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Add missing include into the tests comparison helper
2020-10-01
Arte
m
Zh
m
u
r
ov
A
d
d mi
s
sing in
c
lude i
n
t
o
the tests c
o
mparison helper
commit
|
commitdiff
|
tree
2020-09-30
Artem Zhmuro
v
Restore
d
estruc
t
or for
G
puTe
s
t and g
m
x_hw_info_t
commit
|
commitdiff
|
tree
2020-09-29
Artem Zhmur
o
v
R
emove two-stage
i
n
it
i
al
i
zat
i
on in DeviceS
t
ream
commit
|
commitdiff
|
tree
2020-09-28
Artem
Z
hm
u
rov
add
d
ete
c
t
ion of
CPX 5
3
0
0 w/ 2F
M
A
s
commit
|
commitdiff
|
tree
2020-09-21
Ar
t
em Zhmurov
Do not run PinnedMem
o
r
yCh
e
ckerTest when there are no
.
.
.
commit
|
commitdiff
|
tree
2020-09-21
Artem Z
h
murov
M
o
ve the messag
e
t
o the depr
E
cation-policy file
commit
|
commitdiff
|
tree
2020-09-20
Artem Zhm
u
rov
Set active d
e
vice wh
e
n the device st
r
e
a
m
m
an
a
ge
r
is
.
.
.
commit
|
commitdiff
|
tree
2020-09-20
A
rtem Zhmurov
Allow usin
g
old environment
varia
b
l
es, but print de
p
recation
.
.
.
commit
|
commitdiff
|
tree
2020-09-17
Artem Zhmur
o
v
Remov
e
the CPU hardware
conte
x
t from
the general list
.
.
.
commit
|
commitdiff
|
tree
2020-09-15
A
r
tem
Zhmurov
Use
common device conte
x
t header f
o
r OpenCL
commit
|
commitdiff
|
tree
2020-09-15
Artem Zhmurov
F
i
x VSite out of r
a
nge erro
r
message
commit
|
commitdiff
|
tree
2020-09-14
Artem Zhmurov
U
se comm
o
n dev
i
ce
c
ontext header for OpenCL
commit
|
commitdiff
|
tree
2020-09-11
Artem
Z
h
m
uro
v
Define
st
u
bs fo
r
GPU da
t
a
struct
u
res in SYCL t
o
make
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
A
rtem Zhmurov
Use common
device context
head
e
r for
Open
C
L
commit
|
commitdiff
|
tree
2020-09-10
Artem
Z
hmurov
Us
e
dev
i
ce information object instead of id
w
h
e
n performing
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
Artem Zhmurov
U
n
ify m
o
re
functions in CUDA and OpenCL
i
mp
l
ement
a
tions
.
.
.
commit
|
commitdiff
|
tree
2020-09-09
A
rte
m
Zhm
u
rov
Resto
r
e GMX_F
O
RCE_U
P
DATE_DEFA
U
LT_GPU
enviro
n
ment varible
.
.
.
commit
|
commitdiff
|
tree
2020-09-07
A
r
te
m
Z
h
murov
Remove in-body
c
o
mm
e
nt
f
rom ini
t
_
for
c
erec(
.
.
.
) fu
n
c
t
i
on
commit
|
commitdiff
|
tree
2020-09-07
A
r
tem Zhmuro
v
Fix clang-format
commit
|
commitdiff
|
tree
2020-09-07
Artem
Zhmu
r
ov
Acces
s
the d
e
v
i
ce sta
t
us
d
irectly, remove the ge
t
ter
commit
|
commitdiff
|
tree
2020-08-24
Artem Zhmurov
Move GPU devices m
a
na
g
ement i
n
t
o
hardware
subfolder
commit
|
commitdiff
|
tree
2020-08-14
Ar
t
em Zhmurov
Fix Device
S
treamM
a
nager
t
ests
commit
|
commitdiff
|
tree
2020-07-29
Artem
Z
hmurov
Revert c++-17 fea
t
u
r
es t
h
at are not supp
o
rted by
C
U
D
A
.
.
.
commit
|
commitdiff
|
tree
2020-07-29
Artem Z
h
murov
Revert c++-17 features th
a
t
are no
t
support
e
d b
y
CUDA
.
.
.
commit
|
commitdiff
|
tree
2020-07-27
Artem
Zhmurov
Fi
x
clang-tidy
warning
commit
|
commitdiff
|
tree
2020-07-15
Artem Zhmurov
Fix
the sus
p
icious strin
g
li
t
eral
e
rror i
n
GPU status
.
.
.
commit
|
commitdiff
|
tree
2020-07-07
Artem Zhm
u
ro
v
Make cl
_
nbparam into
a struct
commit
|
commitdiff
|
tree
2020-06-26
Artem Zhmurov
Make
h
o
l
der for sim
u
l
a
tion configuration
commit
|
commitdiff
|
tree
2020-06-25
Artem Zhmur
o
v
Make
cl_nbpa
r
am into
a
str
u
ct
commit
|
commitdiff
|
tree
2020-06-24
Artem Zh
m
u
rov
Fi
x
minor
n
it-pick
s
commit
|
commitdiff
|
tree
2020-06-22
Artem
Zhm
u
rov
Remove D
e
v
i
ce
S
tream inclu
d
e from GPU traits
commit
|
commitdiff
|
tree
2020-06-16
Artem Zhmuro
v
Add missing
e
nd-of-l
i
ne in
the GPU up
d
ate assi
g
nment
.
