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Make SD stuff private for update.cpp
2020-06-09
Artem Zh
m
urov
Make SD stu
f
f
pr
i
vate
for updat
e
.
cpp
commit
|
commitdiff
|
tree
2020-06-09
Artem
Zhmur
o
v
Mak
e
SD
s
tu
f
f
p
riv
a
t
e
f
or
u
p
dat
e
.
cpp
commit
|
commitdiff
|
tree
2020-06-08
Artem Zhm
u
r
ov
Move constr
a
ints related logic to constraints
f
ile
commit
|
commitdiff
|
tree
2020-06-08
A
rt
e
m Zhmurov
Uni
f
y
V
dW a
n
d
Electrost
a
t
i
c kernel en
u
m
erations in
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
Ar
t
em Zhmuro
v
Move calculation of ki
n
e
t
ic en
e
rgy to md
_
sup
p
ort
commit
|
commitdiff
|
tree
2020-06-04
Arte
m
Zhmurov
Make a error message less confusing
commit
|
commitdiff
|
tree
2020-06-04
Ar
t
em Z
h
murov
Cool quote
commit
|
commitdiff
|
tree
2020-05-29
Ar
t
em
Zhmuro
v
Unify initialization of GPU
and
CPU SETT
L
E
commit
|
commitdiff
|
tree
2020-05-26
Artem Zhmurov
Remove the depe
n
dence on Cons
t
raints
o
bject on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-25
Artem Zh
m
u
r
o
v
Remove depen
d
enc
e
on t
_
m
d
at
o
ms from GPU
v
ersion of
.
.
.
commit
|
commitdiff
|
tree
2020-05-23
Artem
Z
hmurov
Re
m
ove de
p
endence on
t_mdatoms from pull code
commit
|
commitdiff
|
tree
2020-05-22
A
rtem Zhmurov
Remove
de
p
endence
of con
s
trai
n
ts on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-22
Artem Z
h
m
u
rov
Remove dependence
of constr
a
ints on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-15
Art
e
m Zhmurov
Uni
f
y C
U
DA and OpenCL
l
ookup-tabl
e
c
r
eation
commit
|
commitdiff
|
tree
2020-05-11
Art
e
m
Z
hmurov
Remo
v
e the du
p
l
icating note f
r
o
m th
e
release notes
commit
|
commitdiff
|
tree
2020-05-11
Artem Zhmurov
Unify CUDA an
d
O
penCL lo
o
kup-table
c
r
e
ation
commit
|
commitdiff
|
tree
2020-05-05
Arte
m
Zhmurov
U
nify
C
UDA an
d
OpenCL lookup-table creation
commit
|
commitdiff
|
tree
2020-05-04
A
rtem Z
h
murov
Unify CUDA
and
O
penCL look
u
p-
t
able creation
commit
|
commitdiff
|
tree
2020-04-29
Artem Zhmurov
Fix
t
he n
u
m
b
er of steps check wh
e
n
c
heck
p
oint is loade
d
commit
|
commitdiff
|
tree
2020-04-27
Artem Zh
m
urov
F
ix the rem
o
val of COM velocity in case of GPU
u
pdate
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Move
PBC setup o
u
t
of the launchKern
e
l(
.
.
.
) in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
A
r
tem Zhmurov
Fix the numb
e
r of steps check when che
c
kpoint
i
s
load
e
d
commit
|
commitdiff
|
tree
2020-04-16
Art
e
m
Zh
m
urov
N
e
w cool quote
commit
|
commitdiff
|
tree
2020-04-16
A
rtem Zhm
u
rov
U
n
i
f
y CUDA a
n
d OpenCL lo
o
kup-tab
l
e creation
commit
|
commitdiff
|
tree
2020-03-25
Artem Zhmurov
Make use of t
h
e DeviceStream
M
an
a
ger
commit
|
commitdiff
|
tree
2020-03-23
Artem Zhm
u
rov
Introduce DeviceSt
r
e
amManager
commit
|
commitdiff
|
tree
2020-03-20
Artem
Z
h
m
urov
Add
O
penCL e
r
r
o
r
rep
o
rt
i
n
g
to GPU region t
i
m
er
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhmur
o
v
S
m
a
ll fixes t
o
the D
e
v
i
ceStr
e
am
commit
|
commitdiff
|
tree
2020-03-19
A
r
tem Z
h
mur
o
v
Sto
r
e DeviceInf
o
rmation inside
t
he Dev
i
ceContext cl
a
ss
commit
|
commitdiff
|
tree
2020-03-19
A
rtem
Z
hmurov
P
ass
D
e
vi
c
eConte
x
t in
s
tead of GPU
runt
i
m
e data wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Artem Zhmurov
Make s
o
m
e
doxyg
e
n
errors
m
ore clear
commit
|
commitdiff
|
tree
2020-03-13
A
r
tem Zhmurov
Combine initialization rou
t
ines for
G
PUs assigned to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Arte
m
Zhmu
r
ov
Remove s
t
ream f
r
om GPU kernel launch
c
o
n
fig
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Use
D
eviceStream i
n
it(
.
