
x
pressure coupling with GPU
u
p
date
commit
|
commitdiff
|
tree
2019-11-27
A
rtem Zhmurov
C
o
mbi
n
e t
w
o booleans in
m
d
loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhm
u
rov
Add m
e
tho
d
f
o
r c
o
ordina
t
es scaling into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
A
r
tem Zhmurov
Remo
v
e the PB
C
manag
e
m
ent f
r
om LINCS, SETTLE
a
nd Le
a
p
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Art
e
m Zhmurov
U
s
e same matrix for Parrinello-Rahman and Beren
d
sen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem
Zhmurov
Fix index mapp
i
ng issue with LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-23
Ar
t
em Zhmu
r
ov
N
e
w cool
quote
commit
|
commitdiff
|
tree
2019-11-20
A
r
tem Zhmuro
v
Add D2H copies for the check
p
oin
t
ing
commit
|
commitdiff
|
tree
2019-11-20
Arte
m
Zhmurov
Move th
e
copy of the velocities for t
h
e o
u
tput clo
s
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix
icc-19 warning in n
i
gh
t
ly matr
i
x
commit
|
commitdiff
|
tree
2019-11-15
Artem Z
h
murov
Removing c
o
de duplications in
S
tatePropa
g
atorDataGp
u
commit
|
commitdiff
|
tree
2019-11-13
A
r
tem Zhmurov
Use same
matrix f
o
r P
a
r
r
in
e
llo-Rahman
a
n
d
Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmurov
R
e
move excessive H2D and D2H copies of
f
orces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Disabl
e
G
PU
up
d
at
e
w
hen coordin
a
tes
s
w
a
p
p
i
ng is e
n
a
b
l
e
d
commit
|
commitdiff
|
tree
2019-10-29
Ar
t
e
m
Zhmuro
v
Switch
t
he GPU buff
e
r ops on when
u
pdate i
s
on GPU
commit
|
commitdiff
|
tree
2019-10-28
Arte
m
Zhmurov
Fix missing coo
r
dinate D2
H
c
o
p
y with GPU update and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem Zhmurov
Add haveCpuLocalFor
c
es
flag to D
o
m
a
inLife
t
imeW
o
rkload
commit
|
commitdiff
|
tree
2019-10-28
Art
e
m
Zhmurov
All
o
w using update flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhm
u
rov
Slight impr
o
vements
to
d
ecid
e
Whether
T
oUseG
p
u
F
orUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem
Zhmur
o
v
Rem
o
v
e
unnecessary CU
D
A
s
tream
s
ynchronization calls
commit
|
commitdiff
|
tree
2019-10-22
A
rtem Zhmu
r
ov
Rename havePosit
i
onRestraints(
.
.
.
) to haveRe
s
traints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Art
e
m Z
h
mur
o
v
Update
t
he copyr
i
ght message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmu
r
ov
Add
env
i
ro
n
men
t
v
a
riable that
c
h
anges t
h
e meaning of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
rtem Zhmurov
Rem
o
ve exces
s
ive H2D
a
n
d D2H coordinates co
p
ie
s
when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem
Z
hmurov
Remove excessive H2
D
and D2H copies of
v
elocities
w
hen
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem
Zhmuro
v
Link GPU for
c
e
produ
c
er and con
s
umer ta
s
ks
commit
|
commitdiff
|
tree
2019-10-15
Ar
t
em Zhm
u
r
o
v
F
ix the
s
ingl
e
-GPU updat
e
-
c
onstraints
commit
|
commitdiff
|
tree
2019-10-14
Arte
m
Z
hmu
r
ov
Add separate cons
t
ructor to S
t
a
tePr
o
pa
g
a
t
orDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zh
m
u
rov
Centralize management of fo
r
ces ready on GPU e
v
ent
commit
|
commitdiff
|
tree
2019-10-12
Ar
t
e
m
Zhmu
r
ov
C
hange
c
opy mo
d
e to
Async in PME only rank
commit
|
commitdiff
|
tree
2019-10-12
Ar
t
em
Z
hmur
o
v
Cent
r
alize management
of coordi
n
ates rea
d
y on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Art
e
m Zhmurov
Wron
g
l
o
ca
l
i
ty was use
d
when
i
gnor
i
n
g
the
P
ME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
A
r
tem Zhmurov
Ad
d
managem
e
nt
for velociti
e
s and forces
c
o
py events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zh
m
urov
Fix
f
or the re
c
ent nigh
t
l
y failure
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
h
murov
Pass the GPU streams to
StatePropaga
t
orDataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zh
m
urov
Clean up t
h
e co
m
ments sections in Up
d
ate-
C
onstrain
commit
|
commitdiff
|
tree
2019-10-07
Artem Zh
m
u
rov
F
i
x
a bug
in
GPU halo exc
h
a
nge initializatio
n
commit
|
commitdiff
|
tree
2019-10-03
Ar
t
em
Zhmurov
Fix the bu
g
with
o
ffloading t
h
e PM
E
-only r
a
nks to GPU
commit
|
commitdiff
|
tree
2019-10-02
Artem Zhm
u
r
ov
Elimi
n
a
te D2D copy in update constra
