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Add missing header and disable failing test
2020-02-22
Artem Zhmurov
Add missing he
a
der and disable f
a
iling
t
est
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmu
r
ov
Refac
t
o
r an
d
enable RVec
t
o f
l
oa
t
convers
i
on test
commit
|
commitdiff
|
tree
2020-02-20
A
r
t
em
Zhmurov
Do no
t
call PME GPU builder in CPU
co
d
e
path
s
commit
|
commitdiff
|
tree
2020-02-20
Art
e
m Zhmurov
U
s
e GROMACS wrappe
r
s
for EXPECT_THROW/NO
_
THROW in P
M
E
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhm
u
r
o
v
Use
CUDA float3
v
ector type instead
o
f fv
e
c
i
n GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Art
e
m Zhmurov
Clean up trivial
functi
o
n and dup
l
icatin
g
macroses
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Arte
m
Zhmurov
Fix the
nightly fail
u
re
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmurov
T
emporary d
i
sable RVec->fl
o
at3
c
o
n
version test t
o
fi
x
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
U
se
R
V
ec instead
o
f
float fo
r
x,
v
a
n
d f device
buffers
commit
|
commitdiff
|
tree
2020-02-06
Ar
t
em Zhmur
o
v
M
o
ve DeviceInfo int
o
GP
U
traits
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
M
a
ke
Ope
n
C
L
Devi
c
eVendor into enum class
a
nd move
t
o
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmur
o
v
M
ove non-bonded
initialization ou
t
of the
fo
r
cerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmu
r
ov
Fix typo in and remove a couple of
d
uplicates from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Art
e
m Zhmu
r
ov
Enable GPU
u
pd
a
te for
s
upported c
a
ses of FEP
commit
|
commitdiff
|
tree
2020-02-01
Arte
m
Z
h
m
urov
Coup
l
e cool quotes
commit
|
commitdiff
|
tree
2020-02-01
Artem Zhmurov
Mer
g
e "
M
erge
b
r
anch
origin/release-2020 in
t
o
master"
commit
|
commitdiff
|
tree
2020-01-30
Artem Zhmurov
Cl
e
a
ning bo
o
leans in NB
N
X
M in OpenC
L
build
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
R
e
o
rganize GP
U
s
t
u
ff initialization
in
P
ME
-
only ranks
commit
|
commitdiff
|
tree
2020-01-29
A
r
tem Zhmurov
Split
a
nd move the c
h
e
ckDevi
c
e
Buffer(
.
.
.
)
function
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmuro
v
Remove the rest of
t
h
e
device coord
i
na
t
e
s mana
g
e
ment
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
A
rtem Zhmurov
R
ename UpdateCons
t
raintsCuda
t
o Upda
t
eCons
t
raintsGpu
commit
|
commitdiff
|
tree
2020-01-23
A
r
te
m
Zhmurov
Fix a co
u
p
le of commas in cool qu
o
tes
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhm
u
rov
Renam
e
S
ettleCuda to Set
t
leGpu
commit
|
commitdiff
|
tree
2020-01-20
A
rtem Zh
m
u
rov
Rename
L
incsC
u
da into
L
incsG
p
u
commit
|
commitdiff
|
tree
2020-01-20
Artem
Z
hmur
o
v
Rename L
e
a
pFrogCuda to LeapFrogG
p
u
commit
|
commitdiff
|
tree
2020-01-13
Art
e
m Z
h
mu
r
o
v
R
epor
t
if u
p
date is running on the GPU or on the CPU
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Change signature of the se
t
Pbc(
.
.
.