.
.
) function to create streams
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Make Devi
c
eStream into
a
cla
s
s
commit
|
commitdiff
|
tree
2020-03-11
Artem
Z
hmu
r
ov
Fix the post-submit failures
commit
|
commitdiff
|
tree
2020-03-11
Artem Zhmurov
Take over
management
o
f
Op
e
n
C
L context from PME and
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Artem Zh
m
urov
U
s
e
init(
.
.
) fu
n
ction to
b
uild
D
evi
c
eContext
commit
|
commitdiff
|
tree
2020-03-09
A
r
tem Zhmuro
v
Make D
e
viceContext
i
nto a
p
roper class
commit
|
commitdiff
|
tree
2020-03-05
Art
e
m Z
h
murov
Finalize
r
enaming of bEnerVir
t
o comput
e
Ene
r
gyAndVir
i
al
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmu
r
ov
Do not count
PME o
n
ly rank when initializing NBNXM
commit
|
commitdiff
|
tree
2020-03-03
A
r
t
em
Z
hmu
r
ov
Move
t
he
PmePPCommGpu initia
l
ization from forcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmur
o
v
Update the message on
w
h
ethe
r
update
and con
s
tr
a
ints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
A
rtem Zhmurov
Fix
the
R
Vec to float3 conversion te
s
t
commit
|
commitdiff
|
tree
2020-02-22
Artem Zhmurov
A
dd
m
issing
h
ea
d
er and dis
a
ble fa
i
l
i
ng test
commit
|
commitdiff
|
tree
2020-02-21
A
rte
m
Zhmu
r
ov
Refacto
r
and enable RVec to
f
l
oat conversion test
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhm
u
rov
D
o not ca
l
l PME GPU builder in
C
PU code paths
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmu
r
ov
Use GROMACS w
r
appers for E
X
PECT_THROW/NO_THROW in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem
Zhmur
o
v
Use CUDA
float3 vector type inste
a
d of
f
v
ec in GP
U
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
C
l
e
an
u
p triv
i
al fun
c
tion and d
u
pl
i
c
ating macro
s
es
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Artem Zhmurov
F
ix the nightly
failure
commit
|
commitdiff
|
tree
2020-02-08
Artem Zh
m
uro
v
Temporary disab
l
e RVec->flo
a
t3
convers
i
on test to f
i
x
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
Us
e
R
Vec instead of
float for
x, v
and
f
device buffe
r
s
commit
|
commitdiff
|
tree
2020-02-06
Artem Zhmurov
Mov
e
Devi
c
eInfo into GPU
t
raits
commit
|
commitdiff
|
tree
2020-02-05
Artem
Z
hmurov
Make OpenCL DeviceVendor into
e
num cl
a
ss and m
o
ve to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
A
r
t
em
Z
hmurov
Move n
o
n
-bonde
d
initi
a
l
i
z
ation out of the f
o
r
c
erec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zh
m
u
r
o
v
F
i
x typo in a
n
d remov
e
a couple of
dupl
i
c
a
tes from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem Zh
m
urov
Enable
GPU update for suppo
r
ted cases of FEP
commit
|
commitdiff
|
tree
2020-02-01
Ar
t
em Zhmurov
Couple
c
ool quote
s
commit
|
commitdiff
|
tree
2020-02-01
Art
e
m Zh
m
urov
Merge "Merge branch origin/releas
e
-2020 into master"
commit
|
commitdiff
|
tree
2020-01-30
Artem Z
h
murov
Clea
n
in
g
booleans in
N
BNXM in
O
p
enCL build
commit
|
commitdiff
|
tree
2020-01-29
Artem
Z
h
m
urov
Reor
g
anize G
P
U stuff initializati
o
n in
P
ME
-
o
n
ly ranks
commit
|
commitdiff
|
tree
2020-01-29
Ar
t
e
m
Zhmurov
S
p
lit
a
nd move
t
he
checkDevice
B
u
f
fer(
.
