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Unify CUDA and OpenCL lookup-table creation
2020-05-05
Artem Z
h
murov
Unify
CUDA
a
nd OpenCL lookup-t
a
ble
c
reation
commit
|
commitdiff
|
tree
2020-05-04
Artem Zhmur
o
v
Unify
C
UDA and OpenCL lookup-table c
r
e
ation
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Move
P
BC setu
p
out of
t
he lau
n
chKer
n
el(
.
.
.
)
i
n GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
Artem Zhmur
o
v
Fix t
h
e
number of steps check when
checkpoint is l
o
aded
commit
|
commitdiff
|
tree
2020-04-16
Artem Zhm
u
r
ov
Ne
w
c
ool qu
o
te
commit
|
commitdiff
|
tree
2020-04-16
Artem
Z
hm
u
r
ov
Un
i
fy C
U
D
A
and OpenCL lookup
-
t
able
cr
e
ation
commit
|
commitdiff
|
tree
2020-03-25
Artem Zhmurov
Mak
e
use
o
f the
DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-23
A
rtem Zhmurov
In
t
roduce DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-20
Arte
m
Zhmu
r
ov
Add OpenCL error reportin
g
to
G
PU region timer
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhmurov
Small f
i
xes to the DeviceSt
r
eam
commit
|
commitdiff
|
tree
2020-03-19
Artem Zhmurov
St
o
r
e D
e
vi
c
e
I
nformation inside
t
he DeviceContext class
commit
|
commitdiff
|
tree
2020-03-19
Ar
t
em Zhmur
o
v
P
ass DeviceConte
x
t instea
d
of GPU runtime data w
h
en
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Artem Zhm
u
rov
M
a
ke some doxygen errors more
c
lear
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Combine initialization
routines for GPU
s
a
ssigned
to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Remove stream from GPU kern
e
l l
a
unch config
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Use DeviceStream init(
.
.
.
) function to
crea
t
e
streams
commit
|
commitdiff
|
tree
2020-03-13
Art
e
m Zhmur
o
v
Make
De
v
ic
e
Stream
in
t
o a
class
commit
|
commitdiff
|
tree
2020-03-11
Ar
t
em Zhmurov
Fix
the po
s
t-submit failures
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhm
u
rov
Take over ma
n
a
gement of OpenCL context from PME
a
nd
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Ar
t
em Z
h
muro
v
Use
i
ni
t
(
.
.
)
func
t
ion to build Devic
e
C
o
nte
x
t
commit
|
commitdiff
|
tree
2020-03-09
Artem Zhmurov
Mak
e
Devic
e
Context into a prop
e
r class
commit
|
commitdiff
|
tree
2020-03-05
Artem Zhm
u
r
o
v
Fin
a
lize
re
n
a
m
ing
of bEnerVir to c
o
m
p
uteE
n
e
r
g
yA
n
dVirial
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
D
o not count PM
E
only rank when i
n
itial
i
z
i
n
g
NBNXM
commit
|
commitdiff
|
tree
2020-03-03
Artem
Zhmurov
M
o
ve the PmePP
C
ommGp
u
initialization fr
o
m fo
r
cerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Arte
m
Zhmurov
Update the message on whe
t
h
e
r up
d
a
te an
d
constraints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Z
h
murov
F
i
x
the RVec to float3 conversion tes
t
commit
|
commitdiff
|
tree
2020-02-22
Ar
t
em Zh
m
u
r
ov
A
dd mis
s
ing header and disable failing test
commit
|
commitdiff
|
tree
2020-02-21
Artem
Z
hmu
r
ov
Refactor
an
d
en
a
ble RVec to float
c
onversion test
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Do not call
PME GPU
builder in CPU cod
e
paths
commit
|
commitdiff
|
tree
2020-02-20
A
r
t
e
m Z
h
murov
Use G
R
O
M
ACS wrappers for EXPECT_THROW/NO_THROW in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem
Zh
m
urov
U
se CUDA f
l
oa
t
3 vect
o
r type instead of fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
C
lean up trivial function and dupli
c
ating macroses
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Art
e
m Zhmurov
Fi
x
the nigh
t
ly f
a
ilure
commit
|
commitdiff
|
tree
2020-02-08
A
r
tem Zhmurov
Tem
p
