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Use signed arithmetic in enumeration helper
2020-07-07
Artem
Zh
m
ur
o
v
Make cl_nbparam into a s
t
ruct
commit
|
commitdiff
|
tree
2020-06-26
Artem Zhm
u
rov
Make
h
olde
r
for
simulation con
f
i
g
uration
commit
|
commitdiff
|
tree
2020-06-25
Artem Zhmurov
Make cl_nb
p
a
r
am into a
s
tru
c
t
commit
|
commitdiff
|
tree
2020-06-24
Ar
t
em Z
h
murov
Fix minor
ni
t
-
p
ick
s
commit
|
commitdiff
|
tree
2020-06-22
Artem Zhmurov
Remove DeviceStream include from GPU t
r
a
i
ts
commit
|
commitdiff
|
tree
2020-06-12
A
rtem Z
h
m
u
rov
Replace compile_cp
p
_
a
s_cuda(
.
.
.
) w
i
th CUDA runtim
e
.
.
.
commit
|
commitdiff
|
tree
2020-06-09
Artem Zhmuro
v
M
a
ke SD stu
f
f private f
o
r
update
.
cpp
commit
|
commitdiff
|
tree
2020-06-09
A
r
tem Zhmu
r
ov
Make SD
s
tuff private for update
.
cpp
commit
|
commitdiff
|
tree
2020-06-08
Artem Zhm
u
r
o
v
Move constraints related logic to
const
r
a
ints file
commit
|
commitdiff
|
tree
2020-06-08
Artem
Z
hmurov
U
nif
y
VdW an
d
Electr
o
static kernel
enumerations in
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
Artem Zhmurov
Move
calculation of kinetic e
n
ergy
to md_support
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmurov
Make a err
o
r
mess
a
ge less confu
s
ing
commit
|
commitdiff
|
tree
2020-06-04
Artem
Z
h
murov
Cool quote
commit
|
commitdiff
|
tree
2020-05-29
A
rtem
Zh
m
u
r
o
v
Unify initializ
a
ti
o
n o
f
GPU and CP
U
SETTLE
commit
|
commitdiff
|
tree
2020-05-26
Artem Zhmurov
Remove the dependence on C
o
nstraints object on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-25
Artem Z
h
murov
R
e
move depe
n
dence on t_mdatoms from GPU
version of
.
.
.
commit
|
commitdiff
|
tree
2020-05-23
Art
e
m
Z
h
murov
Rem
o
v
e depen
d
e
n
ce on t
_
mdatoms fr
o
m pull code
commit
|
commitdiff
|
tree
2020-05-22
Artem Zhmu
r
o
v
R
e
move de
p
endence
of constraints o
n
t_mdatoms
commit
|
commitdiff
|
tree
2020-05-22
A
r
te
m
Zhmuro
v
Re
m
ove de
p
ende
n
ce of
c
o
n
straint
s
on t_md
a
t
oms
commit
|
commitdiff
|
tree
2020-05-15
Ar
t
em Zhmurov
Unif
y
CU
D
A and OpenCL looku
p
-table creation
commit
|
commitdiff
|
tree
2020-05-11
Artem Zhmurov
R
e
move th
e
duplicating note
from the r
e
lease notes
commit
|
commitdiff
|
tree
2020-05-11
A
r
tem Zhmurov
Un
i
fy
CUDA and Open
C
L lookup-table
creation
commit
|
commitdiff
|
tree
2020-05-05
A
r
tem Zhmurov
Unify CUDA
a
n
d
Open
C
L loo
k
up-t
a
ble
creation
commit
|
commitdiff
|
tree
2020-05-04
Artem Zhmurov
Unif
y
CUDA and
O
p
e
nCL lookup-table
creation
commit
|
commitdiff
|
tree
2020-04-29
Artem Zhmur
o
v
Fix
the number of steps che
c
k w
h
en checkpoint is loaded
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Fix the rem
o
val of COM
velocity in case of
G
P
U upda
t
e
commit
|
commitdiff
|
tree
2020-04-27
Art
e
m
Z
hmurov
Move PBC
setup o
u
t of the launchKernel(
.
.
.
