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Unify CUDA and OpenCL lookup-table creation
2020-04-16
Artem
Z
hmurov
Unify CUDA and
O
penCL
l
o
o
kup-table
c
reation
commit
|
commitdiff
|
tree
2020-03-25
Artem
Z
hmurov
M
ake use of the DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-23
Ar
t
em Zhmurov
Intro
d
uce DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhmurov
Add OpenCL error repo
r
t
ing
to GPU region timer
commit
|
commitdiff
|
tree
2020-03-20
A
r
t
e
m
Zhm
u
ro
v
Sm
a
ll
f
i
xes to t
h
e
DeviceStream
commit
|
commitdiff
|
tree
2020-03-19
Arte
m
Zhmur
o
v
S
t
ore
D
eviceInformation inside the D
e
vic
e
Context
class
commit
|
commitdiff
|
tree
2020-03-19
A
r
tem Zhmurov
Pass DeviceContext
i
nstead of
G
P
U runtime
d
a
t
a when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
A
rtem Zhmurov
Make some do
x
ygen e
r
rors more cl
e
ar
commit
|
commitdiff
|
tree
2020-03-13
Ar
t
em
Zhmurov
Comb
i
n
e initialization routines for GPUs assig
n
ed to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Arte
m
Z
h
murov
R
e
m
ove str
e
am fro
m
GPU k
e
rnel la
u
n
c
h co
n
fig
commit
|
commitdiff
|
tree
2020-03-13
Artem Zh
m
u
rov
Use
D
eviceStrea
m
init(
.
.
.
) functio
n
to create streams
commit
|
commitdiff
|
tree
2020-03-13
Ar
t
em Zhmur
o
v
Make DeviceStream into a class
commit
|
commitdiff
|
tree
2020-03-11
A
rtem Zhmur
o
v
Fix the post-submit fail
u
res
commit
|
commitdiff
|
tree
2020-03-11
Artem
Z
hmurov
Take over management of Open
C
L conte
x
t from PME and
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Ar
t
e
m
Zhmurov
Use
i
nit(
.
.
)
f
unction to build Devic
e
Cont
e
xt
commit
|
commitdiff
|
tree
2020-03-09
Art
e
m Zhmuro
v
Make Devi
c
eContext into a p
r
oper class
commit
|
commitdiff
|
tree
2020-03-05
Ar
t
em Zhmurov
Final
i
ze renaming
of bEnerVir to compute
E
ner
g
yAndVir
i
al
commit
|
commitdiff
|
tree
2020-03-04
Ar
t
em
Z
hmurov
Do
not
c
o
un
t
PME
only ran
k
when initia
l
izing NBNXM
commit
|
commitdiff
|
tree
2020-03-03
Artem Zhmurov
Move
th
e
PmePPCommGpu ini
t
ializati
o
n from forcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmur
o
v
U
p
d
ate the
mes
s
age on whether update a
n
d constraints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Zh
m
u
r
o
v
Fix
t
he RVec to flo
a
t
3
conversion test
commit
|
commitdiff
|
tree
2020-02-22
Artem
Z
hm
u
rov
Ad
d
m
i
ssing header and
disabl
e
failing test
commit
|
commitdiff
|
tree
2020-02-21
Artem Z
h
mur
o
v
Re
f
a
ctor and enabl
e
R
Vec to
floa
t
conversion
t
est
commit
|
commitdiff
|
tree
2020-02-20
A
rtem
Z
hmur
o
v
Do not call PME
G
PU builder
in CP
U
code
p
aths
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Us
e
GRO
M
ACS wr
a
ppe
r
s
for EXPECT_THROW/NO_
T
HROW i
n
PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhm
u
rov
Use CUDA
f
loat3 vector type instead of fve
c
in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
A
rtem Zhmuro
v
Clean u
p
t
r
ivia
l
funct
i
o
n
and du
p
lic
a
ting mac
r
os
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
Fi
x
the
nightly
f
ailure
commit
|
commitdiff
|
tree
2020-02-08
Art
e
m Zhmurov
Temporary
d
is
a
ble RVec
-
>
f
loat3
c
onv
e
rsi
o
n test to fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmur
o
v
Use RV
e
c inste
a
d of float for x,
v
and f device buffers
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
Move DeviceInfo in
t
o GPU traits
commit
|
commitdiff
|
tree
2020-02-05
Arte
m
Z
h
m
urov
M
a
ke OpenCL Devic
e
Vendor i
n
to enum class and move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Art
e
m Zhm
u
ro
v
Move non-bonded i
n
i
tializati
o
n out of the f
o
rcerec
commit
|
commitdiff
|
tree
2020-02-05
A
rtem
Zhmuro
v
Fix typo
in
and
