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Use init(..) function to build DeviceContext
2020-03-10
Arte
m
Zhmu
r
ov
Use init(
.
.
) function to bu
i
ld
DeviceContex
t
commit
|
commitdiff
|
tree
2020-03-09
Artem Zhmurov
M
ake DeviceContext
into a
p
rop
e
r
cl
a
ss
commit
|
commitdiff
|
tree
2020-03-05
Artem
Z
hmu
r
ov
Final
i
z
e renam
i
n
g of
bEnerVir to
computeEnergyAndVirial
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
Do not count
PM
E
o
nly rank when initializin
g
NBN
X
M
commit
|
commitdiff
|
tree
2020-03-03
Artem Zhmurov
Move the PmePPCommG
p
u initializa
t
ion from force
r
ec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem
Zhmurov
Upda
t
e
the message on
wh
e
ther update a
n
d
constra
i
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Art
e
m Zhmur
o
v
Fix the RVe
c
t
o
float3 conversion test
commit
|
commitdiff
|
tree
2020-02-22
Artem Zhm
u
rov
Add
missing header a
n
d
dis
a
ble faili
n
g
test
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmur
o
v
Refact
o
r
and enable RVec to float co
n
version tes
t
commit
|
commitdiff
|
tree
2020-02-20
A
rtem
Z
hmur
o
v
Do not
call P
M
E GPU build
e
r in CPU
c
o
d
e
p
a
ths
commit
|
commitdiff
|
tree
2020-02-20
Art
e
m Zh
m
urov
Use GROMACS wrappers for EXPECT_T
H
ROW/NO_THROW i
n
P
M
E
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
A
rtem Zhmuro
v
U
se CUD
A
float3
vector type
i
n
stead of fv
e
c in
G
PU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Arte
m
Zhmurov
Cle
a
n
up t
r
iv
i
al functio
n
and dupli
c
ating ma
c
ro
s
es
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem
Z
hmurov
Fi
x
the nightl
y
fail
u
re
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmurov
Temporary
d
i
sable RVec->float3 c
o
nversion
t
est to fi
x
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem
Z
hmurov
Use RVec ins
t
ead of flo
a
t for x,
v and f device buf
f
ers
commit
|
commitdiff
|
tree
2020-02-06
Artem
Zhmurov
Move
DeviceI
n
fo int
o
G
P
U
traits
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
Make
O
p
e
nCL Dev
i
ceVendor into
e
n
u
m
c
l
ass a
n
d
m
ove to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Art
e
m
Z
hmur
o
v
Mov
e
non-bonded
initialization
o
u
t
of
the forcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmu
r
ov
Fix typo in
and remove a co
u
ple of dupli
c
ate
s
fr
o
m
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
A
rtem Zhmu
r
ov
En
a
ble GPU update for s
u
pported cases
o
f
F
EP
commit
|
commitdiff
|
tree
2020-02-01
Artem
Z
hmurov
Couple cool
q
uotes
commit
|
commitdiff
|
tree
2020-02-01
Artem Zhmurov
Merg
e
"
M
erge branch
origin/relea
s
e-202
0
into
master"
commit
|
commitdiff
|
tree
2020-01-30
Ar
t
em Z
h
murov
Cleaning
b
ooleans in
NBN
X
M
i
n OpenCL build
commit
|
commitdiff
|
tree
2020-01-29
A
r
t
em
Zhmurov
R
eo
r
ga
n
ize GPU
stuff initialization in P
M
E-only ranks
commit
|
commitdiff
|
tree
2020-01-29
A
rtem Zhmurov
Split
and move the checkDeviceBuffer(
.
.
.
)
function
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
A
r
t
em
Z
h
m
urov
Remove
the rest
o
f th
e
devi
c
e coordinates man
a
gement
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
A
rtem Zhmurov
Rename UpdateConstraintsCuda to
Up
d
ateConstraint
s
Gpu
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhmurov
F
i
x a couple of c
o
mmas in cool quotes
commit
|
commitdiff
|
tree
2020-01-20
Arte
m
Zhmurov
R
e
na
m
e
S
e
ttle
C
uda to Settle
G
p
u
commit
|
commitdiff
|
tree
2020-01-20
Art
e
m
Z
hmuro
v
Rename Li
n
c
sCu
d
a int
o
LincsG
p
u
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmu
r
ov
Rename Le
a
pFrogCuda to
Le
a
pFrogGp
u
commit
|
commitdiff
|
tree
2020-01-13
Artem Zhmurov
Report if u
p
d
a
te i
s
runn
i
n
g
on the GPU
o
r on the CPU
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Ch
a
nge signature of the
s
etPbc(
.
