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Update instructions in containers.rst
2020-02-21
A
rt
e
m
Z
h
m
urov
Refactor
a
nd enable RV
e
c to
f
l
oat conve
r
sion test
commit
|
commitdiff
|
tree
2020-02-20
Artem
Zhmurov
Do not call PME
G
PU builder in CPU code paths
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Use GROMACS
w
rappers for EXPEC
T
_THR
O
W
/
NO_T
H
R
O
W
in
P
M
E
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhm
u
rov
U
se CUDA floa
t
3 vecto
r
type ins
t
ead of fvec in
G
PU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
A
r
tem Z
h
m
urov
Clean up
t
r
i
vial function and
d
uplicat
i
ng macr
o
s
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Arte
m
Z
h
murov
Fix the nightly failure
commit
|
commitdiff
|
tree
2020-02-08
Artem
Z
hmu
r
ov
Temporar
y
disab
l
e R
V
ec->float3 conv
e
r
s
i
on t
e
s
t
to
fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Art
e
m Zhmurov
Use RV
e
c in
s
t
e
ad of float for
x, v
a
nd
f d
e
vi
c
e buffers
commit
|
commitdiff
|
tree
2020-02-06
Art
e
m Zhmurov
Move DeviceI
n
fo into GPU t
r
aits
commit
|
commitdiff
|
tree
2020-02-05
Ar
t
em Zhmur
o
v
M
ake OpenCL De
v
i
c
e
V
e
ndor into
enum clas
s
a
n
d
m
o
ve to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Art
e
m Zhmu
r
ov
Move no
n
-
b
ond
e
d in
i
tia
l
ization out of the
f
orc
e
rec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhm
u
r
ov
Fix ty
p
o
in and remove a couple of du
p
licate
s
from
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem Zhmurov
E
n
a
ble GPU update for supported cas
e
s of FEP
commit
|
commitdiff
|
tree
2020-02-01
Artem Zhmurov
Couple co
o
l qu
o
tes
commit
|
commitdiff
|
tree
2020-02-01
Artem Z
h
murov
Merg
e
"Mer
g
e branch or
i
gin/release-202
0
into master"
commit
|
commitdiff
|
tree
2020-01-30
Artem Zhmurov
Cleani
n
g
boo
l
eans in NB
N
XM
in OpenCL build
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmuro
v
Reorga
n
i
ze GPU stuff
initialization in PME-only ranks
commit
|
commitdiff
|
tree
2020-01-29
A
rtem
Z
hmurov
Split and
m
o
v
e
t
h
e chec
k
Device
B
uffer(
.
.
.
)
function
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Arte
m
Zhmurov
Re
m
ove the
rest of the d
e
vi
c
e coo
r
di
n
ates management
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem
Zh
m
urov
Rena
m
e UpdateConstr
a
intsC
u
da to UpdateCons
t
raintsGpu
commit
|
commitdiff
|
tree
2020-01-23
A
r
tem Zhmurov
Fix a
c
oupl
e
of co
m
mas
i
n
c
o
o
l
q
uo
t
es
commit
|
commitdiff
|
tree
2020-01-20
A
r
t
e
m Zhmur
o
v
Re
n
ame SettleCuda
to SettleGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
R
ename LincsC
u
da
i
nto Linc
s
Gpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Rename LeapF
r
ogCu
d
a to LeapFrog
G
pu
commit
|
commitdiff
|
tree
2020-01-13
Art
e
m Zhmur
o
v
Rep
o
rt if updat
e
is
r
u
nnin
g
on the GPU
o
r on the CPU
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Change sign
a
ture of th
e
setPbc(
.
.
.
) m
e
th
o
d
in update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Art
e
m Zhmurov
M
a
ke PBC type enumer
a
tio
n
into
P
bcType enum class
commit
|
commitdiff
|
tree
2019-12-31
A
rtem Zhmurov
I
n
form user
why
f
orcing GP
U
up
d
ate is not pos
s
ible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmur
o
v
Add des
c
ription of GMX_FORCE_UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em Zhmurov
Fix g
p
u
update matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmurov
Change the be
h
avior of t
h
e GPU update UI
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
A
dd a note
to
t
he log f
i
le when
-
update
g
pu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
A
rte
m
Zh
m
urov
Cle
a
n bad auto-form
a
t
in decide
g
puusa
g
e
d
oxygen
c
omment
s
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmu
r
ov
Clean-up buffer-ops CU
D
A kernels
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmu
r
ov
Clean
up outdated c
o
mments in md
.
