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Fix clang-format
2020-09-07
Artem
Zhmurov
Fix clang-fo
r
mat
commit
|
commitdiff
|
tree
2020-09-07
Artem
Z
h
m
urov
Acce
s
s the device statu
s
directly, remove the gett
e
r
commit
|
commitdiff
|
tree
2020-08-24
Artem
Z
hmu
r
ov
Move GPU devices
m
anag
e
m
ent into hardware s
u
b
f
ol
d
er
commit
|
commitdiff
|
tree
2020-08-14
Art
e
m Zhmuro
v
Fix DeviceStream
M
anage
r
tests
commit
|
commitdiff
|
tree
2020-07-29
Artem Zhm
u
r
ov
R
evert
c
++-17 f
e
atures that are not supported by CUDA
.
.
.
commit
|
commitdiff
|
tree
2020-07-29
Ar
t
em Zhmurov
Revert c++-17 features that are not supported
by C
U
DA
.
.
.
commit
|
commitdiff
|
tree
2020-07-27
Artem Zhmurov
Fix clang-tidy war
n
i
ng
commit
|
commitdiff
|
tree
2020-07-15
Art
e
m Zhmu
r
ov
Fix the su
s
picious string literal e
r
ror in GPU status
.
.
.
commit
|
commitdiff
|
tree
2020-07-07
Artem Zhmurov
Ma
k
e
cl_nbp
a
r
am into a struc
t
commit
|
commitdiff
|
tree
2020-06-26
Artem
Z
hmurov
M
a
ke hold
e
r
for simulation conf
i
guration
commit
|
commitdiff
|
tree
2020-06-25
Ar
t
em
Zhmurov
Make cl_nb
p
a
r
am into a s
t
ru
c
t
commit
|
commitdiff
|
tree
2020-06-24
Artem Zhmurov
Fix minor nit-picks
commit
|
commitdiff
|
tree
2020-06-22
A
r
tem Zhmurov
Remove D
e
viceS
t
ream in
c
lude fro
m
GPU tr
a
its
commit
|
commitdiff
|
tree
2020-06-16
Artem Zhm
u
rov
Add missing end-of-line in the GPU update assignment
.
.
.
commit
|
commitdiff
|
tree
2020-06-12
A
r
te
m
Zhm
u
rov
Repl
a
ce compile_cpp_a
s
_cuda(
.
.
.
) with CUDA runtime
.
.
.
commit
|
commitdiff
|
tree
2020-06-09
Artem Zhmurov
Ma
k
e SD stuff private for update
.
c
p
p
commit
|
commitdiff
|
tree
2020-06-09
Art
e
m Zhmurov
Make SD stuff private for update
.
cp
p
commit
|
commitdiff
|
tree
2020-06-08
Artem
Z
hmurov
Move constraints
relat
e
d logic to constraints file
commit
|
commitdiff
|
tree
2020-06-08
Ar
t
em
Z
h
m
ur
o
v
Uni
f
y VdW and El
e
ctro
s
tatic ke
r
ne
l
enu
m
erati
o
ns in
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
A
r
tem Zhmur
o
v
M
o
v
e calculat
i
on of kineti
c
ener
g
y to md_support
commit
|
commitdiff
|
tree
2020-06-05
Artem Zhmurov
Make a error message
l
ess confusing
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmuro
v
Ma
k
e a error message less confu
s
i
n
g
commit
|
commitdiff
|
tree
2020-06-04
A
r
tem Zhmurov
Update the release notes
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmurov
C
o
ol quote
commit
|
commitdiff
|
tree
2020-05-29
Art
e
m Z
h
murov
Unify initialization
o
f
GPU
a
nd CPU SE
T
TLE
commit
|
commitdiff
|
tree
2020-05-26
Artem Zhmu
r
o
v
Remove the depe
n
dence on Constraints object on t
_
m
d
a
t
oms
commit
|
commitdiff
|
tree
2020-05-25
A
r
tem Zhmurov
Remov
e
dependence on
t_
m
datoms from GPU version of
.
.
