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Fixed bug in orires code that was checking too strict.
2020-01-23
Artem Zhmurov
Fix a co
u
ple o
f
co
m
m
a
s in coo
l
qu
o
te
s
commit
|
commitdiff
|
tree
2020-01-13
Artem Zhmurov
R
e
p
o
r
t
i
f
update is running
o
n the GPU or o
n
the CP
U
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhmurov
Inform use
r
why forcing GPU updat
e
is not
p
oss
i
ble
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Add description of GMX_FORCE_
U
PDATE_DEFAULT_G
P
U
dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem Zhm
u
rov
Fix g
p
uupdate matrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zhmuro
v
C
hange the beh
a
vior of
t
he GPU update
U
I
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Add a note to the log
f
ile when
-
u
p
date gpu was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem
Z
hmurov
C
l
e
an b
a
d auto-format in decidegpuusage doxygen co
m
ments
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
Clean-up b
u
ffer
-
ops
C
UDA kernels
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmurov
Clean up outdated comments in md
.
c
p
p
commit
|
commitdiff
|
tree
2019-12-12
Artem Zhm
u
rov
Allow using GPU
updat
e
with DD and upda
t
e
groups
commit
|
commitdiff
|
tree
2019-12-11
Art
e
m Zh
m
urov
Enable most of the pu
l
ling flavors
w
ith GPU u
p
d
a
te
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmurov
Cla
r
ify what s
e
tting z
e
ro to some
output
m
d
p op
t
ions
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Set GPU update to false in case of a
re
r
u
n
commit
|
commitdiff
|
tree
2019-12-06
Artem
Zhmurov
Pass array ref ins
t
e
ad of casting
to basic
array
i
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhm
u
rov
Print Open
C
L
e
rror
i
n
fo in case
of
f
a
i
led asse
r
tion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Make Le
a
p
-
Frog CUDA kernel selection
s
af
e
r
commit
|
commitdiff
|
tree
2019-11-29
A
r
t
em Zhmuro
v
Ren
a
me som
e
variables in GPU
U
pdate
commit
|
commitdiff
|
tree
2019-11-28
Artem Zh
m
ur
o
v
Clear d
e
v
ice
force buff
e
r if it was reallocated
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhm
u
r
o
v
F
i
x
p
res
s
u
r
e
c
o
upling with GPU updat
e
commit
|
commitdiff
|
tree
2019-11-27
Arte
m
Zhmu
r
o
v
Co
m
bine two bool
e
a
ns in
m
d loop
commit
|
commitdiff
|
tree
2019-11-27
Artem
Z
hmurov
Add
m
eth
o
d for coordi
n
ate
s
s
c
a
l
ing into GPU
update
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhmurov
Use
sam
e
matrix for Parr
i
n
e
llo-Rahm
a
n and
B
erendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Arte
m
Zhmurov
Fix index mapping i
s
sue with LINCS o
n
GPU
commit
|
commitdiff
|
tree
2019-11-23
Art
e
m Zhmurov
N
ew
co
o
l
quo
t
e
commit
|
commitdiff
|
tree
2019-11-20
Arte
m
Zhmurov
Ad
d
D2H copi
e
s
for the checkpoin
t
ing
commit
|
commitdiff
|
tree
2019-11-20
A
r
tem Zhmurov
M
o
ve th
e
c
opy of the v
e
locities for the output closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
A
r
tem
Zhmurov
Fix icc-19 warn
i
ng in
n
igh
t
ly matrix
commit
|
commitdiff
|
tree
2019-10-31
A
rtem Zhmurov
Rem
o
ve ex
c
e
ss
i
ve H2D a
n
d D2H copies of forces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
A
r
tem Zhmu
r
o
v
Disa
b
l
e GPU update
w
hen
coordinat
e
s swapping is enabled
commit
|
commitdiff
|
tree
2019-10-29
Artem
Zhmu
r
ov
Switch the GPU
b
uffer ops on when update is
o
n GPU
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem
Z
h
mur
o
v
F
i
x missi
n
g coordinate
D
2
H copy with
G
PU upda
t
e and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Add haveCpuLocalF
o
rces flag t
o
Doma
i
nLi
f
etim
e
W
o
rkl
o
ad
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Al
l
ow using update
f
lag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmurov
Slight improvem
e
nts to decideWh
e
therToUseGp
u
F
o
rUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmu
r
ov
Re
m
ove un
n
ecessa
r
y
C
UDA stream s
y
nchr
o
niz
a
ti
o
n
c
alls
commit
|
commitdiff
|
tree
2019-10-22
Ar
t
em Zh
m
urov
Rename hav
e
P
o
sitionRestra
i
n
ts(
.