c
pp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
Allow usi
n
g GPU update
w
ith DD
a
nd
update group
s
commit
|
commitdiff
|
tree
2019-12-11
A
r
t
em
Zh
m
urov
Enable
m
ost of
t
h
e
pullin
g
flavors with
G
P
U up
d
ate
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem Zhmurov
Clarify what
s
etting
z
ero to so
m
e outpu
t
mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Ar
t
em Zhm
u
r
o
v
Avoid unn
e
cessary reinterpr
e
t_cast of
c
oor
d
i
nate
s
buffer
commit
|
commitdiff
|
tree
2019-12-10
A
r
tem Zhmurov
Set GP
U
upda
t
e to fal
s
e in case of a rerun
commit
|
commitdiff
|
tree
2019-12-06
Artem Z
h
muro
v
Pass array ref instead o
f
casting to basic arra
y
in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Pri
n
t OpenCL e
r
ror
i
nfo in case of failed assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Make Leap-Frog CUDA ke
r
nel selection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmu
r
ov
R
ename some variables in GPU Update
commit
|
commitdiff
|
tree
2019-11-28
A
rtem Zhmur
o
v
Cl
e
ar
devi
c
e
force
b
uffer if it w
a
s realloc
a
ted
commit
|
commitdiff
|
tree
2019-11-28
Artem
Z
h
m
urov
Fi
x
pres
s
ure coupling
w
i
th GPU update
commit
|
commitdiff
|
tree
2019-11-27
Artem
Zhmurov
C
omb
i
ne tw
o
booleans in
md loop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmur
o
v
Add
method for
c
oordinates sca
l
i
n
g int
o
G
P
U up
d
a
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Arte
m
Zhmurov
Remo
v
e the P
B
C management from LI
N
CS, SET
T
L
E
an
d
Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use
sam
e
m
a
trix for Parrinello-
R
ahman a
n
d
Berends
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
A
r
tem Zhmur
o
v
Fix index mapping issue with L
I
NCS
on GPU
commit
|
commitdiff
|
tree
2019-11-23
Artem
Z
hmurov
New cool
qu
o
te
commit
|
commitdiff
|
tree
2019-11-20
Artem Zh
m
urov
Add D
2
H cop
i
es
for t
h
e check
p
oint
i
ng
commit
|
commitdiff
|
tree
2019-11-20
Artem Zh
m
ur
o
v
Move the c
o
py
of the velocities f
o
r
t
h
e output
c
loser
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix icc-19 war
n
ing
i
n night
l
y m
a
trix
commit
|
commitdiff
|
tree
2019-11-15
Artem
Z
hmurov
Removing c
o
de duplica
t
ions in
StateProp
a
gatorDat
a
Gpu
commit
|
commitdiff
|
tree
2019-11-13
Ar
t
em Zhmurov
Use
s
ame matrix fo
r
P
arrinello-Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmurov
Remove excessive H2
D
and
D2H copies of forces whe
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zh
m
urov
Disable GPU update when coor
d
i
nates
s
w
appin
g
is enabled
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Swi
t
ch the GP
U
buffer ops on
when update is on GPU
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem Zhm
u
rov
Fix missing c
o
ordina
t
e
D2H cop
y
with GPU update and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Ar
t
em Z
h
mur
o
v
Add ha
v
e
Cp
u
L
ocalForces flag to D
o
m
ain
L
ifetimeWor
k
l
o
ad
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Allow
u
sing update flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmurov
S
ligh
t
improv
e
ments to
d
ecideWhetherToUseGpuForUpda
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Arte
m
Zhmu
r
ov
Rem
o
ve unnece
s
sary CU
D
A
strea
m
sync
h
ronization calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Rename h
a
vePositionRestraints(
.
.
.
