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Fixed bug in orires code that was checking too strict.
2020-01-23
Artem
Z
h
m
urov
Fix a couple of commas
i
n cool quo
t
e
s
commit
|
commitdiff
|
tree
2020-01-13
Artem
Z
hmuro
v
Report if
update i
s
running
o
n
the
GPU or on the CPU
commit
|
commitdiff
|
tree
2019-12-31
Art
e
m Zhmurov
I
nform user why for
c
ing GPU upd
a
te is not possible
commit
|
commitdiff
|
tree
2019-12-31
Art
e
m Zhmurov
Add description of G
M
X_FORCE_UPDATE_DEFAULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem
Z
h
murov
Fix
g
puupd
a
t
e
ma
t
rix
commit
|
commitdiff
|
tree
2019-12-28
A
r
tem Z
h
murov
Chang
e
the behav
i
or of th
e
GPU upd
a
te UI
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m
Zhmurov
Ad
d
a not
e
t
o
the log file when
-up
d
ate gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Arte
m
Zhmurov
Cl
e
an
b
a
d auto-format in decideg
p
uus
a
g
e
doxyge
n
c
o
mments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
C
l
e
an-up buffer-op
s
CUD
A
ke
r
nel
s
commit
|
commitdiff
|
tree
2019-12-13
A
r
t
e
m Zh
m
urov
C
l
ean up outdated commen
t
s i
n
md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Ar
t
em Z
h
m
urov
All
o
w
u
s
ing
G
PU
u
pdate wi
t
h DD a
n
d update groups
commit
|
commitdiff
|
tree
2019-12-11
Ar
t
em Zhm
u
rov
Ena
b
le
m
ost
o
f
t
he
p
ulling flav
o
rs
with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-12-11
A
r
t
e
m Zhmurov
Cl
a
rify what s
e
ttin
g
zer
o
t
o
some
outp
u
t m
d
p options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Set
GPU updat
e
to false in case of a rerun
commit
|
commitdiff
|
tree
2019-12-06
A
rtem Zhm
u
rov
Pass array ref ins
t
ead of casting
to basic array
i
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhm
u
rov
Print
O
penCL er
r
or info
i
n case
o
f failed assertion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
e
m
Z
h
mur
o
v
Make Le
a
p-Frog CUDA kern
e
l selec
t
ion safer
commit
|
commitdiff
|
tree
2019-11-29
Artem Zh
m
ur
o
v
Rename some variabl
e
s in GPU Upd
a
t
e
commit
|
commitdiff
|
tree
2019-11-28
Artem
Zhmurov
C
lear device force buffer if it
w
as r
e
alloc
a
ted
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmu
r
o
v
Fix
p
ressure coupling with GP
U
update
commit
|
commitdiff
|
tree
2019-11-27
Arte
m
Zhmurov
C
o
m
bine two bool
e
ans in md loop
commit
|
commitdiff
|
tree
2019-11-27
Artem
Zhmurov
Add method for coordi
n
at
e
s scaling into GPU upda
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zh
m
urov
U
s
e sa
m
e
m
a
trix for Parrinello-Rahman
a
nd Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmur
o
v
Fix index mapping i
s
sue wi
t
h LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
N
e
w
c
ool quote
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Z
h
murov
Add D2H
c
opies for the check
p
ointing
commit
|
commitdiff
|
tree
2019-11-20
A
rtem Zhmurov
M
ove t
h
e cop
y
o
f
t
h
e velocities
f
or
t
he output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmuro
v
Fix
i
cc-19 warning
i
n nightly ma
t
rix
commit
|
commitdiff
|
tree
2019-10-31
Ar
t
e
m Zhmurov
R
e
move ex
c
essive H2D and
D
2H copie
s
o
f
f
orce
s
wh
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Z
h
murov
Disab
l
e GPU updat
e
when coordinates
s
w
appin
g
is enable
d
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Swit
c
h the GP
U
buffer
ops
o
n
w
hen update is on GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem
Z
h
m
urov
Fix mi
s
s
i
ng coo
r
di
n
ate D2H cop
y
with GPU update a
n
d
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem
Zhmuro
v
Add haveCpuLocalForce
s
flag
to DomainLif
e
timeWorkload
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Al
l
ow using
update flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmu
r
ov
Slight i
m
provem
e
nt
s
to decideW
h
etherToUseG
p
u
Fo
r
Up
d
a
te
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem
Z
hmu
r
ov
Remove unnecessary CUDA stream
syn
c
hroniz
a
tion calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmu
r
ov
Rename have
P
osit
i
onRe
s
traints(
.
