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Rename SettleCuda to SettleGpu
2020-01-20
Artem Zhmurov
Rename SettleCud
a
to SettleGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Rena
m
e LincsCuda into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhm
u
r
ov
Renam
e
LeapF
r
o
gC
u
da
to LeapFr
o
g
Gpu
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Change signature of
the setPbc
(
.
.
.
) method in update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem Zh
m
urov
Make PBC t
y
pe enumeration into PbcType en
u
m
class
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inf
o
rm user
w
hy
forci
n
g GP
U
update is not
p
ossible
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
hmurov
Add description o
f
GMX_FORCE_UPDATE_DEFAULT
_
GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zhm
u
r
o
v
Fix
g
puupdat
e
matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmuro
v
Change the
behavior of the G
P
U
upda
t
e
UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Ad
d
a
note to the log fi
l
e when
-upd
a
te gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhm
u
ro
v
Clean bad auto-format in
decidegpuusage doxyge
n
comments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zh
m
urov
C
lean-up
b
u
f
fer-ops CUD
A
kernels
commit
|
commitdiff
|
tree
2019-12-13
Art
e
m Zhmurov
C
l
e
an up outdated comments in md
.
c
p
p
commit
|
commitdiff
|
tree
2019-12-12
A
r
tem Zhm
u
rov
Allow usin
g
GPU u
p
date with
D
D
an
d
u
p
date gro
u
ps
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Enab
l
e
mos
t
of the pul
l
i
n
g flavors wi
t
h
G
P
U
update
commit
|
commitdiff
|
tree
2019-12-11
Arte
m
Zhmurov
Clarify wha
t
sett
i
ng zero to some o
u
t
p
ut mdp
o
ption
s
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Z
h
murov
Avoid unnecessar
y
r
ei
n
terp
r
et_cast of
c
oordinates buffer
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmuro
v
Set GPU update to false in
case
o
f a rerun
commit
|
commitdiff
|
tree
2019-12-06
A
r
tem Zhmurov
P
ass
a
rray ref instead
o
f casting
to basic
a
rray in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem
Z
h
m
u
r
ov
Print OpenCL error in
f
o in ca
s
e of failed
a
ssertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
M
ake Leap-Frog CUDA kernel s
e
lection safer
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
em Zhmurov
Rename some var
i
ables
in GP
U
Update
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clear
d
evice force buffer if it
w
a
s reallocated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zh
m
urov
Fix p
r
essure c
o
upling
w
ith
G
PU updat
e
commit
|
commitdiff
|
tree
2019-11-27
A
r
tem Zhmuro
v
Combi
n
e two booleans in md loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
Add method for coo
r
dinates scaling into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
A
r
te
m
Zhm
u
rov
Rem
o
ve the PBC man
a
ge
m
ent from LI
N
CS, SETTLE
and Le
a
p
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use
same
matrix for Parrinello-Rahman and
Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem
Z
h
m
u
r
ov
Fix
i
n
dex map
p
ing issue w
i
th LINC
S
on
G
PU
commit
|
commitdiff
|
tree
2019-11-23
Artem
Z
hmurov
New
cool
q
u
o
te
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Add D2H copies for
t
he check
p
oin
t
ing
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m
Zh
m
urov
Move th
e
cop
y
of the velocit
i
es for the
output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
A
r
tem Zhmu
r
ov
F
i
x icc-19
w
a
r
ning in nightly matrix
commit
|
commitdiff
|
tree
2019-11-15
Art
e
m Zhm
u
rov
Remov
i
ng co
d
e dupl
i
ca
t
ions in St
a
tePropag
a
torDataG
p
u
commit
|
commitdiff
|
tree
2019-11-13
Ar
t
em
Zhmur
o
v
Use same matri
x
for Parrinell
o
-Rahman an
d
Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Ar
t
e
m Zhmurov
Remove excessive H2D and D2
H
copies of forces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhm
u
rov
Disable
G
PU update
w
hen coordinates swappin
g
is enabl
e
d
commit
|
commitdiff
|
tree
2019-10-29
A
r
tem
Z
hmurov
Switch t
h
e
GPU buffer ops
o
n
when upda
t
e
is on GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem
Zhmurov
Fix missing
coordinate D2H copy wi
t
h
GPU updat
e
and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem
Z
hm
u
rov
A
dd ha
v
eCpuLocalForces flag to
D
omainLifetimeWorkload
commit
|
commitdiff
|
tree
2019-10-28
Ar
t
em Zhmurov
Allow using upd
a
te flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zh
m
urov
Slight impr
o
v
eme
n
ts
to decide
W
he
t
herToUs
e
Gp
u
For
U
pda
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Arte
m
Zhm
u
rov
R
emove unnecessar
y
C
UD
A
stream synchroni
z
ation
c
a
lls
commit
|
commitdiff
|
tree
2019-10-22
Ar
t
em Zhmu
r
ov
Rename havePosit
i
onRestraints
(
.