) method in update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhm
u
r
ov
Make PBC
type e
n
umeration into PbcType enum class
commit
|
commitdiff
|
tree
2019-12-31
A
rte
m
Zhm
u
rov
Inform
u
ser why
f
orcing GPU update is no
t
p
o
ssi
b
l
e
commit
|
commitdiff
|
tree
2019-12-31
Artem Zh
m
u
r
o
v
Add de
s
cription o
f
GMX_FO
R
CE_UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Z
h
muro
v
Fix gpuupda
t
e
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change the beha
v
i
o
r of the GPU updat
e
UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Ad
d
a note to the lo
g
file when
-upda
t
e
gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
A
r
t
em
Zhmurov
Clean bad auto-for
m
at in decid
e
gpuusag
e
doxygen comments
commit
|
commitdiff
|
tree
2019-12-17
Ar
t
em Zhmurov
Cle
a
n-up buffer-ops CUDA k
e
rnels
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmurov
C
l
ean up
o
utdated comment
s
in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Art
e
m Zhmu
r
ov
Allow using
G
P
U
u
pdate wit
h
DD
and update gro
u
ps
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhm
u
rov
Enab
l
e
mo
s
t
of the p
u
l
l
i
n
g
f
l
avors with GPU updat
e
commit
|
commitdiff
|
tree
2019-12-11
A
r
t
em Zhmu
r
ov
Clari
f
y w
h
a
t setting zero to some outp
u
t mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
A
v
oid un
n
ecessar
y
r
e
inte
r
pret_cast of coordinates buffe
r
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
S
e
t GP
U
update to false in case of a
re
r
un
commit
|
commitdiff
|
tree
2019-12-06
Artem Zh
m
urov
Pass array ref i
n
stead of cas
t
in
g
to basic
a
rray in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhm
u
rov
Print Op
e
nCL erro
r
info in case of failed asse
r
tion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Make Leap-Fro
g
C
U
DA kernel selection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Renam
e
so
m
e variables in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhmurov
Clear device force bu
f
fer i
f
it was
r
eallocated
commit
|
commitdiff
|
tree
2019-11-28
Art
e
m Zhmur
o
v
Fix pressure
coupling with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
Combine two
b
ooleans
in md lo
o
p
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhm
u
rov
Add meth
o
d
f
or coor
d
in
a
tes scaling int
o
GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Arte
m
Zhmurov
Remove the P
B
C
managemen
t
from
LI
N
CS,
SETTL
E
and Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
A
rtem
Zhmurov
Use
s
ame matrix for Parrinello-Rahm
a
n and
B
e
r
endsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem
Z
hmurov
F
ix
i
ndex map
p
ing issue wit
h
LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
New
c
oo
l
quote
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Z
h
murov
Add D2H c
o
pies for the che
c
kp
o
in
t
ing
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhm
u
rov
Move the c
o
py
o
f
the velocities
f
or the output close
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix icc-
1
9 w
a
rning in nightly matrix
commit
|
commitdiff
|
tree
2019-11-15
Artem
Zhmurov
Removing code duplicati
o
ns in S
t
a
t
e
Propagato
r
D
ataGpu
commit
|
commitdiff
|
tree
2019-11-13
Artem Zh
m
urov
Us
e
s
a
m
e matr
i
x for Parrinello-Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmurov
R
e
mov
e
exc
e
ssive H2D and D2H copies
o
f f
o
rces whe
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
D
i
s
abl
e
GPU update when coordi
n
ates
swapping is enabled
commit
|
commitdiff
|
tree
2019-10-29
Art
e
m Zhm
u
rov
Switch the GPU buffer ops on w
h
en upd
a
t
e is on GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem Z
h
murov
F
i
x
missing co
o
rdinate D2H copy with
GPU upd
a
t
e and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmuro
v
Add ha
v
eCp
u
LocalF
o
rc
e
s fl
a
g to Doma
i
n
LifetimeWorkload
commit
|
commitdiff
|
tree
2019-10-28
Art
e
m Zh
m
ur
o
v
Allow usi
n
g
upd
a
te flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmurov
S
light
improvements to decideWhetherTo
U
seG
p
uForUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Remove unnecessary CUDA st
r
eam
s
ynchronization calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
R
ename havePo
s
itionRe
s
t
raints(
.
.
.
