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Update the release notes
2020-06-04
Artem
Zhmur
o
v
Upda
t
e th
e
re
l
ease
n
otes
commit
|
commitdiff
|
tree
2020-04-29
A
r
tem
Z
h
mu
r
ov
Fix th
e
number of
s
teps check when checkp
o
int is
loaded
commit
|
commitdiff
|
tree
2020-04-27
Ar
t
em
Zhmurov
F
ix the removal of COM
v
e
l
o
c
ity
in case of G
P
U u
p
date
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmurov
Update the m
e
ssag
e
on
w
hether update and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-01-23
Artem Zhmurov
Fix a couple of commas in cool quotes
commit
|
commitdiff
|
tree
2020-01-13
Artem Zhmurov
Re
p
ort i
f
upd
a
te is ru
n
ning
o
n the GPU
o
r
o
n the CPU
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Inf
o
rm use
r
why forcing GP
U
update is not possible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Add description of GMX_FORCE_UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmu
r
ov
Fix
g
p
uupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem
Z
hmu
r
ov
Ch
a
nge the
behavior of th
e
G
PU update
UI
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zhmu
r
o
v
Add a note to t
h
e log file when
-
u
pdate g
p
u
was
set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem
Z
h
m
ur
o
v
Cle
a
n b
a
d auto-format in decidegpuus
a
ge doxygen comme
n
t
s
commit
|
commitdiff
|
tree
2019-12-17
A
rte
m
Zhmurov
Clean-up b
u
ffer-op
s
CUDA kernels
commit
|
commitdiff
|
tree
2019-12-13
Artem Z
h
m
urov
C
lean u
p
outd
a
te
d
comments
in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhmurov
A
llow using GPU update
w
ith DD and
up
d
ate groups
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Enable
most of the
p
ulling
f
lavors with GPU
u
pdate
commit
|
commitdiff
|
tree
2019-12-11
Arte
m
Zhmuro
v
Clarify what setting zero to so
m
e
ou
t
put mdp option
s
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
A
r
t
e
m Zhmurov
Set GPU u
p
date to
f
a
l
se in case
of a reru
n
commit
|
commitdiff
|
tree
2019-12-06
Ar
t
em Zhmurov
Pas
s
array ref instead of cas
t
ing to
basic a
r
ray in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmur
o
v
Print
Op
e
nCL
erro
r
info in
c
ase of fai
l
ed assertio
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
A
rt
e
m Zhmurov
Make Leap-Frog CUDA kernel s
e
lection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem
Zhmurov
Rename so
m
e variab
l
e
s in
GPU Update
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmu
r
ov
Clear
d
ev
i
ce f
o
rce buffer if it was
r
eallocated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmur
o
v
Fix pressure coupling with GPU update
commit
|
commitdiff
|
tree
2019-11-27
A
rtem Zhmurov
Combine
two boolean
s
in md loo
p
commit
|
commitdiff
|
tree
2019-11-27
Artem Z
h
murov
Add meth
o
d for coordinates scaling
into GPU upd
a
te
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmuro
v
Use same
matrix for Par
r
inello-Rahm
a
n a
n
d
Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Art
e
m Zhm
u
rov
F
ix index mapping issue with LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-23
Art
e
m Zhmurov
Ne
w
cool
quote
commit
|
commitdiff
|
tree
2019-11-20
Artem
Z
hmurov
A
d
d D2
H
copies
f
or the chec
k
p
o
inting
commit
|
commitdiff
|
tree
2019-11-20
Arte
m
Zhmu
r
o
v
Move
t
he copy of the velocities for the output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmur
o
v
F
i
x
icc-19 warning in nig
h
tly matrix
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmurov
Remo
v
e
e
xcess
i
ve H2D and
D
2
H
copi
e
s
of forces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Art
e
m Zhmurov
D
i
sab
l
e GPU upd
a
t
e
when
coordinate
s
swapping is enab
l
ed
commit
|
commitdiff
|
tree
2019-10-29
A
r
t
em
Z
hmur
o
v
Switch th
e
G
P
U
b
uffer ops o
n
when update is on GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Fi
x
mi
s
sing coordinate
D2H c
o
py with G
P
U update
a
nd
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
A
r
te
m
Zhmur
o
v
Add haveCpuLocalForces flag to DomainLi
f
etimeWorkload
commit
|
commitdiff
|
tree
2019-10-28
Artem Z
h
mu
r
o
v
Allow using update flag
commit
|
commitdiff
|
tree
2019-10-23
A
rtem Zhmurov
Slight im
p
roveme
n
ts to decideW
h
etherToUseGpu
F
orU
p
date
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmu
r
ov
R
e
move unnecessary CUDA stream synchronizatio
n
calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmu
r
o
v
Renam
e
h
a
vePositi
o
nRe
s
t
raints(
.