orary disable RVec->float3 con
v
er
s
ion tes
t
to fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Ar
t
em Zh
m
urov
Use RVec instead
of floa
t
for x
,
v
and
f device bu
f
fers
commit
|
commitdiff
|
tree
2020-02-06
A
r
t
em Zhm
u
rov
Mo
v
e
DeviceInfo into GPU trait
s
commit
|
commitdiff
|
tree
2020-02-05
Artem
Zhmu
r
ov
M
a
ke
O
p
e
nCL DeviceVendor into enum
class a
n
d m
o
ve to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Artem Zh
m
u
r
ov
Move non-bonded initia
l
ization out
of th
e
forcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
Fix typ
o
i
n an
d
r
emove a couple o
f
d
uplicates from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem
Z
h
m
u
r
ov
E
nab
l
e
G
PU update fo
r
s
u
pported cases of FEP
commit
|
commitdiff
|
tree
2020-02-01
Ar
t
em Zhmu
r
ov
C
o
uple
c
o
o
l
q
uotes
commit
|
commitdiff
|
tree
2020-02-01
A
r
tem Zhmurov
M
e
rge "Me
r
g
e branch origin/release-2020 into master
"
commit
|
commitdiff
|
tree
2020-01-30
Artem Zhmurov
Clea
n
ing
bool
e
ans in NBNXM in Open
C
L build
commit
|
commitdiff
|
tree
2020-01-29
A
r
tem Zh
m
uro
v
Reorganize GPU
stuff initialization in PME-o
n
ly
ranks
commit
|
commitdiff
|
tree
2020-01-29
Artem
Z
hmurov
Spli
t
and mov
e
the ch
e
ckDeviceBuff
e
r
(
.
.
.
) f
u
nction
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
R
emove
t
h
e
rest of the device co
o
r
d
i
nates m
a
nagement
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Art
e
m Zhmurov
Rename
UpdateC
o
nstr
a
int
s
Cuda to Upd
a
teConstrain
t
sGpu
commit
|
commitdiff
|
tree
2020-01-23
Arte
m
Zh
m
ur
o
v
Fix a couple of commas in cool quotes
commit
|
commitdiff
|
tree
2020-01-20
Artem
Zhmurov
Rename SettleCuda to S
e
ttle
G
p
u
commit
|
commitdiff
|
tree
2020-01-20
Art
e
m Zhmurov
Renam
e
LincsCuda
i
nto LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
A
r
tem Zhmurov
R
ename Lea
p
FrogCu
d
a to Leap
F
r
ogGpu
commit
|
commitdiff
|
tree
2020-01-13
Artem Z
h
m
u
rov
R
eport i
f
upd
a
te
i
s running
on the GPU or on
the CPU
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Cha
n
ge sig
n
ature
of
the s
e
tPbc
(
.
.
.
) method in updat
e
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem
Zhm
u
rov
Mak
e
PB
C
type enumeration into Pb
c
T
y
pe enum class
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
hmurov
Inform user why forcing GPU updat
e
is not possib
l
e
commit
|
commitdiff
|
tree
2019-12-31
Artem Z
h
m
u
rov
Add descriptio
n
of GMX_
F
O
R
CE_UPDATE_DEFAULT_GPU
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zhmurov
Fix
g
puupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
A
r
t
e
m
Zhmurov
Change the behav
i
or of the GPU u
p
date UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
A
dd a no
t
e to the log file when -update
gp
u
w
a
s
set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m Zhmur
o
v
Clean bad auto-format
i
n decidegpuusage doxygen
com
m
ents
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhm
u
rov
C
l
e
a
n-up
b
uffer-o
p
s
CUDA kernels
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmu
r
ov
Clean up out
d
at
e
d comments in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhm
u
r
ov
Allow using GPU update with DD and update groups
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem Zhmurov
Enable mos
t
of the pulling fl
a
vors with
G
PU
u
pdate
commit
|
commitdiff
|
tree
2019-12-11
Arte
m
Z
h
murov
Clarify what se
t
ting zero
t
o some
o
utput mdp op
t
ions
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Ar
t
em Zhmu
r
o
v
Avoid unnecessar
y
re
i
nterpret_cas
t
o
f co
o
rdinates buffer
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Set GPU u
p
d
a
te
to false in case of a