.
.
commit
|
commitdiff
|
tree
2020-06-12
Art
e
m Zhmurov
Replac
e
compi
l
e_cpp_as
_
cuda(
.
.
.
) w
i
th
C
UDA run
t
ime
.
.
.
commit
|
commitdiff
|
tree
2020-06-09
Ar
t
em Zhmurov
Make
S
D
stuf
f
private for updat
e
.
cpp
commit
|
commitdiff
|
tree
2020-06-09
Ar
t
em
Z
hmurov
Mak
e
SD st
u
f
f
p
rivate for
u
pd
a
te
.
cpp
commit
|
commitdiff
|
tree
2020-06-08
Artem Zhmur
o
v
Move
constra
i
n
t
s related logic to con
s
traints file
commit
|
commitdiff
|
tree
2020-06-08
Artem Zhmurov
Unif
y
V
dW and Electrostatic ker
n
el enumerations in
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
Artem Zh
m
urov
Mo
v
e calculat
i
on of k
i
netic ene
r
g
y to md_su
p
p
ort
commit
|
commitdiff
|
tree
2020-06-05
Artem
Zhmurov
Make
a
e
rro
r
messag
e
le
s
s confusing
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmur
o
v
Make a error message less confu
s
ing
commit
|
commitdiff
|
tree
2020-06-04
A
r
t
em Zhm
u
rov
Updat
e
the rele
a
se notes
commit
|
commitdiff
|
tree
2020-06-04
A
r
te
m
Z
hmurov
Cool q
u
ote
commit
|
commitdiff
|
tree
2020-05-29
Artem Zhmurov
Unify
i
nit
i
a
lization
o
f
GPU and C
P
U SETTLE
commit
|
commitdiff
|
tree
2020-05-26
Artem Zhm
u
rov
Remove th
e
dependence o
n
Constraints o
b
ject on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-25
Artem Zhmu
r
ov
Remove dependence on t_
m
dato
m
s from
G
PU vers
i
o
n
of
.
.
.
commit
|
commitdiff
|
tree
2020-05-23
Art
e
m Zhm
u
r
o
v
Remove d
e
pende
n
ce on t_m
d
atoms from pull c
o
de
commit
|
commitdiff
|
tree
2020-05-22
A
r
tem Zhm
u
rov
Remove
d
e
pendence of con
s
traints on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-22
Artem Zhmurov
Rem
o
ve depen
d
ence of constraint
s
o
n
t_mdatom
s
commit
|
commitdiff
|
tree
2020-05-15
Artem
Z
hmurov
Unify CUDA
and OpenC
L
look
u
p-table cre
a
tion
commit
|
commitdiff
|
tree
2020-05-11
Art
e
m
Zhmurov
Remove the duplicating note from
th
e
relea
s
e not
e
s
commit
|
commitdiff
|
tree
2020-05-11
Artem Zhmuro
v
Unify CU
D
A
and Op
e
n
CL
l
o
o
k
u
p-
t
able
c
r
e
ation
commit
|
commitdiff
|
tree
2020-05-05
Artem Zhmurov
Unify CUDA and OpenCL lookup-table c
r
eation
commit
|
commitdiff
|
tree
2020-05-04
Artem Zhmurov
Unify CUDA an
d
O
penCL lookup-tab
l
e creation
commit
|
commitdiff
|
tree
2020-04-29
Artem Zhmurov
Fi
x
the numbe
r
of st
e
ps check whe
n
c
h
eckp
o
i
n
t is l
o
aded
commit
|
commitdiff
|
tree
2020-04-27
A
rtem Zhmurov
F
i
x the
r
emova
l
of COM velocity in case
of GPU
u
pdate
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Move PBC setup out of the launch
K
ernel(
.
.
.
)
in G
P
U
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
A
rtem Zhm
u
r
ov
F
i
x the numbe
r
o
f
steps
chec
k
when check
p
o
i
n
t is loade
d
commit
|
commitdiff
|
tree
2020-04-16
Artem
Z
hmurov
New c
o
ol quote
commit
|
commitdiff
|
tree
2020-04-16
A
r
tem Zhmurov
Unify
CUDA and OpenC
L
lookup-tab
l
e creation
commit
|
commitdiff
|
tree
2020-03-25
A
r
tem Zhmurov
Make u
s
e of
t
he De
v
ic
e
StreamManage
r
commit
|
commitdiff
|
tree
2020-03-23
Artem Z
h
m
u
r
o
v
Introduce DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhm
u
ro
v
Add OpenCL er
r
or reporting to GPU region timer
commit
|
commitdiff
|
tree
2020-03-20
Artem
Z
hmuro
v
Small
f
ixes
to
t
he Devi
c
e
S
t
ream
commit
|
commitdiff
|
tree
2020-03-19
Art
e
m Zhmurov
Store De
v
iceInformation inside the D
e
viceCo
n
text class
commit
|
commitdiff
|
tree
2020-03-19
Ar
t
em Zhm
u
r
o
v
Pass Device
C
o
nt
e
xt instead of
G
PU runtime data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Artem Zhmurov
Make some do
x
y
gen er
r
ors
m
ore clear
commit
|
commitdiff
|
tree
2020-03-13
Art
e
m
Z
h
m
u
r
o
v
Combine initializa
t
i
on
routin
e
s for GPUs assigned
t
o
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
A
r
tem Zhmurov
Remove
s
tream from G
P
U
k
ernel launch config
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
U
se
D
eviceStream init(
.