r
emove a co
u
ple of dupl
i
cates from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem Zhmurov
E
n
able
GPU update for sup
p
orted cas
e
s of FEP
commit
|
commitdiff
|
tree
2020-02-01
A
r
tem
Z
hm
u
r
o
v
C
o
up
l
e cool
q
u
otes
commit
|
commitdiff
|
tree
2020-02-01
A
rtem Zhmurov
Mer
g
e "M
e
rge
b
ra
n
ch origi
n
/relea
s
e-2020
into
mas
t
er"
commit
|
commitdiff
|
tree
2020-01-30
A
r
tem Zhmurov
Clea
n
ing
booleans in NB
N
XM
i
n
OpenCL bui
l
d
commit
|
commitdiff
|
tree
2020-01-29
Ar
t
em Zhmurov
Reorgan
i
ze GPU stuff initia
l
i
zatio
n
in PME-
o
nly ra
n
ks
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Sp
l
it
and
move the c
h
e
ckDeviceBuffer(
.
.
.
) function
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmu
r
ov
Remo
v
e
th
e
rest of t
h
e
device co
o
rdinates ma
n
age
m
ent
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Ar
t
em Zhmurov
Re
n
ame Upda
t
eCo
n
straintsCu
d
a to
UpdateConstrai
n
tsGpu
commit
|
commitdiff
|
tree
2020-01-23
Artem Z
h
murov
Fix a coup
l
e o
f
commas in cool quotes
commit
|
commitdiff
|
tree
2020-01-20
A
r
tem Zh
m
urov
Rename SettleCuda to SettleGpu
commit
|
commitdiff
|
tree
2020-01-20
Art
e
m Zhmurov
Ren
a
me LincsCuda into LincsGp
u
commit
|
commitdiff
|
tree
2020-01-20
Artem Zh
m
urov
Rename LeapFrog
C
ud
a
to
L
e
apFrogGpu
commit
|
commitdiff
|
tree
2020-01-13
Artem
Zhmu
r
ov
Report if upda
t
e
is running o
n
the GPU
or on the CPU
commit
|
commitdiff
|
tree
2020-01-09
A
rtem Zhmu
r
ov
C
h
ange sig
n
ature
o
f
t
h
e s
e
tP
b
c(
.
.
.
) method in updat
e
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Ar
t
em Zhmurov
Make
P
BC type enu
m
eration
i
nto
P
bcType
e
n
u
m
clas
s
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em
Z
hmur
o
v
Inform u
s
er why forc
i
ng GPU
u
pdat
e
i
s
not pos
s
i
ble
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmuro
v
Add description of GM
X
_F
O
R
C
E_UPD
A
TE_DEFAULT
_
GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmurov
Fix
g
puupdate
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change
the be
h
avior of th
e
GPU u
p
date U
I
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Add a note
t
o the l
o
g file when -update gpu was
set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
C
l
ean
b
a
d
auto-forma
t
in decidegpuusage doxyg
e
n
c
o
mments
commit
|
commitdiff
|
tree
2019-12-17
A
rtem Zhm
u
rov
Clean-up buffer-ops C
U
DA
k
erne
l
s
commit
|
commitdiff
|
tree
2019-12-13
A
r
tem Zhmu
r
o
v
Clean up outd
a
ted comments in m
d
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allo
w
using GPU updat
e
wi
t
h D
D
and update groups
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Enable mo
s
t of the pulling flav
o
rs with GPU update
commit
|
commitdiff
|
tree
2019-12-11
Arte
m
Z
h
m
u
rov
Clari
f
y what
setting ze
r
o to some output mdp optio
n
s
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Arte
m
Zhmurov
Avoid u
n
neces
s
ary reinte
r
pret_cast o
f
co
o
rd
i
nates buff
e
r
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmuro
v
Set GPU update to false
i
n
cas
e
of
a
r
e
r
un
commit
|
commitdiff
|
tree
2019-12-06
Artem Zhmurov
P
ass array ref in
s
t
e
ad of
c
asting
to basi
c
array in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Print OpenCL er
r
o
r
info in
case of failed a
s
se
r
tion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Art
e
m Zhmurov
Make Leap-Frog CUDA kernel selection saf
e
r
commit
|
commitdiff
|
tree
2019-11-29
Artem
Z
hmurov
Rename some variables
in GPU
Update
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhmurov
Clear de
v
ice force buffer if it was
realloca
t
ed
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhm
u
r
ov
Fix pre