.
.
) to haveRestraints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
A
rtem
Z
h
murov
Update t
h
e c
o
py
r
ight mes
s
age
commit
|
commitdiff
|
tree
2019-10-21
Art
e
m
Zhmurov
A
d
d
env
i
r
o
nm
e
n
t var
i
a
b
le that changes the mean
i
ng of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
r
t
em Zhmur
o
v
R
emove
excessiv
e
H2D
a
nd D2H coordin
a
tes cop
i
es when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Z
h
murov
Remove e
x
cess
i
ve H2D
and
D
2H copies of velocities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zh
m
urov
L
i
nk
G
PU
f
o
rce
prod
u
cer a
n
d consumer tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhm
u
rov
F
i
x the s
i
ngle-GPU u
p
date
-
constr
a
ints
commit
|
commitdiff
|
tree
2019-10-14
Art
e
m
Z
hmurov
Add separ
a
te constructor to
StatePr
o
pagatorDataGp
u
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Zhmurov
C
e
ntralize mana
g
ement of forces
r
e
a
d
y
on
GPU even
t
commit
|
commitdiff
|
tree
2019-10-12
Artem Z
h
mu
r
ov
Cha
n
ge copy m
o
de to
A
s
y
nc in PME only
r
ank
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmu
r
o
v
C
entralize manag
e
ment of co
o
rdinate
s
rea
d
y
o
n GPU event
commit
|
commitdiff
|
tree
2019-10-11
Artem Zh
m
urov
Wrong loc
a
l
i
ty was used w
h
en
igno
r
ing the PM
E
for
c
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
A
rt
e
m Zhmuro
v
Add manage
m
ent f
o
r
v
elocities and forces copy
e
v
e
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem
Zhm
u
rov
F
ix for
t
he
recent night
l
y
fail
u
re
commit
|
commitdiff
|
tree
2019-10-07
Artem Zh
m
urov
Pass the GPU stream
s
to StatePr
o
pag
a
t
orDataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Artem
Zhmurov
Clean u
p
the
c
omments sections in U
p
date
-
Constrai
n
commit
|
commitdiff
|
tree
2019-10-07
Ar
t
em
Z
hmurov
Fi
x
a bug in GPU halo ex
c
hange initia
l
ization
commit
|
commitdiff
|
tree
2019-10-03
Artem
Z
hmurov
Fix
t
h
e
b
ug with
o
f
floa
d
ing
the PME-only r
a
nks to GP
U
commit
|
commitdiff
|
tree
2019-10-02
Artem Zhmurov
Elimina
t
e D2
D
cop
y
in update const
r
aints
commit
|
commitdiff
|
tree
2019-10-01
Artem Z
h
mur
o
v
Stat
e
PropagatorD
a
ta
G
p
u o
b
ject t
o
manage GP
U
f
orc
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Arte
m
Zhmurov
Slight improve
m
ents to GPU update/
c
onst
r
aints init
i
aliz
a
tion
commit
|
commitdiff
|
tree
2019-09-27
Ar
t
em Zhmurov
Intr
o
duc
e
stream management to GPU Update-Constra
i
nts
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhm
u
r
o
v
D
isable GP
U
update/constraints when nei
t
h
e
r
P
ME n
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem
Zhmurov
Change Pa
d
de
d
Vector to PaddedHostVect
o
r for for
c
e CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhm
u
rov
F
i
x
for the post-submit
f
a
ilure
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmur
o
v
D
e
couple G
P
U
force
buffer management
from
b
u
f
fer o
p
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem
Z
hmurov
Decouple c
o
ordinates
buffer managemen
t
from buff
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Art
e
m Zhmurov
Reorg
a
nize
PME code:
commit
|
commitdiff
|
tree
2019-09-10
Art
e
m Zhmurov
Making Device