.
.
) f
u
ncti
o
n to create strea
m
s
commit
|
commitdiff
|
tree
2020-03-13
Artem Zh
m
urov
Make DeviceStream into a class
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhmuro
v
F
i
x the post-sub
m
i
t failures
commit
|
commitdiff
|
tree
2020-03-11
A
r
tem Z
h
murov
T
a
k
e over management of OpenC
L
co
n
tex
t
from P
M
E
a
nd
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Art
e
m Zhm
u
rov
Use i
n
i
t(
.
.
)
f
unc
t
ion to build De
v
ic
e
Context
commit
|
commitdiff
|
tree
2020-03-09
Artem
Z
hmurov
Make
DeviceContext
into a proper class
commit
|
commitdiff
|
tree
2020-03-05
Artem Zh
m
urov
Finalize
r
enaming of bEnerVir to computeEnergyA
n
dViria
l
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
D
o
n
ot count
PME on
l
y r
a
nk when initializ
i
ng NB
N
XM
commit
|
commitdiff
|
tree
2020-03-03
A
r
te
m
Zhmur
o
v
Move the PmePPCommGp
u
i
nitiali
z
a
tion from forcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmuro
v
Update
t
he
m
essage
o
n whether update
a
nd
con
s
traints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Zhmu
r
ov
Fix the R
V
ec to fl
o
at3 con
v
ersion test
commit
|
commitdiff
|
tree
2020-02-22
A
rtem Zhmurov
Add mis
s
ing h
e
ader
a
nd
d
is
a
ble
failin
g
test
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmurov
R
e
factor
a
nd
e
n
a
ble RVec to fl
o
at convers
i
on test
commit
|
commitdiff
|
tree
2020-02-20
A
r
t
e
m Zhmurov
Do not
call PME GPU builder in CPU
code paths
commit
|
commitdiff
|
tree
2020-02-20
A
r
tem Zhmuro
v
Use G
R
OMACS
wrappers fo
r
EXP
E
CT_THROW/
N
O
_THR
O
W in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
A
r
tem Zhmurov
Use CU
D
A f
l
oat
3
vector ty
p
e instea
d
of fvec
i
n G
P
U
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem
Zhmurov
Clean up tri
v
ial
fun
c
tio
n
and duplicating
macro
s
es
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Z
h
murov
Fix the n
i
ghtly failure
commit
|
commitdiff
|
tree
2020-02-08
Artem
Z
hmurov
T
emporary
disable RV
e
c->float3 conversion tes
t
to
f
ix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem Z
h
mu
r
o
v
Use
R
Ve
c
instead of float for x, v and
f
d
e
vice buf
f
ers
commit
|
commitdiff
|
tree
2020-02-06
Ar
t
em Z
h
m
urov
Mov
e
Devic
e
Info in
t
o GPU
t
ra
i
t
s
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmuro
v
Make OpenCL DeviceVendor into enum cla
s
s
a
n
d
move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Artem Z
h
m
u
rov
Move
n
on-bonded initi
a
lization out of the forcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
F
i
x typo
i
n and remove a
c
ouple of dupli
c
a
t
e
s f
r
om
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem
Z
h
m
urov
Enable GPU update fo
r
s
u
pported cases of
F
EP
commit
|
commitdiff
|
tree
2020-02-01
Arte
m
Zhmurov
Couple c
o
ol
q
uotes
commit
|
commitdiff
|
tree
2020-02-01
Artem Zhmurov
Merge "M
e
rge branch origin/release-
2
020 into master
"
commit
|
commitdiff
|
tree
2020-01-30
Artem Zhmurov
Cleanin
g
boolean
s
in NBNXM in OpenCL build
commit
|
commitdiff
|
tree
2020-01-29
A
r
tem Zhmuro
v
Reorgan
i
ze GPU stuf
f
initialization in PME-on
l
y ran
k
s
commit
|
commitdiff
|
tree
2020-01-29
Artem Z
h
m
u
rov
S
plit and move the chec
k
De
v
iceBuffer(
.
.
.
)
function
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem
Z
hmur
o
v
R
e
m
ove
t
h
e re
s
t of the device coordina
t
e
s
managem
e
nt
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem
Z
h
murov
Re
n
ame UpdateC
o
nstraintsCuda to UpdateCon
s
traintsGpu
commit
|
commitdiff
|
tree
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