.
.
) method in upda
t
e
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Art
e
m Zhmurov
Ma
k
e P
B
C
type enumerat
i
o
n in
t
o Pbc
T
yp
e
enum cla
s
s
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zhmurov
Info
r
m user
why forcing GPU update
is
n
ot possible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhm
u
r
o
v
Ad
d
descr
i
ption of GMX
_
F
O
RCE_UPDATE_
D
EFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
e
m
Zhmurov
F
ix gpuup
d
ate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmur
o
v
Change t
h
e behavior o
f
the GPU updat
e
UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmur
o
v
A
d
d a note to the log file when
-
update gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
A
r
tem Z
h
m
u
rov
Clean bad auto-format in decidegpuusage
doxygen comments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
Clean-up buffer-o
p
s CUDA kernels
commit
|
commitdiff
|
tree
2019-12-13
A
r
tem Zhmuro
v
Clean up ou
t
dated co
m
ments in
md
.
c
pp
commit
|
commitdiff
|
tree
2019-12-12
Art
e
m
Zhmurov
Allow usin
g
GPU
update with DD and
u
pdate
g
roups
commit
|
commitdiff
|
tree
2019-12-11
Artem
Z
h
m
urov
En
a
ble most
of t
h
e pulling flavors wi
t
h GP
U
u
p
d
ate
commit
|
commitdiff
|
tree
2019-12-11
A
rtem Zhmurov
Clarify what setti
n
g zero
t
o
s
ome
outp
u
t
m
dp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem
Z
h
m
urov
Avoid unnecessary rei
n
terpret_cast of
coordinates buf
f
er
commit
|
commitdiff
|
tree
2019-12-10
A
r
tem Z
h
m
u
rov
Set GPU update
to false in cas
e
o
f
a rerun
commit
|
commitdiff
|
tree
2019-12-06
A
rtem Zhmuro
v
Pass
a
rr
a
y ref inste
a
d of casting to ba
s
ic arr
a
y
in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Pri
n
t OpenCL
error i
n
fo in
c
ase of failed assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem
Z
hm
u
rov
M
ak
e
Leap-
F
rog
C
UDA kernel sel
e
cti
o
n
s
a
fer
commit
|
commitdiff
|
tree
2019-11-29
A
r
t
em
Zhmurov
Re
n
a
me some va
r
iable
s
in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clear dev
i
ce force buffer if it was reallo
c
ated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhm
u
rov
Fix p
r
e
ssure coupl
i
ng with
G
PU update
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Comb
i
ne two
boolea
n
s in
md
loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhm
u
rov
Add method for
co
o
rd
i
n
at
e
s scaling i
n
t
o GPU updat
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Art
e
m Z
h
m
ur
o
v
Rem
o
ve the PBC management from LINCS, SETTL
E
an
d
Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zh
m
u
r
ov
Use sam
e
matrix for Pa
r
rinello-R
a
hman
and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zh
m
urov
F
i
x index mapping iss
u
e with LIN
C
S
on GPU
commit
|
commitdiff
|
tree
2019-11-23
Ar
t
em Zhmurov
New c
o
ol q
u
ote
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hmurov
Add
D2
H
copies for the che
c
kp
o
in
t
in
g
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
M
ove
t
he copy of the veloc
i
ties f
o
r th
e
output cl
o
ser
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Art
e
m Z
h
murov
Fix icc-19 war
n
ing in ni
g
htly ma
t
rix
commit
|
commitdiff
|
tree
2019-11-15
A
rtem Zhmurov
Removing code dupl
i
cation
s
in StatePropagatorDataGpu
commit
|
commitdiff
|
tree
2019-11-13
Ar
t
em Zhmu
r
o
v
U
s
e same
matrix f
o
r
P
arrinello-Rahman and
B
erend
s
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zh
m
urov
Remove excessive H2D and
D2H
copies of forces whe
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
A
rt
e
m
Zhmurov
Disable GPU update
w
hen coordinates swapping is enabled
commit
|
commitdiff
|
tree
2019-10-29
A
r
tem
Zh
m
urov
Switch t
h
e GPU
b
uffe
r
ops on when upd
a
te is on G
P
U
commit
|
commitdiff
|
tree
2019-10-28
Artem Z
h
m
u
rov
Fix miss
i
ng coordinate D2H copy with GPU up
d
ate and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Art
e
m Zhmurov
Ad
d
h
ave
C
p
u
LocalForces f
l
ag to
D
omainL
i
f
etimeW
o
rklo
a
d
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Allow us
i
ng update flag
commit
|
commitdiff
|
tree
2019-10-23
Artem
Z
hmuro
v
Slight improvements to d
e
cideWhe
t
herToU
s
eGpuFo
r
Upd
a
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem
Z
hmurov
Remo
v
e
unnecessar
y
CUDA stream
s
ynchronization calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Rena
m
e hav
e
Posi
t
ionRestraints(
.