) t
o
h
a
veRes
t
raints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem
Z
hmurov
Upda
t
e the copy
r
ight message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmuro
v
Add en
v
ir
o
nment variable t
h
a
t
changes
t
he mean
i
ng
o
f
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Art
e
m Z
h
murov
Rem
o
ve exc
e
ssiv
e
H2D a
n
d D2H coordinates copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Art
e
m
Z
hmurov
Remove
e
xcessive H2D a
n
d
D2H cop
i
es of
v
elocities wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem
Z
hmurov
Link GPU force pr
o
ducer and consumer tas
k
s
commit
|
commitdiff
|
tree
2019-10-15
A
r
tem Z
h
murov
Fix th
e
s
ingle-GPU update-constraints
commit
|
commitdiff
|
tree
2019-10-14
A
r
t
em
Z
hmurov
Add separ
a
te constructor t
o
St
a
tePro
p
agat
o
r
Data
G
pu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhm
u
rov
Centraliz
e
man
a
gement of f
o
r
ces
r
eady on
GPU event
commit
|
commitdiff
|
tree
2019-10-12
A
rt
e
m Zhmur
o
v
Change c
o
py mode to Async in PME
only rank
commit
|
commitdiff
|
tree
2019-10-12
Art
e
m
Zhmurov
Centrali
z
e management of coor
d
inates ready on GPU even
t
commit
|
commitdiff
|
tree
2019-10-11
Artem Zhmurov
Wron
g
locality wa
s
used
when igno
r
i
n
g
the PM
E
force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Art
e
m Zhmurov
Add management for vel
o
cities and forces copy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zhmu
r
ov
Fix fo
r
the recent nigh
t
l
y
failure
commit
|
commitdiff
|
tree
2019-10-07
A
r
te
m
Zhm
u
rov
Pass the GPU
s
t
ream
s
to StatePr
o
p
a
gatorDataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Clean up the c
o
mments sections i
n
Upd
a
t
e
-
C
onst
r
ain
commit
|
commitdiff
|
tree
2019-10-07
Arte
m
Zhm
u
rov
Fix
a bug in GPU halo exch
a
n
g
e initialization
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix
t
he
bug w
i
th offl
o
ad
i
ng the PME-only ranks to GPU
commit
|
commitdiff
|
tree
2019-10-02
Artem Z
h
murov
Elimin
a
te D2D
c
opy in
upda
t
e constraints
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmuro
v
S
t
a
tePropag
a
torDataGpu ob
j
ect to manage
G
PU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Sli
g
ht impr
o
vements
t
o GPU upda
t
e/c
o
nstraints
initializ
a
t
ion
commit
|
commitdiff
|
tree
2019-09-27
A
r
tem Zh
m
urov
Int
r
o
duce stream m
a
nagement t
o
GPU Upd
a
te-Con
s
traints
commit
|
commitdiff
|
tree
2019-09-22
A
r
t
em Zhmur
o
v
Disable GPU update/constraints w
h
en
ne
i
the
r
PME no
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Arte
m
Zhmu
r
ov
Chan
g
e PaddedV
e
ctor to Pa
d
de
d
Ho
s
tVector for force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhm
u
rov
Fix
for the
p
o
st-su
b
mit failu
r
e
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmurov
Decou
p
le GPU force buffer management
f
r
om buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
D
ecouple
c
oordin
a
t
es buffer
m
anag
e
ment from buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
rtem Zhmu
r
ov
Reorganize
P
ME code:
commit
|
commitdiff
|
tree
2019-09-10
A
rtem
Zhmurov
Making Dev
i
c
eBuffer availib
l
e
i
n non-GP
U
builds
commit
|
commitdiff
|
tree
2019-09-03
Art
e
m Zhmurov
Add Parrinello-Ra
h
man pre
s
sure coupling
to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Ar
t
em Zhmurov
Add temp
e
ratur
e
c
oupl
i
ng to CUDA
L
eap-Frog
inte
g
rator
commit
|
commitdiff
|
tree
2019-08-25
Arte
m
Zhmurov
Make use of recent changes
t
o pre
p
areKe
r
ne
l
Argum
e
n
t
s
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Misc
e
leneous improvem
e
nts to the L
e
ap
F
rog tests
commit
|
commitdiff
|
tree
2019-08-14
Artem Zhm
u
rov
B
u
g
F
ix: Zer
o
ing the padded area of coord
i
nate
s
vecto
r
s
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmurov
M
a
k
e u
s
e of reference data
in
i
nt
e
grator t
e
st
s
commit
|
commitdiff
|
tree
next