)
i
n GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
Arte
m
Zh
m
ur
o
v
Fix t
h
e
numb
e
r of st
e
p
s chec
k
when checkpoint
is loade
d
commit
|
commitdiff
|
tree
2020-04-16
Artem Zhmurov
New co
o
l quote
commit
|
commitdiff
|
tree
2020-04-16
Artem Zhmuro
v
Un
i
fy C
U
DA
a
nd O
p
enC
L
lookup-table cre
a
tion
commit
|
commitdiff
|
tree
2020-03-25
Artem Zhmurov
Make
u
s
e of the DeviceStreamM
a
n
ag
e
r
commit
|
commitdiff
|
tree
2020-03-23
Ar
t
em Zhmurov
Int
r
oduce
De
v
i
c
e
S
t
reamManager
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhmurov
Add OpenCL error
r
e
p
orting
t
o G
P
U region timer
commit
|
commitdiff
|
tree
2020-03-20
Artem Z
h
murov
S
mall
f
ixes to the De
v
iceStream
commit
|
commitdiff
|
tree
2020-03-19
Artem Zh
m
urov
Store
Devic
e
I
nf
o
rmation
i
nside the Devi
c
eCon
t
ext class
commit
|
commitdiff
|
tree
2020-03-19
A
r
tem Zhmurov
P
a
ss DeviceC
o
n
text instead of G
P
U r
u
ntime data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Artem Zhmurov
Mak
e
s
ome d
o
xyge
n
errors more clea
r
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Combine initialization routi
n
es for GPUs assi
g
ned to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Rem
o
ve stream fr
o
m
GPU kernel launch config
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Use
DeviceS
t
ream init(
.
.
.
) fun
c
t
i
on to c
r
e
ate str
e
ams
commit
|
commitdiff
|
tree
2020-03-13
Arte
m
Zh
m
urov
Make DeviceStr
e
am into a class
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhmurov
Fix the
p
ost-submit failures
commit
|
commitdiff
|
tree
2020-03-11
Artem
Zhmurov
Take over ma
n
agement of OpenCL c
o
nte
x
t from PME
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Arte
m
Zhmur
o
v
U
se in
i
t(
.
.
) function to bu
i
l
d
DeviceConte
x
t
commit
|
commitdiff
|
tree
2020-03-09
Art
e
m
Zhmurov
Make DeviceC
o
ntext in
t
o a proper cla
s
s
commit
|
commitdiff
|
tree
2020-03-05
Artem Z
h
m
urov
Finali
z
e renaming of b
E
nerVir to computeE
n
ergyAndVirial
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
Do not co
u
nt P
M
E only r
a
nk when
i
nitializi
n
g NBNX
M
commit
|
commitdiff
|
tree
2020-03-03
Artem
Z
hmur
o
v
M
o
ve the P
m
ePPCommGpu initializat
i
on from forcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Z
h
murov
Update the
m
es
s
ag
e
o
n whether
u
pdate a
n
d constraints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Ar
t
e
m Zhmurov
Fix
the RVec to flo
a
t
3
conversion test
commit
|
commitdiff
|
tree
2020-02-22
Artem Zhmurov
Add mis
s
i
ng header and disable failing tes
t
commit
|
commitdiff
|
tree
2020-02-21
A
r
tem Zhmur
o
v
Refactor and
enable RVec to fl
o
at conv
e
rsion test
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
D
o
not
call PM
E
GPU
b
uilde
r
in CPU co
d
e p
a
ths
commit
|
commitdiff
|
tree
2020-02-20
A
rtem Zhmuro
v
Use
G
ROMAC
S
wr
a
p
p
ers for
E
XPEC
T
_THROW/N
O
_THROW in PM
E
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem
Z
h
mur
o
v
U
s
e CUDA
float3 vector type
i
nstead
o
f fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
A
r
tem Zhmurov
Clean up trivia
l
function and duplicating macroses
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem
Zhmurov
Fix the nightly fai
l
u
r
e
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmurov
Temp
o
rary disable RVe
c
->fl
o
a
t3 c
o
n
version test
to fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
A
r
t
e
m Zhmurov
Use RVec inst
e
a
d of float for x,
v
and f d
e
vice buffers
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmuro
v
M
o
ve DeviceInfo int
o
GPU
traits
commit
|
commitdiff
|
tree
2020-02-05
A
rtem Zhm
u
rov
Make OpenCL Dev
i
ceVe
n
dor into
enum class and move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Art
e
m
Z
hmurov
Move non-
b
on
d
ed initi
a
lization out o
f
the f
o
rcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem
Zhmurov
Fix
typo in and re
m
o
v
e a couple of dupl
i
ca
t
es
f
ro
m
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem
Zhmurov
Enable GPU update
f
or su
p
ported case
s
of FEP
commit
|
commitdiff
|
tree
2020-02-01
A
rtem Zhmurov
Couple cool quote
s
commit
|
commitdiff
|
tree
2020-02-01
A
r
tem Zhmurov
Merge
"
M
e
rge
b
r
a
n
ch origin/release-2020 in
t
o mas
t
e
r"
commit
|
commitdiff
|
tree
2020-01-30
A
rtem
Z
hmurov
C
leaning boo
l
ea
n
s in NBNXM in Open
C
L
b
u
il
d
commit
|
commitdiff
|
tree
2020-01-29
Arte
m
Z
h
murov
Reorg
a
nize GP
U
s
tuff
initiali
z
ation in PME
-
only
r
an
k
s
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Spl
i
t and move the che
c
k
D
evice
B
uf
f
e
r
(
.