.
commit
|
commitdiff
|
tree
2020-05-23
A
rtem
Zhmu
r
ov
Remove dependence o
n
t_md
a
toms from pull co
d
e
commit
|
commitdiff
|
tree
2020-05-22
Artem Zhmurov
Remove dep
e
ndenc
e
of co
n
str
a
ints on t_mdato
m
s
commit
|
commitdiff
|
tree
2020-05-22
Artem Z
h
murov
Rem
o
ve dependence of c
o
nstraints on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-15
A
r
t
e
m
Zh
m
urov
U
n
ify C
U
DA and
OpenC
L
lookup-t
a
ble creatio
n
commit
|
commitdiff
|
tree
2020-05-11
A
r
tem
Z
h
mu
r
ov
Remov
e
the
duplicating
not
e
from the
r
eleas
e
note
s
commit
|
commitdiff
|
tree
2020-05-11
A
rte
m
Zhmurov
U
nify CUDA and OpenCL lookup-table cre
a
tion
commit
|
commitdiff
|
tree
2020-05-05
Artem
Zhmuro
v
Unify C
U
D
A
and OpenCL lookup-table
c
reati
o
n
commit
|
commitdiff
|
tree
2020-05-04
A
rtem
Zhmurov
Unify
CUDA and OpenCL lookup-t
a
bl
e
c
r
e
ation
commit
|
commitdiff
|
tree
2020-04-29
Art
e
m Zhmurov
Fix t
h
e number
o
f steps chec
k
when che
c
kpoint i
s
l
o
a
d
ed
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
F
i
x the rem
o
val of COM velocity i
n
c
ase of
GPU update
commit
|
commitdiff
|
tree
2020-04-27
Art
e
m Zhmuro
v
M
ove PBC setup out of
the la
u
nchK
e
r
n
el(
.
.
.
) in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
A
r
tem Zhmurov
Fi
x
t
he number of
s
teps
c
heck when
c
hec
k
point is
loaded
commit
|
commitdiff
|
tree
2020-04-16
A
r
tem Zhmur
o
v
New
c
oo
l
quote
commit
|
commitdiff
|
tree
2020-04-16
Artem Zhmu
r
ov
Uni
f
y
C
UDA and OpenCL lookup-table creation
commit
|
commitdiff
|
tree
2020-03-25
Art
e
m Zhmurov
Make use of th
e
DeviceS
t
r
e
a
m
M
a
n
ager
commit
|
commitdiff
|
tree
2020-03-23
Artem Zhm
u
rov
Int
r
oduce DeviceStreamMa
n
ag
e
r
commit
|
commitdiff
|
tree
2020-03-20
Artem
Zhmur
o
v
Add OpenCL
e
r
r
or repor
t
in
g
to GPU
r
egion
t
imer
commit
|
commitdiff
|
tree
2020-03-20
Ar
t
em
Z
hmurov
Small fixes to the
D
eviceStream
commit
|
commitdiff
|
tree
2020-03-19
A
rt
e
m Zhmurov
Store
DeviceInformation inside the Devi
c
eContext cla
s
s
commit
|
commitdiff
|
tree
2020-03-19
A
r
t
e
m
Zhmu
r
ov
Pass
DeviceContext instea
d
of GPU
r
untime data when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Art
e
m Zh
m
urov
M
a
ke so
m
e doxyg
e
n err
o
rs mor
e
clear
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmu
r
ov
Combine i
n
itia
l
i
z
a
tion routin
e
s for GPUs a
s
signed t
o
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Ar
t
em
Z
hmu
r
ov
R
emove stream from G
P
U kernel launch con
f
ig
commit
|
commitdiff
|
tree
2020-03-13
A
r
t
em Zhmurov
Use DeviceStream ini
t
(
.
.
.
) func
t
i
o
n
t
o
create streams
commit
|
commitdiff
|
tree
2020-03-13
A
rtem Zh
m
urov
Make Devi
c
eStr
e
am into
a cl
a
ss
commit
|
commitdiff
|
tree
2020-03-11
A
r
tem Zhmu
r
o
v
Fix the post-submit failure
s
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhmurov
Take over managem
e
n
t
of OpenCL context
from PME and
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Artem
Zhmurov
U
se init(
.
.