.
.
) to h
a
veRestraints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
A
rt
e
m
Zhmu
r
ov
U
pdat
e
the copy
r
i
ght message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem
Z
hmurov
Add environment
variable that
changes t
h
e meaning of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
Re
m
o
v
e exces
s
iv
e
H
2D and D2H coo
r
dina
t
e
s
copi
e
s when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
Remove
e
xcessive
H
2D and D2H cop
i
es of
velocities whe
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
A
r
tem Zhmu
r
ov
Link
G
PU f
o
r
c
e p
r
o
d
ucer a
n
d consumer tasks
commit
|
commitdiff
|
tree
2019-10-15
Arte
m
Zh
m
urov
F
ix the
s
i
ngle-GPU u
p
dat
e
-
c
o
n
st
r
a
ints
commit
|
commitdiff
|
tree
2019-10-14
Ar
t
e
m
Z
h
m
urov
Add separa
t
e constructor to
S
tatePropagatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem
Z
h
m
urov
Centralize ma
n
agem
e
nt of force
s
ready on
G
PU event
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmuro
v
Change cop
y
m
o
de
t
o Async in PME only rank
commit
|
commitdiff
|
tree
2019-10-12
Art
e
m Zhmurov
Centr
a
l
i
ze mana
g
ement of coordinates ready on GPU e
v
ent
commit
|
commitdiff
|
tree
2019-10-11
A
rtem Zhm
u
rov
W
r
on
g
l
o
c
ality was used w
h
en ignoring
the P
M
E force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Artem
Zhmur
o
v
Ad
d
man
a
ge
m
ent for velo
c
ities and f
o
rces copy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Art
e
m Zhmu
r
ov
F
ix for the recent nightly f
a
ilur
e
commit
|
commitdiff
|
tree
2019-10-07
A
rtem Zhmurov
Pass the GPU
streams to State
P
ropag
a
torData
G
pu con
s
tructor
commit
|
commitdiff
|
tree
2019-10-07
A
rtem Z
h
murov
Clea
n
up the com
m
ents sections
in Update-Constrain
commit
|
commitdiff
|
tree
2019-10-07
A
rtem Zhmur
o
v
Fix a bug in GPU h
a
l
o
exchang
e
initializ
a
t
i
o
n
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix the
bug with
off
l
oading th
e
PME-only ranks to G
P
U
commit
|
commitdiff
|
tree
2019-10-02
A
r
tem Zhmurov
Eliminate D2D copy
i
n u
p
date constra
i
nts
commit
|
commitdiff
|
tree
2019-10-01
Artem
Z
hmurov
State
P
ropagato
r
DataGpu ob
j
ect
to man
a
ge GPU
f
o
rc
e
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Arte
m
Zhmurov
Slig
h
t improvements to GPU
up
d
a
t
e
/co
n
st
r
aints initia
l
ization
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Introduce s
t
ream management t
o
GPU Upd
a
t
e-Constraints
commit
|
commitdiff
|
tree
2019-09-22
Ar
t
e
m
Zhmurov
Disable GPU up
d
ate/const
r
aints when neithe
r
PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Arte
m
Z
hmurov
Cha
n
ge PaddedV
e
c
tor to PaddedHo
s
tV
e
ctor for fo
r
ce CP
U
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Fix
f
or t
h
e post-
s
u
bmit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
D
e
coupl
e
G
PU forc
e
buffer ma
n
age
m
ent from bu
f
f
er ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zh
m
urov
Decoupl
e
c
oordinates buff
e
r manag
e
men
t
from buf
f
er
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Z
h
muro
v
R
e
o
rgan
i
ze PME co
d
e:
commit
|
commitdiff
|
tree
2019-09-10
Artem Zhmu
r
ov
Making
DeviceBu
f
f
er availible in non-GPU builds
commit
|
commitdiff
|
tree
2019-09-03
Artem Z
h
m
urov
Add Par
r
inello-Rahm
a
n pr
e
ssure coup
l
in
g
to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Arte
m
Zhmurov
A
dd te
m
p
e
r
a
ture coupling to
CUDA Leap-
F
rog
i
n
t
egr
a
t
o
r
commit
|
commitdiff
|
tree
2019-08-25
A
r
tem Zhmurov
M