.
.
) f
u
nctio
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Remo
v
e t
h
e
rest
o
f the device coordinates manage
m
en
t
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Z
h
murov
Rename UpdateC
o
nstraintsCuda to Updat
e
Constrain
t
sGp
u
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhmuro
v
Fix a
c
o
u
pl
e
o
f
co
m
mas in cool quot
e
s
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Rename
S
ettleCuda to SettleG
p
u
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Rename Li
n
csC
u
da i
n
to LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
A
rtem Zhmur
o
v
R
e
name Leap
F
rogCuda to L
e
apFr
o
gGpu
commit
|
commitdiff
|
tree
2020-01-13
Artem Z
h
murov
R
e
p
o
rt
if up
d
ate i
s
running o
n
the GPU or on the CPU
commit
|
commitdiff
|
tree
2020-01-09
A
rtem Zhmurov
Change signa
t
ure of the set
P
bc
(
.
.
.
) method in u
p
da
t
e
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
M
ake PBC type enum
e
ration
i
nto PbcType enum class
commit
|
commitdiff
|
tree
2019-12-31
Art
e
m Zh
m
urov
Info
r
m user why fo
r
cin
g
GP
U
upda
t
e is not po
s
sible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Add desc
r
iption of G
M
X
_FORCE_UPDATE_DEFAULT
_
GPU
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zh
m
urov
Fix
g
p
u
u
p
da
t
e matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change t
h
e
be
h
avior
o
f the GPU
u
p
date UI
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m Zhmurov
Add a n
o
te to the log
f
i
le when -update gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem
Zhmu
r
ov
Clean
bad auto-f
o
rmat in decidegpuusage doxygen comm
e
n
ts
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
Clean-
u
p buf
f
er-ops CUDA kernels
commit
|
commitdiff
|
tree
2019-12-13
Artem
Z
hmur
o
v
Clean up o
u
tdated comment
s
in
m
d
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allow u
s
ing GPU
update w
i
th DD and update groups
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
En
a
b
l
e mos
t
o
f the
pullin
g
flavor
s
with GPU update
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Clarif
y
what s
e
tting z
e
ro to some o
u
tp
u
t mdp o
p
tions
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Ar
t
em Zh
m
uro
v
Avoi
d
unnecessary reinterpret_cas
t
of
coordinates buffer
commit
|
commitdiff
|
tree
2019-12-10
A
r
tem
Zhmuro
v
Set GPU upd
a
te
t
o fals
e
in cas
e
of
a rer
u
n
commit
|
commitdiff
|
tree
2019-12-06
Artem Zhm
u
rov
Pass arra
y
ref
i
n
s
t
e
a
d
of casting to
b
asic array in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Arte
m
Zh
m
urov
P
r
int OpenC
L
er
r
or
i
nf
o
i
n case of failed
assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
em Zhmurov
M
ake
Lea
p
-
Frog CUDA
kernel select
i
on safer
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Rename some variable
s
in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Clear device force buffer if it w
a
s rea
l
lo
c
at
e
d
commit
|
commitdiff
|
tree
2019-11-28
Artem
Z
hmurov
Fix
pressur
e
co
u
pling with
G
PU update
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
C
o
mbine
two b
o
oleans in md loop
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Zhmurov
Add
m
e
thod for coordinates scaling into GPU update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Artem Zh
m
urov
Rem
o
ve the
PBC mana
g
e
ment from LINCS, SETTLE a
n
d Leap
.
.
.
commit
|
commitdiff
|
tree
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