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Store DeviceInformation inside the DeviceContext class
2020-03-19
Artem
Z
hmurov
Store De
v
iceInformatio
n
ins
i
de the
D
evi
c
eCont
e
xt class
commit
|
commitdiff
|
tree
2020-03-19
Artem
Zhmurov
Pass
D
eviceC
o
ntex
t
in
s
tead of GPU runtime dat
a
when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Art
e
m
Z
h
murov
Mak
e
some doxygen
e
rrors
more cl
e
ar
commit
|
commitdiff
|
tree
2020-03-13
Arte
m
Zhmurov
Combine in
i
ti
a
l
i
z
a
t
i
on routines for GPU
s
assigned to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Artem Zh
m
urov
R
e
move
stream from
G
PU kernel launch config
commit
|
commitdiff
|
tree
2020-03-13
Arte
m
Z
h
murov
Use D
e
viceStream init(
.
.
.
) function to create
streams
commit
|
commitdiff
|
tree
2020-03-13
A
r
t
e
m Z
h
mu
r
ov
Make Devic
e
Stream in
t
o a class
commit
|
commitdiff
|
tree
2020-03-11
Artem
Z
hmurov
Fix the post-su
b
mit failures
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhmur
o
v
T
a
ke ov
e
r mana
g
emen
t
o
f OpenCL context from PME and
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
A
rte
m
Zhmurov
Use init(
.
.
)
f
unction
to build DeviceContext
commit
|
commitdiff
|
tree
2020-03-09
A
rtem Z
h
murov
Make Device
C
ontext i
n
to a
p
roper class
commit
|
commitdiff
|
tree
2020-03-05
Artem Zhmurov
Fi
n
a
liz
e
renaming of bEnerVir to computeEnergy
A
ndVirial
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
Do not
c
ount PME only
rank when initializi
n
g NBNX
M
commit
|
commitdiff
|
tree
2020-03-03
Artem Zhm
u
rov
Move the PmePPCo
m
m
G
p
u initial
i
zation from
f
orcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
A
rtem Zhmuro
v
U
p
date the me
s
sage
o
n whether
up
d
a
t
e
a
n
d cons
t
rain
t
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
A
rtem Zhmurov
Fix th
e
RVec to
f
loat3 conversion
test
commit
|
commitdiff
|
tree
2020-02-22
Art
e
m
Zhmuro
v
A
d
d missing header and dis
a
ble fail
i
ng
t
e
st
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmurov
Refactor and enable
RVec
to fl
o
a
t
c
onv
e
rsion test
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmur
o
v
Do not call PME GPU b
u
ilder i
n
CPU code paths
commit
|
commitdiff
|
tree
2020-02-20
A
rtem Zhmuro
v
Use GRO
M
ACS
w
rap
p
ers fo
r
EXPECT_
T
H
R
O
W
/NO_THRO
W
i
n
PM
E
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Use C
U
DA float3 vector ty
p
e instead of fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
Cle
a
n up tr
i
vial function and
d
upli
c
ati
n
g
ma
c
r
o
s
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmur
o
v
Fix the n
i
ghtly fa
i
lure
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhm
u
r
ov
Temporary disable
RVe
c
->float3 conversion test
t
o f
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Art
e
m Zhmurov
Use RVec i
n
stead o
f
float fo
r
x, v and
f
d
e
vic
e
buffers
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
M
ove Devic
e
Info into GPU trai
t
s
commit
|
commitdiff
|
tree
2020-02-05
A
rtem Zhmurov
Make Open
C
L
D
e
vic
e
V
endor into enum
c
las
s
a
n
d move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
A
rtem Zhmurov
Move non-bonde
d
in
i
tiali
z
ation out o
f
th
e
f
o
rcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
Fi
x
typ
o
in and remove
a couple
of duplicates from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem Zhmur
o
v
Enable
G
P
U update
f
or sup
p
orte
d
cases of FEP
commit
|
commitdiff
|
tree
2020-02-01
Ar
t
em
Z
h
mu
r
ov
Cou
p
le cool quotes
commit
|
commitdiff
|
tree
2020-02-01
A
r
t
em Zhmurov
Merge "Merge branc
h
origin/r
e
lease-2020 into master"
commit
|
commitdiff
|
tree
2020-01-30
Art
e
m
Zhmurov
Cleaning b
o
oleans i
n
NBNXM in OpenCL b
u
ild
commit
|
commitdiff
|
tree
2020-01-29
Ar
t
em Zhmurov
Reorganize
GPU
stuff
in
i
tializati
o
n in PME-only ranks
commit
|
commitdiff
|
tree
2020-01-29
A
rtem Zhmur
o
v
Split and move the
c
heckDevi
c
eBuffer(
.