.
.
) to
haveRestraints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmurov
Update
the copyri
g
ht m
e
s
s
a
ge
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
A
rtem Zhmurov
A
dd
e
nvironment varia
b
le th
a
t
c
hanges the meaning o
f
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Z
h
murov
Remov
e
excess
i
ve H2D and D
2
H coordinates cop
i
es when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmur
o
v
R
emo
v
e excessive H2D and D2H
copies o
f
v
elocities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
A
r
tem Zhmur
o
v
Link
G
PU
f
o
r
ce
producer and consume
r
tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem
Zhmurov
Fix
the single-GPU up
d
ate
-
constraints
commit
|
commitdiff
|
tree
2019-10-14
A
rtem
Z
h
murov
Add separate
constructor to StatePro
p
a
gator
D
ataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Centr
a
liz
e
manage
m
ent
of force
s
re
a
dy on GPU
e
ve
n
t
commit
|
commitdiff
|
tree
2019-10-12
Ar
t
em Zhmurov
C
h
ange copy mode to Async in PME only rank
commit
|
commitdiff
|
tree
2019-10-12
A
rtem Zh
m
urov
Centralize management of coordinat
e
s
r
eady on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Artem
Z
hmurov
Wrong locality was used when
igno
r
ing the PME forc
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmu
r
ov
Add management
for velociti
e
s
and forces copy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zhmurov
F
ix for the recent nightly
f
a
i
lure
commit
|
commitdiff
|
tree
2019-10-07
A
r
tem Zhm
u
r
ov
Pass the GPU
strea
m
s to StatePropaga
t
o
rDataGpu co
n
st
r
uctor
commit
|
commitdiff
|
tree
2019-10-07
Artem
Zhm
u
r
o
v
Cle
a
n
u
p
the comments sec
t
ions
in Update-Constrain
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmu
r
o
v
Fix a bug in GPU halo exch
a
nge initializa
t
ion
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix
t
h
e bug with offloading the PME-onl
y
ranks t
o
GPU
commit
|
commitdiff
|
tree
2019-10-02
A
rtem Zh
m
urov
E
limina
t
e D2D c
o
py
in update
constra
i
nts
commit
|
commitdiff
|
tree
2019-10-01
Art
e
m Z
h
m
u
rov
StatePropagatorDataGpu
o
bject
t
o manage GPU forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Ar
t
em Zhmuro
v
S
light improvements to GP
U
update/constraint
s
in
i
tialization
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmur
o
v
I
n
troduc
e
stream manageme
n
t to GPU Update-Constrai
n
ts
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmurov
Di
s
able GPU upda
t
e/co
n
straints when
n
e
ither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem
Z
hmurov
Change
P
ad
d
edVector to PaddedHostVector for fo
r
ce CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Fix for the po
s
t-submit fai
l
u
r
e
commit
|
commitdiff
|
tree
2019-09-11
Arte
m
Zhmurov
De
c
ouple GPU force buf
f
e
r
m
anage
m
ent
from buffer
o
p
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Z
h
m
u
rov
Decouple coo
r
di
n
ates buffer manag
e
ment from buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
rt
e
m
Z
h
murov
Reorganize
P
ME code
:
commit
|
commitdiff
|
tree
2019-09-10
Artem Z
h
murov
Making
D
evice
B
uffer ava
i
l
ib
l
e
in non-GP
U
builds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add Parrinello-Rahman pressure coupl
i
ng
t
o CUDA Le
a
p
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
A
r
tem
Z
hm
u
r
o
v
Add tem
p