) t
o
haveRestraint
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhm
u
r
ov
Up
d
ate
the copyright message
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmur
o
v
A
dd environment variable
t
hat
ch
a
nges the m
e
an
i
ng of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem
Zhmurov
Remov
e
exc
e
ssive H2D and D2H coordinates
c
opies w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmur
o
v
R
emov
e
excessive H2D an
d
D2H copie
s
of veloc
i
t
ies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Ar
t
em Zh
m
urov
Li
n
k GP
U
for
c
e producer a
n
d consumer tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmur
o
v
Fix th
e
single-GPU
updat
e
-constr
a
ints
commit
|
commitdiff
|
tree
2019-10-14
Art
e
m Zhmurov
Ad
d
sep
a
rate constructor
t
o St
a
tePropagatorDataG
p
u
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem
Zhmurov
Centralize
manag
e
ment
of forces rea
d
y on GPU event
commit
|
commitdiff
|
tree
2019-10-12
Artem Z
h
murov
Change copy mo
d
e to Async in PME
o
n
l
y rank
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Centralize mana
g
ement
of coordinates ready
o
n GP
U
event
commit
|
commitdiff
|
tree
2019-10-11
Artem
Zhmurov
W
r
ong locality w
a
s used when ignorin
g
the P
M
E
force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
A
r
tem Zhmurov
Add management fo
r
velocities and
f
or
c
es copy e
v
ents
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zhmur
o
v
Fix
for t
h
e recent nig
h
tly f
a
i
l
ure
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Pass the GPU streams to Sta
t
eP
r
o
pagatorDat
a
Gpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Art
e
m Zhmurov
Clean up the comme
n
ts sections
in Update-Co
n
strain
commit
|
commitdiff
|
tree
2019-10-07
Artem
Zhmurov
F
i
x a bug in GP
U
halo ex
c
hange initial
i
zation
commit
|
commitdiff
|
tree
2019-10-03
A
r
te
m
Zhmurov
Fi
x
the bug with offl
o
ading
the P
M
E-only ranks to GPU
commit
|
commitdiff
|
tree
2019-10-02
Artem Zhmurov
E
liminate D2D
co
p
y
i
n u
p
date c
o
n
straints
commit
|
commitdiff
|
tree
2019-10-01
Ar
t
em Zhm
u
ro
v
S
t
atePropag
a
tor
D
a
taGpu ob
j
ect
to manage GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Art
e
m
Zhm
u
rov
Slight improvements to
GPU updat
e
/constraints in
i
tialization
commit
|
commitdiff
|
tree
2019-09-27
Arte
m
Zhmurov
I
n
troduce stream management to GP
U
Update-C
o
nstrai
n
ts
commit
|
commitdiff
|
tree
2019-09-22
A
r
tem
Zh
m
uro
v
Disab
l
e GPU update/co
n
s
tr
a
ints whe
n
neither PME n
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
A
r
t
em Zhm
u
r
o
v
Cha
n
ge
P
a
d
d
e
dV
e
c
t
or t
o
Pa
d
dedHostVector for
force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
rtem Zhmurov
F
ix f
o
r
the p
o
s
t
-submit fa
i
lure
commit
|
commitdiff
|
tree
2019-09-11
Art
e
m Zhmurov
D
ecoup
l
e GPU force buffer management from buf
f
er ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Z
hmurov
Decouple
c
o
ordinates buff
e
r managemen
t
f
r
om buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmuro
v
Reorganiz
e
PME
code:
commit
|
commitdiff
|
tree
2019-09-10
A
rtem Zhmurov
M
a
king DeviceBuffer
a
va
i
lible in non-
G
PU bui
l
ds
commit
|
commitdiff
|
tree
2019-09-03
Ar
t
e
m Zhmurov
A
dd Parrinello-Rahman pressure
c
oupling
to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Artem Zh
m
urov
Add temperature coupling t
o
CUD
A
L
eap-Frog
i
ntegrat
o
r
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
M
ake use
of r
e
c
e
nt c
h
ange
s
to prepareKernelArguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
A
r
te
m
Zhmurov
Misce
l
e
n
e
o
u
s improvements to t
h
e
L
eap
Fr
o
g te
s
ts
commit
|
commitdiff
|
tree
2019-08-14
Art
e
m Zhmurov
B
u
g
F
ix: Zeroing the padded area
o
f coordinat
e
s
vect
o
rs
.
.
.
commit
|
commitdiff
|
tree
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