)
f
unction to build
Dev
i
ceContext
commit
|
commitdiff
|
tree
2020-03-09
Arte
m
Z
hmurov
Make Devic
e
Context into a p
r
oper class
commit
|
commitdiff
|
tree
2020-03-05
A
r
tem Zhmurov
Fin
a
liz
e
r
enaming of bE
n
erV
i
r to computeEner
g
yAnd
V
irial
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
Do not co
u
nt PME onl
y
rank when initializing NB
N
XM
commit
|
commitdiff
|
tree
2020-03-03
A
r
te
m
Zh
m
urov
Move the PmePPCommGpu in
i
tialization from fo
r
cerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmurov
Up
d
ate
t
he message on whether
update
and c
o
nstra
i
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Zhmurov
F
i
x the
R
Vec to float3 c
o
nversion t
e
s
t
commit
|
commitdiff
|
tree
2020-02-22
Art
e
m Zhmurov
Add missi
n
g heade
r
and d
i
sab
l
e faili
n
g
tes
t
commit
|
commitdiff
|
tree
2020-02-21
A
r
t
e
m Z
h
m
u
rov
Refactor and en
a
bl
e
RVec to flo
a
t c
o
n
v
ersi
o
n te
s
t
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Do not
c
all
P
M
E
G
PU builder
in CPU code
pa
t
h
s
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Use GROMACS wrappers f
o
r EXP
E
CT
_
THROW/NO
_
T
H
ROW in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem
Z
hm
u
r
ov
Use CUDA
f
l
oat3 vector
t
y
p
e
inste
a
d of fvec in GP
U
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zh
m
urov
Cl
e
a
n up trivial
f
unction an
d
d
u
pl
i
ca
t
i
ng macroses
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
Fix the nightly failure
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmurov
T
e
m
p
orary
d
isable RV
e
c->float3 c
o
n
v
er
s
ion t
e
st to fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem Zh
m
urov
Use RVec ins
t
ead of f
l
oat for x,
v and f
d
e
vice buffers
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
Move De
v
iceInfo into GPU tr
a
i
ts
commit
|
commitdiff
|
tree
2020-02-05
Ar
t
em Zhmurov
Make OpenCL D
e
viceVendor into enum clas
s
and move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Artem Zh
m
urov
Move
no
n
-bonde
d
ini
t
ia
l
i
z
a
t
ion
out o
f
the for
c
e
r
e
c
commit
|
commitdiff
|
tree
2020-02-05
Arte
m
Zhmur
o
v
Fix
typo
in and remo
v
e a co
u
ple of duplicates from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem Zhmurov
Enable GPU update for supp
o
rted cases o
f
FEP
commit
|
commitdiff
|
tree
2020-02-01
Ar
t
e
m Zhmuro
v
Couple c
o
ol quotes
commit
|
commitdiff
|
tree
2020-02-01
A
r
t
em Zhmu
r
ov
Merge "Me
r
ge branch or
i
g
in/
r
e
lease-2020 into
mast
e
r"
commit
|
commitdiff
|
tree
2020-01-30
Artem Zhmurov
C
l
eaning
b
ooleans
in
NBNXM in
O
penCL build
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmu
r
ov
Reorgani
z
e GPU stuff initi
a
lization in PME-only ranks
commit
|
commitdiff
|
tree
2020-01-29
A
r
tem Zhm
u
rov
Sp
l
it and move the
ch
e
ckDeviceBuf
f
er(
.
.
.
) functio
n
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
R
e
move t
h
e res
t
of the device coordinates managemen
t
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Rename Up
d
a
t
eConstraints
C
u
da to UpdateConstrain
t
sGpu
commit
|
commitdiff
|
tree
2020-01-23
A
r
tem Zhmuro
v
F
ix a couple of comma
s
in cool quotes
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
R
ename Settl
e
Cud
a
to SettleGp
u
commit
|
commitdiff
|
tree
2020-01-20
Artem
Z
h
mur
o
v
R
e
n
a
me LincsC
u
d
a
into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
A
rt
e
m Zhmurov
Re
n
ame
L
eapF
r
ogC
u
da to Leap
F
rogGpu
commit
|
commitdiff
|
tree
2020-01-13
A
rtem Zhmurov
Report
i
f
u
p
date i
s
running
on
the GPU or
o
n the
CPU
commit
|
commitdiff
|
tree
2020-01-09
A
rtem Zh
m
u
rov
Change signature of
the setPbc(
.
.
.
)
method in update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Make PBC ty
p
e
e
n
umeration int
o
PbcType enum class
commit
|
commitdiff
|
tree
2019-12-31
A
r
t
e
m
Zhmur
o
v
I
nform user why forcing GPU update is not possible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Add descr
i
pti
o
n of GM
X
_FORCE_UPDATE_DE
F
AULT_GP
U
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zh
m
urov
Fix gpuupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmu
r
ov
Change t
h
e behavior
of the GPU upd
a
te UI
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zhmurov
Add a not
e
to the l
o
g
file when -update gpu w
a
s
set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zh
m
ur
o
v
Clean bad auto-format in decid
e
g
puus
a
ge doxy
g
en
c
o
mmen
t
s
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
Clean-u
p
b
u
ffe
r
-
ops CUDA k
e
r
nels
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmurov
C
lean up outd
a
ted
c
o
mments
i
n md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
A
rtem Zhmu
r
ov
A
llo
w
using GPU update
w
i
t
h
DD and u
p
da
t
e gro
u
p
s
commit
|
commitdiff
|
tree
2019-12-11
Artem Zh
m
urov
E
n
able most of t
h
e pulling
flavors with GPU update
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Clarify
wh
a
t
s
et
t
ing z
e
ro to some
output mdp options
.
.
.
commit
|
commitdiff
|
tree
next