.
.
) functio
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Remov
e
the
r
es
t
of the device coordinates m
a
nag
e
me
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Rename UpdateConstraintsCuda to UpdateConstraintsGpu
commit
|
commitdiff
|
tree
2020-01-23
A
rtem Zhmurov
Fix
a couple of com
m
as in cool
q
u
o
t
es
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Ren
a
me SettleCuda
t
o Sett
l
eG
p
u
commit
|
commitdiff
|
tree
2020-01-20
A
rt
e
m Zhmurov
Rena
m
e
Lin
c
s
Cuda into Li
n
c
s
G
pu
commit
|
commitdiff
|
tree
2020-01-20
Artem
Zhmurov
Rename Leap
F
rogCuda to Leap
F
rogGpu
commit
|
commitdiff
|
tree
2020-01-13
Art
e
m Zhmu
r
ov
Re
p
ort if update is running on
t
he G
P
U or on the CPU
commit
|
commitdiff
|
tree
2020-01-09
Arte
m
Zhmurov
Change signatur
e
of t
h
e setPbc(
.
.
.
) meth
o
d in updat
e
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmur
o
v
Make
P
BC
t
ype e
n
umeration into PbcTyp
e
enum class
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Inform user
w
hy forcing GPU update is not possible
commit
|
commitdiff
|
tree
2019-12-31
A
r
te
m
Zhmu
r
ov
Add
description of G
M
X_FORCE_UPDATE_DEFAULT_G
P
U
d
ev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Fix gpu
u
pdate matri
x
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Chang
e
the behav
i
or of the GPU update UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Z
h
murov
A
dd
a no
t
e
t
o
the log f
i
l
e when
-update gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmu
r
ov
Cl
e
an bad auto-format in
decidegpuusage
doxygen
c
o
mments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
C
lean-u
p
bu
f
fer-ops
C
UDA
k
ernels
commit
|
commitdiff
|
tree
2019-12-13
Artem Z
h
mu
r
o
v
Clean u
p
ou
t
dated
com
m
ents
in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allow
u
sing GPU
update with DD and u
p
date gr
o
ups
commit
|
commitdiff
|
tree
2019-12-11
Art
e
m Zhmurov
Enable most of the pulling flavors
with GPU update
commit
|
commitdiff
|
tree
2019-12-11
Artem Z
h
murov
Clarif
y
w
hat s
e
tting zero to some ou
t
put
mdp optio
n
s
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
A
r
t
e
m Zhmurov
A
v
oid unnecessa
r
y
r
e
interpret_c
a
st of coo
r
di
n
ates
bu
f
fer
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmu
r
ov
Set GP
U
update to
fals
e
in
c
as
e
of a rerun
commit
|
commitdiff
|
tree
2019-12-06
Artem
Z
h
m
uro
v
P
a
ss array ref instead of casting to basic array in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Arte
m
Z
hmur
o
v
Print Open
C
L error in
f
o in case of failed assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem
Zhm
u
rov
Make Leap-Frog
C
UDA
k
e
r
n
e
l se
l
ection
sa
f
er
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Rename some varia
b
les
in GPU
Upd
a
te
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clear device for
c
e buffe
r
if it
w
as reallocated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Fix press
u
re coupling with GPU
u
p
date
commit
|
commitdiff
|
tree
2019-11-27
Arte
m
Zhm
u
ro
v
Combine two bo
o
leans in md
loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Z
h
mur
o
v
Add
method for coo
r
d
i
nates sc
a
ling into GPU u
p
date
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Artem Zhmu
r
o
v
Remove th
e
PBC manageme
n
t from LINCS, SETTLE
and
Lea
p
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zh
m
urov
Use same
m
atrix for
P
arrinel
l
o-R
a
hman and Ber
e
ndsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Fix index mapping is
s
ue wit
h
L
INC
S
on GPU
commit
|
commitdiff
|
tree
2019-11-23
Arte
m
Zhmurov
N
ew cool quote