ake us
e
of rece
n
t changes
to prepa
r
eKernelA
r
guments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
A
rtem Zh
m
u
rov
Miscelen
e
ous impr
o
vements to th
e
Lea
p
Frog t
e
s
t
s
commit
|
commitdiff
|
tree
2019-08-14
Artem Zhmurov
BugFix: Ze
r
oing the
p
ad
d
e
d area of coo
r
dinates
v
ecto
r
s
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmurov
Make use of
re
f
erence dat
a
in integrator t
e
sts
commit
|
commitdiff
|
tree
2019-08-13
A
r
tem Z
h
murov
M
a
ke use of reference data in S
E
T
TLE tests
commit
|
commitdiff
|
tree
2019-08-09
Arte
m
Zhmurov
P
r
epare
U
pdat
e
and Constraints f
o
r Domain Decompositio
n
commit
|
commitdiff
|
tree
2019-08-09
A
rtem Zhm
u
rov
Refacto
r
ing of the SET
T
LE tests
commit
|
commitdiff
|
tree
2019-08-08
Artem
Z
hmu
r
ov
Re
f
a
ctor Leap-Frog tests
an
d
conne
c
t them to CPU version
commit
|
commitdiff
|
tree
2019-08-06
Ar
t
em Zhm
u
rov
Fix for cma
k
e lists in mdlib tests
commit
|
commitdiff
|
tree
2019-08-06
A
r
tem Zhmurov
Remov
e
PIm
p
l scaffo
l
di
n
g
from CUDA
v
ersion of Leap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Change the file structu
r
e
in con
s
tra
i
nts t
e
st
s
commit
|
commitdiff
|
tree
2019-07-31
Ar
t
em Zhmu
r
o
v
Intr
o
du
c
e function that
checks if the computations
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Ar
t
em Zhmurov
Remove PImpl scaffolding
fr
o
m CUDA
versio
n
of SETTL
E
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmurov
Remove PImpl scaffolding from CUDA version of LINCS
commit
|
commitdiff
|
tree
2019-07-04
Ar
t
em Zhmurov
Us
e
reallocate
D
evice
B
u
ff
e
r(
.
.
.
)
i
n CUDA versi
o
n of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Ea
r
l
y exit
f
o
r CUDA
versions of SETTLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Mem
o
ry manageme
n
t
f
i
xe
s
in CUDA version of LI
N
CS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Co
m
bin
e
CUD
A
Leap-Frog, LIN
C
S
and SETTLE
.
II
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Z
h
murov
Combine CUDA Leap-Frog, LINCS a
n
d SET
T
L
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem
Zhmuro
v
B
u
g fix: Constrai
n
t
s
tests a
r
e no
t
instantiated with
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
Art
e
m
Z
h
m
urov
Clarify which of the main ene
r
gy t
e
rms are printed
.
commit
|
commitdiff
|
tree
2019-05-24
Ar
t
em Zhmurov
Clarify
t
he EnergyOutput
III
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clarify the EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhmurov
Clarify the EnergyOutput
I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmurov
CUDA ver
s
i
on of Leap-Frog in
t
egr
a
tor
with basic tes
t
s
commit
|
commitdiff
|
tree
2019-05-06
Arte
m
Z
hm
u
rov
F
ixing
mino
r
memory issues in MDLib
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhmurov
Use tes
t
with pa
r
am
e
ters for E
n
ergy
O
u
tput
commit
|
commitdiff
|
tree
2019-04-30
Artem Zhmurov
CUD
A
version of
SETTLE al
g
orithm with basic tests
commit
|
commitdiff
|
tree
2019-04-29
Arte
m
Zhmurov
F
i
x for the CUD
A
ver
s
ion of LIN
C
S
commit
|
commitdiff
|
tree
2019-04-28
A
rtem Z
h
murov
CUDA version of LIN
C
S constraints
.
commit
|
commitdiff
|
tree
2019-04-25
Arte
m
Zhmurov
Improvements
for energ
y
output test
.
commit
|
commitdiff
|
tree
2019-04-16
Artem
Z
hmurov
Fix for the memory a
c
cess error in co
n
strain
t
s
t
es
t
.
commit
|
commitdiff
|
tree
2019-04-04
A
rtem Zhm
u
rov
Re
m
ove isPressureC
o
u
p
lingSte
p
(
.
.
.
)
commit
|
commitdiff
|
tree
next