i
nts
commit
|
commitdiff
|
tree
2019-10-01
Ar
t
em
Z
hmurov
S
t
atePropagatorDataGpu obj
e
ct to manage GPU force
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Artem Z
h
murov
Sl
i
ght improvement
s
t
o
GP
U
update/constra
i
nts in
i
tialization
commit
|
commitdiff
|
tree
2019-09-27
Art
e
m
Zhmurov
I
ntr
o
duce stream mana
g
ement to
GPU Update-Co
n
straint
s
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmurov
D
isa
b
le GPU update/constraints when neither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem
Z
h
m
ur
o
v
Chang
e
P
adde
d
Vector to Padde
d
HostVector for force C
P
U
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhm
u
rov
Fix for the po
s
t
-
submit
f
ailure
commit
|
commitdiff
|
tree
2019-09-11
A
r
tem Zhmurov
D
e
c
oupl
e
G
P
U force bu
f
fe
r
m
a
nagem
e
n
t
from buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
r
tem
Zhmurov
Decoupl
e
c
o
o
rdin
a
tes buffer ma
n
agement fro
m
buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Ar
t
e
m
Zhmurov
Reorga
n
ize PME code:
commit
|
commitdiff
|
tree
2019-09-10
Arte
m
Z
h
muro
v
Makin
g
DeviceBuffer availibl
e
in non-GPU
b
uilds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhm
u
rov
A
dd Parrinello
-
Rahman pr
e
ssure
c
o
u
pling to CU
D
A Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
A
d
d
tempe
r
a
t
ure coupling to CUDA Lea
p
-Fr
o
g int
e
g
rato
r
commit
|
commitdiff
|
tree
2019-08-25
A
r
t
e
m
Z
h
mu
r
ov
Ma
k
e use of
recent
changes to p
r
e
pare
K
ernelArguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
A
r
t
em Zhmurov
M
i
scel
e
neous improvements to the Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-14
Art
e
m Zhmuro
v
BugF
i
x
: Zeroin
g
the
p
ad
d
ed
area of coordin
a
tes v
e
ctors
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Ar
t
em Zhmurov
Mak
e
u
s
e of refere
n
ce
data in integrator te
s
ts
commit
|
commitdiff
|
tree
2019-08-13
Arte
m
Zhmurov
Mak
e
use of refere
n
ce data in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
Arte
m
Zhmurov
Prepa
r
e Update and C
o
nstraints for Domain Decompositi
o
n
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
R
efactori
n
g of the SETTLE
tests
commit
|
commitdiff
|
tree
2019-08-08
Artem Zhmuro
v
Re
f
actor Lea
p
-Frog tests and connect them
t
o
CPU vers
i
on
commit
|
commitdiff
|
tree
2019-08-06
Artem Zh
m
urov
Fix
for c
m
ak
e
lis
t
s in mdlib te
s
ts
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmurov
Remove PImpl
s
c
a
ffolding from CUDA version of Leap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Change the file s
t
ru
c
ture in
constraints t
e
sts
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhm
u
rov
Introduce funct
i
on that
che
c
k
s
if the co
m
p
utations
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
A
rt
e
m Z
h
murov
Re
m
ove PImpl scaf
f
o
lding from
C
UDA version of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Ar
t
em Zhm
u
rov
R
emove PImp
l
scaff
o
ldi
n
g from CUDA version
o
f
LINCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhm
u
rov
Use realloc
a
teDeviceBuffer(
.
.
.
) in CUD
A
versi
o
n of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Z
h
m
u
r
o
v
Early exit
for CUDA ve
r
sions of SETTLE and LINC
S
commit
|
commitdiff
|
tree
2019-07-03
Artem Z
h
murov
M
e
mory management
fixes
in
C
U
DA v
e
r
sio
n
of LINCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhm
u
rov
Com
b
ine C
U
DA Leap-Frog, LINCS and S
E
TTLE
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
A
r
tem Zhmurov
Combine CU
D
A
L
eap-Frog, LINCS and SETT
L
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmurov
Bug fix: Constr
a
ints
tests are not instant
i
ated
with
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
C
larify w
h
ich of the
m
ain energy term
s
ar
e
printed
.
commit
|
commitdiff
|
tree
2019-05-24
Art
e
m Zhmuro
v
Clarify th
e
EnergyOutput III
commit
|
commitdiff
|
tree
2019-05-24
Artem
Zhmurov
Clarify the EnergyOutpu
t
II
commit
|
commitdiff
|
tree
2019-05-13
Artem
Z
hm
u
rov
Clarify the Ener
g
yOutput
I
commit
|
commitdiff
|
tree
2019-05-12
Ar
t
em Zhmurov
C
UDA
v
ersion
o
f L
e
ap
-
Fr
o
g int
e
grator with b
a
sic tests
commit
|
commitdiff
|
tree
2019-05-06
Artem Zhmurov
Fixing
m
i
no
r
memory issues in
M
DLib
commit
|
commitdiff
|
tree
next