.
.
) funct
i
on
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Ar
t
e
m
Zhmurov
R
e
move the
rest o
f
the devi
c
e coordinates ma
n
agement
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
Rename U
p
dateConstraints
C
uda to Up
d
ateCons
t
ra
i
n
tsG
p
u
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhmur
o
v
Fix a couple of
c
o
m
m
as i
n
co
o
l qu
o
tes
commit
|
commitdiff
|
tree
2020-01-20
Artem
Z
hmur
o
v
Rename Settle
C
u
da to SettleGpu
commit
|
commitdiff
|
tree
2020-01-20
Arte
m
Zhmurov
Rename Lincs
C
u
da into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmur
o
v
Ren
a
m
e Le
a
p
Fr
o
gCu
d
a t
o
LeapFrogGpu
commit
|
commitdiff
|
tree
2020-01-13
Artem Zhmurov
R
eport if update is ru
n
ning
on
the GP
U
or o
n
the CP
U
commit
|
commitdiff
|
tree
2020-01-09
Artem
Z
hmurov
Change signature
o
f the setPbc(
.
.
.
)
m
e
th
o
d in
update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Art
e
m Zhmurov
Make PB
C
ty
p
e enumeration in
t
o PbcType enum cl
a
s
s
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Info
r
m user why forcing
G
PU
update is not pos
s
ib
l
e
commit
|
commitdiff
|
tree
2019-12-31
Artem Z
h
murov
Add d
e
scription of GMX_FOR
C
E_UPDATE_DEFAULT_GPU
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Fix gpuu
p
dat
e
matri
x
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change the behavior
o
f the
GPU
update UI
commit
|
commitdiff
|
tree
2019-12-27
Ar
t
em Zh
m
uro
v
Add
a
n
o
t
e t
o
t
h
e log file
w
h
en -update gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Clean bad auto-form
a
t
i
n decidegp
u
usage doxygen
co
m
m
e
nts
commit
|
commitdiff
|
tree
2019-12-17
Art
e
m Zhmurov
Clean-up buffer-ops CUDA kern
e
l
s
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmu
r
ov
Cl
e
a
n
up
o
utdated comments in md
.
c
p
p
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allo
w
using GPU update with DD and updat
e
grou
p
s
commit
|
commitdiff
|
tree
2019-12-11
Artem
Zhmurov
Enable
most
o
f
t
he pulling flavors with G
P
U update
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmur
o
v
C
larify wha
t
setting zero to some output mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Avoid
u
n
necess
a
ry reinterpret_cast of coordinates buffer
commit
|
commitdiff
|
tree
2019-12-10
Artem Zh
m
urov
Set GPU update to false in
c
ase of a rerun
commit
|
commitdiff
|
tree
2019-12-06
Arte
m
Zhmu
r
o
v
Pass array
r
e
f
instead of
casting to b
a
sic array
in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zhmurov
Print
Ope
n
CL error
i
n
f
o i
n
case of
f
aile
d
assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem
Z
h
murov
Make L
e
ap-Frog
C
UD
A
k
e
rnel selection safer
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zh
m
urov
R
ename some var
i
ables in GPU
Update
commit
|
commitdiff
|
tree
2019-11-28
Ar
t
em Zhmu
r
ov
Clea
r
d
e
vice force buffer if
it was
r
eallocated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmuro
v
Fix p
r
essure cou
p
li
n
g with GPU upd
a
te
commit
|
commitdiff
|
tree
2019-11-27
A
r
tem Z
h
mu
r
ov
C
o
mbine
t
wo bo
o
l
eans i
n
md
l
oo
p
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
Add meth
o
d for coordinates scaling into GPU
update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Artem Zhmurov
R
e
m
ove
t
he PBC mana
g
e
ment
from LINCS,
SE
T
TLE a
n
d Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmu
r
ov
Use sam
e
matrix for
P
a
rrinello-Rahman and Berend
s
en
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Fix
i
n
dex mapping issue
with
L
I
N
CS on
G
PU
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
New
cool quote
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Add D2H copies for the checkpointing
commit
|
commitdiff
|
tree
2019-11-20
A
r
tem Zhmurov
Move
the copy of
t
he v
e
locities for th
e
output clos
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
A
rtem
Zhmurov
Fix icc-19 wa
r
ni
n
g in nightly ma
t
rix
commit
|
commitdiff
|
tree
next