s
sure coupling with
GPU update
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmu
r
ov
Co
m
bine two b
o
olean
s
in md loo
p
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Zhmu
r
o
v
Add meth
o
d for coordinates s
c
aling into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Ar
t
em Zhmur
o
v
Remove the P
B
C ma
n
agem
e
nt from LINCS, SETTL
E
and L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
A
rte
m
Zh
m
u
r
ov
Use same matri
x
f
or Parrinello-Ra
h
man and Bere
n
dsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
A
r
tem Zhmurov
Fix index mappi
n
g
issue with
LIN
C
S on GPU
commit
|
commitdiff
|
tree
2019-11-23
Artem Zh
m
urov
Ne
w
cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hmurov
A
d
d D2H
co
p
ies for the checkpointing
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m
Zhm
u
r
o
v
Move th
e
copy o
f
the
velocities for the output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Ar
t
em Zhmur
o
v
Fix ic
c
-19 warning in n
i
g
htl
y
m
a
trix
commit
|
commitdiff
|
tree
2019-11-15
A
r
te
m
Zhmurov
R
e
m
o
ving code duplications in StatePro
p
ag
a
torDataGpu
commit
|
commitdiff
|
tree
2019-11-13
Artem Zhmurov
Use same matr
i
x fo
r
Parrinello-Rah
m
a
n
and Be
r
endsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Arte
m
Zhmurov
Remove exces
s
ive H2
D
and D2H copies of f
o
rces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem
Z
hmurov
Disable GPU
u
pdate
when
c
oordina
t
es
swapping is enabled
commit
|
commitdiff
|
tree
2019-10-29
Artem Z
h
murov
Switch the
GPU buffer ops o
n
when
upda
t
e is
o
n GPU
commit
|
commitdiff
|
tree
2019-10-28
Ar
t
e
m
Zhmurov
Fix missing coordinate D2H copy with GPU
u
p
date a
n
d
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Add haveCpuLocalFor
c
es flag
to DomainLifetimeWo
r
kload
commit
|
commitdiff
|
tree
2019-10-28
A
rtem Zhmurov
Allow
u
sing update fl
a
g
commit
|
commitdiff
|
tree
2019-10-23
A
rte
m
Zhmurov
S
light i
m
p
r
ovements to
d
ec
i
d
eWh
e
ther
T
oUseGpuForUp
d
at
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem
Z
hmurov
Remove un
n
e
cessary C
U
DA stream synchroniz
a
tion
c
alls
commit
|
commitdiff
|
tree
2019-10-22
Ar
t
em
Z
h
m
urov
Rename havePositionRestraints(
.
.
.
) to ha
v
eRestraints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem
Z
h
mu
r
ov
Updat
e
the copyr
i
ght m
e
ssa
g
e
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmuro
v
Add environm
e
nt variable that ch
a
nges
the meaning of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhm
u
rov
Remove e
x
cessive H2D and D2H
coordinates copies
w
hen
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
R
emove excessiv
e
H2D
and D2
H
copies of
v
e
l
oc
i
ties when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmu
r
ov
Link GP
U
force prod
u
cer a
n
d
c
onsumer task
s
commit
|
commitdiff
|
tree
2019-10-15
Arte
m
Zhmurov
Fix the
single-GPU u
p
date-con
s
traint
s
commit
|
commitdiff
|
tree
2019-10-14
Ar
t
em Zhmur
o
v
A
d
d sepa
r
ate co
n
structor to StatePropag
a
to
r
Dat
a
Gpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
Cent
r
alize management of forces ready on
G
P
U
e
v
e
n
t
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Zhmurov
Ch
a
n
g
e
c
opy mode
t
o
A
sync in PME only r
a
nk
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmur
o
v
Ce
n
tralize managem
e
nt
o
f coordinates read
y
on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Artem Zhmur
o
v
Wrong
locality was used when ignoring the PME for
c
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmuro
v
Add management for velo
c
ities a
n
d forces
co
p
y even
t
s
.
.
.
commit
|
commitdiff
|
tree
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