B
uffer availible in n
o
n-GPU
b
uilds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmu
r
ov
Add Parrinello-Rahman pre
s
sure co
u
pling to
C
UDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Art
e
m
Zhmuro
v
Add tempe
r
ature coupl
i
ng to CUDA Leap
-
Frog int
e
g
rator
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Make use of
r
ecent
c
hanges to prep
a
reKerne
l
Argumen
t
s
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zh
m
urov
Mis
c
elene
o
us imp
r
o
vements to the Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-14
A
r
tem Zhmur
o
v
BugF
i
x: Zeroing
t
he padded area of coordi
n
at
e
s
vect
o
rs
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
A
rtem Zhmurov
Make u
s
e of refe
r
ence data in integrat
o
r
t
ests
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhm
u
rov
M
ake u
s
e of referen
c
e data in SETT
L
E
tests
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Pre
p
are Update
a
nd
C
o
n
s
train
t
s
for Domain Decompos
i
tion
commit
|
commitdiff
|
tree
2019-08-09
Arte
m
Z
hmurov
R
efa
c
toring of the SETTLE tests
commit
|
commitdiff
|
tree
2019-08-08
Artem Zh
m
urov
Refactor Lea
p
-Frog tests and connect them to CPU versi
o
n
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmur
o
v
Fix for cm
a
ke
l
i
st
s
in mdlib tes
t
s
commit
|
commitdiff
|
tree
2019-08-06
A
r
tem
Z
h
murov
Remov
e
PImpl
s
caff
o
lding from CUDA versi
o
n
o
f Leap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
C
hange the file struc
t
ure in constraints tests
commit
|
commitdiff
|
tree
2019-07-31
Ar
t
em Z
h
murov
I
n
trod
u
ce
f
un
c
tion that checks
i
f
the
c
omputa
t
ions
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zh
m
urov
Remove P
I
mpl
scaffolding
f
r
o
m C
U
D
A version
o
f SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Artem Zh
m
urov
Remove PIm
p
l scaff
o
lding
f
r
om CUDA versi
o
n o
f
LINCS
commit
|
commitdiff
|
tree
2019-07-04
Ar
t
em Zhmu
r
ov
U
se rea
l
locateDeviceBuffer(
.
.
.
)
in CUDA versi
o
n
o
f
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
A
rtem Zhmurov
Early exi
t
for CUDA versions of SETTLE and LI
N
CS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Memory manag
e
ment fixes in CUDA version of LIN
C
S
commit
|
commitdiff
|
tree
2019-07-03
Arte
m
Zhmuro
v
Combi
n
e
CUD
A
Leap-Fro
g
, LINCS and SETT
L
E
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
Arte
m
Zhmurov
Combine C
U
DA Leap-Frog,
LINC
S
and SETT
L
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Z
h
m
u
rov
Bug fix: Constraints tests
a
re not instantiated wit
h
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clarify which o
f
the m
a
in en
e
rgy
t
er
m
s
a
re printed
.
commit
|
commitdiff
|
tree
2019-05-24
Art
e
m
Z
hmu
r
ov
Clarify the
E
nerg
y
Out
p
ut
II
I
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clarify the EnergyOut
p
ut II
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhmurov
Clarif
y
the EnergyOutput I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmurov
C
UDA
v
ersi
o
n of
L
eap
-
Frog
in
t
egrator with
basic
tests
commit
|
commitdiff
|
tree
2019-05-06
Artem Zh
m
u
r
ov
Fi
x
ing m
i
nor memo
r
y issu
e
s
in MDLib
commit
|
commitdiff
|
tree
next