commit
|
commitdiff
|
tree
2019-11-20
A
rte
m
Zhmuro
v
A
dd D2H copies for the checkp
o
in
t
ing
commit
|
commitdiff
|
tree
2019-11-20
Artem
Zhmurov
M
o
ve the co
p
y of the vel
o
cities
for the output c
l
os
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem
Z
hmurov
F
i
x icc-
1
9 war
n
ing in nightly matrix
commit
|
commitdiff
|
tree
2019-11-15
Artem Z
h
m
u
r
o
v
Removing code
dup
l
ic
a
tions in StatePropaga
t
o
rData
G
pu
commit
|
commitdiff
|
tree
2019-11-13
Art
e
m
Z
hmu
r
ov
Use
same matrix f
o
r P
a
rrinell
o
-R
a
hman and Be
r
endsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Art
e
m Z
h
murov
R
emove exces
s
ive H2
D
and D2H copies of forc
e
s w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Arte
m
Zhmurov
D
i
s
a
ble
G
P
U upd
a
te when coo
r
d
inates s
w
apping is
e
nabled
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmur
o
v
Switch
the GPU buffer
ops o
n
when update is
o
n G
P
U
commit
|
commitdiff
|
tree
2019-10-28
Art
e
m Zh
m
urov
Fix missing c
o
ordinate D2H copy w
i
th GPU update
a
nd
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Ar
t
em Zhmurov
A
d
d
h
a
v
e
C
p
uLocalForc
e
s flag
t
o
DomainLifetimeW
o
rkloa
d
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Allow using updat
e
flag
commit
|
commitdiff
|
tree
2019-10-23
Ar
t
e
m
Z
hmu
r
ov
Slight improvements
t
o decideW
h
eth
e
rToUseGpuForU
p
date
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhm
u
rov
Remo
v
e unnecessar
y
CUD
A
st
r
eam synch
r
onization calls
commit
|
commitdiff
|
tree
2019-10-22
A
r
tem Zhmurov
Ren
a
me hav
e
PositionRestraints(
.
.
.
) to
haveR
e
straints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
A
rtem Z
h
murov
Update t
h
e copyri
g
h
t
m
e
ssag
e
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmurov
Add environ
m
e
n
t var
i
able that
changes t
h
e mean
i
ng of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem
Zhmurov
Remove excessive H2D and D2H c
o
or
d
inates copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhm
u
rov
Remove
excessive H2D and D2
H
copies of velo
c
ities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Art
e
m Zhmurov
L
i
n
k
G
P
U f
o
rce producer an
d
consum
e
r tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmurov
F
ix
the single-GPU up
d
ate-constra
i
n
ts
commit
|
commitdiff
|
tree
2019-10-14
A
rtem Zh
m
urov
Add separat
e
constructor
to
StatePropagatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
A
rtem Zhmuro
v
Centralize management of
fo
r
ces
r
eady
o
n GPU even
t
commit
|
commitdiff
|
tree
2019-10-12
A
rtem Zhmurov
Cha
n
g
e copy mo
d
e to Asyn
c
in P
M
E only rank
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
Centralize mana
g
ement
of
c
oordinates ready
on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Ar
t
e
m Zhmur
o
v
Wron
g
locali
t
y wa
s
used wh
e
n ignor
i
ng th
e
P
ME f
o
rce
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem
Zhmurov
A
dd manageme
n
t for ve
l
o
cities and f
o
rces
c
opy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zhmurov
Fix for the recent night
l
y failure
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
h
m
u
r
ov
Pass
the GPU s
t
r
eam
s
to State
P
ropagato
r
DataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Clean up the com
m
ents sec
t
ions in Update-Cons
t
rain
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Fix a b
u
g in
GPU
halo exch
a
nge initi
a
lizatio
n
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmuro
v
Fix t
h
e bug with
offloading
the PME-only ranks to GPU
commit
|
commitdiff
|
tree
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