.
.
) to have
R
e
stra
i
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem
Zhm
u
rov
Update t
h
e cop
y
right m
e
ssage
commit
|
commitdiff
|
tree
2019-10-21
Ar
t
em Zhm
u
rov
Add envi
r
onm
e
n
t variable that changes th
e
mea
n
ing of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Ar
t
em Zhmuro
v
Remo
v
e ex
c
essive H2D an
d
D2
H
coor
d
inates copies w
h
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
rtem Zh
m
u
r
o
v
Remo
v
e excessive H2D and D2H copies of velocitie
s
when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmurov
L
ink GPU f
o
rce producer and c
o
nsumer
t
asks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmurov
F
i
x the single-G
P
U update-constraints
commit
|
commitdiff
|
tree
2019-10-14
A
rtem
Zhmurov
Add
s
eparat
e
construc
t
or
to St
a
tePropagatorDataGp
u
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
Cen
t
ra
l
ize
m
anagem
e
n
t
o
f forces ready on GPU
e
vent
commit
|
commitdiff
|
tree
2019-10-12
A
r
tem Zhmurov
C
han
g
e c
o
py mode to
Async in PME only rank
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Zhmuro
v
Centralize management of co
o
r
dina
t
es ready on GPU e
v
ent
commit
|
commitdiff
|
tree
2019-10-11
Artem Zhmu
r
ov
Wrong locality
was used when i
g
noring the PME f
o
rce
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmurov
Add managem
e
n
t
for velocities a
n
d forces c
o
py events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Art
e
m
Z
h
murov
Fix fo
r
the rece
n
t nigh
t
ly
f
ailure
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhm
u
rov
Pass the GPU streams to StateP
r
o
p
agatorData
G
pu con
s
tr
u
ctor
commit
|
commitdiff
|
tree
2019-10-07
A
r
tem Zhmurov
Cle
a
n up th
e
commen
t
s secti
o
ns in Update-Constrai
n
commit
|
commitdiff
|
tree
2019-10-07
Ar
t
em Zhmurov
Fix
a
bug in GPU halo e
x
c
h
ange initialization
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
F
ix the
b
ug wit
h
of
f
loading the PME-onl
y
ra
n
ks to GP
U
commit
|
commitdiff
|
tree
2019-10-02
Arte
m
Zhmuro
v
Eliminate D2D co
p
y in update co
n
straints
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
StatePropagato
r
DataG
p
u objec
t
to manage
G
PU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Art
e
m Z
h
m
urov
Slight
improvements to G
P
U update/constraint
s
ini
t
ializatio
n
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Introdu
c
e stream ma
n
agement to
G
P
U
Upda
t
e-Co
n
straints
commit
|
commitdiff
|
tree
2019-09-22
Arte
m
Zhmurov
D
is
a
ble GPU update/co
n
s
traints when
n
eit
h
er P
M
E
n
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmurov
Ch
a
nge Padded
V
ector to PaddedHos
t
Vector f
o
r
force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Ar
t
em Zh
m
urov
Fix fo
r
the post-submit failur
e
commit
|
commitdiff
|
tree
2019-09-11
Art
e
m Z
h
murov
Decouple GPU
f
orce buffer management from
b
u
ff
e
r ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zh
m
urov
Decoup
l
e coo
r
d
inates buffer management
from buffer
.
.
.
commit
|
commitdiff
|
tree
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