.
.
) to haveR
e
st
r
aint
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmur
o
v
Update the copyri
g
ht message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zh
m
urov
A
dd env
i
ronment varia
b
le
t
h
at changes the meaning o
f
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem
Z
hmurov
Remove excess
i
ve H2D and D2H c
o
ordin
a
tes copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
Remove excessi
v
e H2D
and D
2
H copi
e
s
o
f
velocities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem
Z
hmu
r
o
v
Link G
P
U
f
orce
p
roduc
e
r an
d
con
s
umer tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmurov
Fix
t
he single-GPU upd
a
te-
c
o
n
s
traint
s
commit
|
commitdiff
|
tree
2019-10-14
Artem Zh
m
urov
Add se
p
arate
construc
t
or to St
a
tePropagatorDa
t
a
G
p
u
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhm
u
ro
v
Centrali
z
e man
a
gement of forces read
y
on GPU event
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
C
hange copy mode to Async in PM
E
only ran
k
commit
|
commitdiff
|
tree
2019-10-12
Art
e
m Zhmurov
Centralize m
a
nagemen
t
of coordi
n
ates ready
o
n GPU ev
e
nt
commit
|
commitdiff
|
tree
2019-10-11
A
rte
m
Zh
m
urov
Wrong locality was use
d
when
i
gnoring
t
he PM
E
f
o
rce
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhm
u
rov
Add
management for velo
c
ities an
d
forces copy event
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Arte
m
Z
hmurov
F
ix for the recent nightly failu
r
e
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmur
o
v
P
ass the GPU streams to S
t
atePropagator
D
a
t
aGpu
c
onst
r
u
ctor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Clean
u
p
th
e
comments sections in Upd
a
t
e-Constrain
commit
|
commitdiff
|
tree
2019-10-07
Artem Z
h
murov
Fix a bug in GPU halo exchange initializat
i
on
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix th
e
bug with
offloading
t
he
PME
-
only ranks to GPU
commit
|
commitdiff
|
tree
2019-10-02
A
r
t
em Zhmurov
Eli
m
inate D2D copy i
n
upda
t
e constraints
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
StatePropa
g
atorD
a
taGpu obj
e
ct
t
o m
a
n
age GP
U
fo
r
ces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhm
u
rov
Slight improvem
e
nts to GPU update/constra
i
n
t
s initial
i
zation
commit
|
commitdiff
|
tree
2019-09-27
A
rte
m
Zhmurov
In
t
ro
d
u
c
e stre
a
m management to GPU Upd
a
t
e-Con
s
t
raints
commit
|
commitdiff
|
tree
2019-09-22
Artem Zh
m
urov
Disable GPU u
p
date/
c
ons
t
raints when nei
t
her PME n
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Artem
Zhmurov
Ch
a
nge PaddedV
e
c
t
o
r
to P
a
ddedHostVec
t
or for for
c
e
CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmuro
v
Fix for the post
-
submit fail
u
re
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmur
o
v
D
e
couple GPU force buf
f
er management
f
rom buffer ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Decouple coord
i
na
t
es buffer manageme
n
t
fr
o
m buffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Reorgan
i
ze PME code:
commit
|
commitdiff
|
tree
2019-09-10
Artem Z
h
murov
Making
D
evi
c
eBuffer
a
v
ai
l
ible
in
non-GPU builds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add Parrinello-Rahman pressure
coupling to CUDA L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhm
u
rov
A
d
d temperature
c
oupling to CUDA L
e
ap
-
F
rog integrator
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
M
ake use of recent chan
g
es to pre
p
areKernelArg
u