erature couplin
g
t
o CUDA Leap-Fr
o
g integrator
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Make use of recent ch
a
ng
e
s t
o
p
r
e
p
areKernelArguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
A
r
t
e
m Zhmurov
Misceleneous improveme
n
ts to the Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-14
A
r
tem Zhmurov
BugFix
:
Zer
o
ing the padde
d
ar
e
a of
c
oo
r
dina
t
e
s
v
e
cto
r
s
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Art
e
m
Zhmurov
Make use of re
f
erence data in i
n
tegra
t
or te
s
t
s
commit
|
commitdiff
|
tree
2019-08-13
Artem Zh
m
urov
Mak
e
use of re
f
erence data in
S
ETTL
E
tests
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
P
r
epar
e
Update
a
nd Co
n
strai
n
ts for Domain D
e
composition
commit
|
commitdiff
|
tree
2019-08-09
Ar
t
em
Z
hmu
r
o
v
Ref
a
ct
o
r
i
ng o
f
th
e
SETTLE tests
commit
|
commitdiff
|
tree
2019-08-08
Artem Zhmuro
v
R
e
factor
L
eap-Frog tests and connect them
t
o CPU
vers
i
on
commit
|
commitdiff
|
tree
2019-08-06
A
rte
m
Zhmurov
Fix for cm
a
k
e
lists in md
l
ib tests
commit
|
commitdiff
|
tree
2019-08-06
Artem
Z
h
muro
v
Remov
e
PImpl sc
a
ff
o
ldin
g
fro
m
CUDA ve
r
sion
o
f L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Z
h
murov
Chang
e
the fi
l
e structure in constrai
n
ts te
s
t
s
commit
|
commitdiff
|
tree
2019-07-31
A
r
tem Zh
m
urov
Intro
d
u
ce function th
a
t
checks i
f
th
e
computa
t
i
ons
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmuro
v
Re
m
ove PImpl sc
a
ffolding from CU
D
A version of
SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmuro
v
Remov
e
P
Impl
s
caffoldin
g
f
rom
CUDA version of
L
INCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmur
o
v
U
s
e r
e
a
llocateDeviceBuf
f
er(
.
.
.
) in CUD
A
version o
f
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem
Z
hm
u
rov
Early exit for CUDA v
e
r
sions
o
f
SETTLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
Art
e
m
Zhm
u
r
o
v
Memory m
a
nag
e
ment
f
i
x
es in CUDA version
o
f LINCS
commit
|
commitdiff
|
tree
2019-07-03
A
rtem Zhmurov
Com
b
ine CUDA
L
ea
p
-Fr
o
g, LIN
C
S and SETTLE
.
I
I
.
commit
|
commitdiff
|
tree
2019-06-18
A
r
tem Zhmurov
C
o
mbine CUDA Leap-Fro
g
, LINCS an
d
SETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Ar
t
em Zhmurov
Bug fix:
Constraints tests
a
r
e not instanti
a
ted with
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clarify which of the
main ene
r
gy te
r
ms
a
re
printed
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Z
h
mu
r
ov
Clarify the
E
nergyOutp
u
t III
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmu
r
ov
Cl
a
rif
y
the Ene
r
gyOutput II
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhmu
r
ov
Clarify the Ene
r
gyOutput
I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhm
u
rov
CU
D
A version o
f
Leap-
F
rog in
t
e
g
rator with basic tests
commit
|
commitdiff
|
tree
2019-05-06
Art
e
m Zhmurov
Fixin
g
minor memory issues
i
n MDL
i
b
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhmur
o
v
Use te
s
t with parame
t
ers for E
n
ergyOu
t
put
commit
|
commitdiff
|
tree
2019-04-30
Ar
t
e
m
Zh
m
urov
CUDA versi
o
n
o
f SETTLE algo
r
ithm w
i
th
basi
c
te
s
ts
commit
|
commitdiff
|
tree
2019-04-29
Artem
Z
hmur
o
v
F
i
x
fo
r
th
e
CUDA version of LI
N
CS
commit
|
commitdiff
|
tree
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