rerun
commit
|
commitdiff
|
tree
2019-12-06
Arte
m
Zhm
u
r
o
v
P
a
ss array
r
ef instead o
f
ca
s
ting to b
a
sic
a
rray i
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
P
rint OpenC
L
error info in ca
s
e of f
a
iled assert
i
on
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
M
a
ke Le
a
p-Frog CUDA kernel selection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zhmurov
Ren
a
me
s
om
e
vari
a
b
l
es i
n
GPU Upd
a
t
e
commit
|
commitdiff
|
tree
2019-11-28
A
r
t
e
m Zh
m
ur
o
v
Clear device force buffe
r
if i
t
was
re
a
llocated
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhmuro
v
Fix
p
r
e
ssure
coupling
with GPU
up
d
ate
commit
|
commitdiff
|
tree
2019-11-27
Artem Z
h
mur
o
v
C
o
mbine t
w
o b
o
olean
s
i
n md loop
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Z
h
murov
Add
m
eth
o
d for
coordinates scaling into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Artem Zhmurov
Re
m
ove
the
P
BC manag
e
ment fro
m
LI
N
CS, SETTLE an
d
Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhm
u
r
o
v
Use
s
ame matrix for
P
ar
r
inel
l
o-Rah
m
an
and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Fix index m
a
p
ping i
s
su
e
with L
I
N
CS on GPU
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
A
d
d D2H c
o
p
ie
s
for the checkpointing
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hmuro
v
Move
t
he copy of the vel
o
c
i
ties
for the
o
utput c
l
os
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
A
r
tem
Z
hmurov
Fix icc-
1
9 war
n
in
g
i
n nightly mat
r
i
x
commit
|
commitdiff
|
tree
2019-11-15
Artem Zhmur
o
v
Rem
o
ving code duplications in StatePropagatorDataGpu
commit
|
commitdiff
|
tree
2019-11-13
Artem Zhmurov
Use same matrix for Parr
i
n
ell
o
-R
a
hman and
B
erend
s
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmurov
Remove
e
xcessive
H
2
D
an
d
D2H copie
s
of
f
orces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhm
u
rov
Disable
G
PU
update when coordinate
s
s
wappi
n
g is enabled
commit
|
commitdiff
|
tree
2019-10-29
Artem
Z
hmu
r
ov
S
witch the GPU buf
f
er
o
ps on when update is on GPU
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem
Z
hm
u
rov
Fix missi
n
g co
o
rdinate D2
H
copy with
G
PU update an
d
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem
Z
h
m
ur
o
v
Add
h
aveCpuLocalForces flag
t
o
DomainLifet
i
meW
o
rkload
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Allow using update
flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmurov
Sli
g
h
t
impr
o
vements to
d
ecid
e
W
he
t
herToUseG
p
uForUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhm
u
rov
Re
m
ove unnecessar
y
C
U
DA stream
s
ync
h
ronization calls
commit
|
commitdiff
|
tree
2019-10-22
Arte
m
Zhm
u
ro
v
Rename
h
avePositionRe
s
t
r
a
ints(
.
.
.
) to
h
a
veRestra
i
nts
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem
Zhmurov
Update the
c
opyright message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
A
r
tem
Zhm
u
rov
A
dd
e
nvironment variab
l
e
t
hat changes the me
a
nin
g
of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
r
tem
Z
h
murov
Remove excessive H2D and D
2
H
coordinates copies w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmu
r
ov
Remove excessive
H
2D
and D2
H
copies
of velocities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmurov
Lin
k
GPU force
p
roduce
r
and con
s
umer
t
asks
commit
|
commitdiff
|
tree
2019-10-15
Artem
Z
h
mur
o
v
Fix
the sin
g
le-GPU
updat
e
-constr
a
ints
commit
|
commitdiff
|
tree
2019-10-14
Arte
m
Zhmur
o
v
Add separate co
n
structor t
o
StatePropagator
D
ataGp
u
.
.
.
commit
|
commitdiff
|
tree
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