ments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zh
m
urov
M
isceleneo
u
s imp
r
oveme
n
ts t
o
t
he Leap Frog
t
ests
commit
|
commitdiff
|
tree
2019-08-14
Artem Z
h
m
ur
o
v
BugF
i
x: Z
e
r
o
i
ng
t
he
p
added area of co
o
rdinates vectors
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Art
e
m Z
h
murov
Make u
s
e
of
r
e
ference data in int
e
gra
t
or tests
commit
|
commitdiff
|
tree
2019-08-13
Artem
Z
hmurov
M
ake use of reference data in SETTLE
t
es
t
s
commit
|
commitdiff
|
tree
2019-08-09
Arte
m
Zhmuro
v
Prepare Update
and Con
s
train
t
s
fo
r
D
o
main Dec
o
m
p
osition
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmurov
Re
f
actori
n
g of the SE
T
T
LE
tests
commit
|
commitdiff
|
tree
2019-08-08
Art
e
m Zhmur
o
v
Refa
c
to
r
L
e
ap-F
r
og tests and conn
e
ct them to CPU version
commit
|
commitdiff
|
tree
2019-08-06
Art
e
m Zhmurov
Fi
x
for cmake lists
i
n mdlib tests
commit
|
commitdiff
|
tree
2019-08-06
Artem
Zhmur
o
v
Remove
P
Impl
s
caffolding from CUDA version of Leap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Change
t
he
f
ile structure in constrain
t
s
t
ests
commit
|
commitdiff
|
tree
2019-07-31
Artem
Zhmur
o
v
In
t
roduce functi
o
n that che
c
ks if
t
he com
p
ut
a
tions
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmurov
R
em
o
ve PImpl scaffolding
from CU
D
A
version of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
A
r
t
e
m Zhmuro
v
R
emove
P
Im
p
l
s
c
affolding fr
o
m
CUD
A
version o
f
LINCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmu
r
ov
Use reallocateDeviceBuff
e
r(
.
.
.
) in CUDA version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Early exit for CUDA vers
i
ons of SETTL
E
an
d
LINC
S
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmuro
v
Memory management fixes in CUDA
v
e
rs
i
o
n of LINC
S
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zhmu
r
o
v
Co
m
bine CUDA Lea
p
-Fr
o
g, LINCS
a
nd SETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
A
r
tem Zhmur
o
v
Combine CUDA Leap-Fro
g
, LI
N
CS and SETTL
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
A
rt
e
m Zhm
u
rov
Bug fix:
C
onstraint
s
t
ests are not instantiate
d
with
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zh
m
urov
Clarify whic
h
of
t
he ma
i
n e
n
erg
y
terms are printed
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Cla
r
ify
th
e
Ene
r
gyOutput III
commit
|
commitdiff
|
tree
2019-05-24
Ar
t
em Zhmurov
Clarify the EnergyOut
p
ut
II
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhm
u
r
ov
C
larify the Ener
g
yOutput I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmuro
v
CUDA v
e
rsi
o
n
of Leap-Frog integrator
w
ith basic tests
commit
|
commitdiff
|
tree
2019-05-06
Artem Zhmurov
Fixing minor
m
emor
y
i
s
su
e
s in MDL
i
b
commit
|
commitdiff
|
tree
2019-05-02
A
rtem Zhmurov
U
s
e t
e
st with parameters
for
EnergyOutput
commit
|
commitdiff
|
tree
2019-04-30
Arte
m
Zhmuro
v
C
UDA
version of SETTLE
algorithm w
i
th basic tests
commit
|
commitdiff
|
tree
2019-04-29
Artem Zhmurov
F
i
x
f
or the CUDA ve
r
s
ion of LIN
C
S
commit
|
commitdiff
|
tree
2019-04-28
Artem Zhmuro
v
CUDA versio
n
of LINCS co
n
straints
.
commit
|
commitdiff
|
tree
2019-04-25
A
r
tem Zhmurov
Improvements for energy o
u
tput test
.
commit
|
commitdiff
|
tree
2019-04-16
A
rtem
Zhmurov
Fix for th
e
memory access error
i
n c
o
nst
r
aint
s
test
.
commit
|
commitdiff
|
tree
2019-04-04
Artem Zh
m
urov
Remov
e
isPressureCoup
l
ingStep(
.
.
.
)
commit
|
commitdiff
|
tree
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