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Fix gmx h2order -d option
2020-10-22
Art
e
m Zhmurov
Use
a
n
d properly initialize PRNG when hardware r
a
n
dom
.
.
.
commit
|
commitdiff
|
tree
2020-09-29
Artem Zhmuro
v
Don't use fah_fsync
commit
|
commitdiff
|
tree
2020-06-16
A
rtem
Z
hmurov
Add mi
s
sing e
n
d-of-line in the
G
PU
up
d
ate assignment
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
A
rtem Zhmuro
v
Make
a
e
rror message less co
n
fu
s
ing
commit
|
commitdiff
|
tree
2020-06-04
A
r
tem Zhmurov
Update the releas
e
n
otes
commit
|
commitdiff
|
tree
2020-04-29
Artem Z
h
murov
Fix the number of steps check whe
n
c
h
eckpoint is loaded
commit
|
commitdiff
|
tree
2020-04-27
A
rtem Zhmu
r
ov
F
i
x the
r
emoval
o
f
CO
M
velocit
y
in case
of GPU upda
t
e
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhmu
r
ov
Update the mes
s
ag
e
on w
h
ether u
p
date and constraints
.
.
.
commit
|
commitdiff
|
tree
2020-01-23
Artem Z
h
muro
v
Fix a
c
oup
l
e
o
f
commas in cool q
u
otes
commit
|
commitdiff
|
tree
2020-01-13
Art
e
m Zhmurov
Report if update
i
s run
n
ing on the G
P
U or o
n
the CP
U
commit
|
commitdiff
|
tree
2019-12-31
Artem
Zhmurov
Inform
u
ser why forcing GPU update is not
possible
commit
|
commitdiff
|
tree
2019-12-31
Artem Zhmurov
Add descr
i
p
t
ion of GMX_FORC
E
_
UPDA
T
E_DE
F
AULT_GPU dev
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem
Zhmurov
Fix gpuu
p
d
a
te
m
atrix
commit
|
commitdiff
|
tree
2019-12-28
Artem Zh
m
urov
Change the behavior
o
f the GPU up
d
ate U
I
commit
|
commitdiff
|
tree
2019-12-27
Artem
Zhmurov
Add a note to the log
file when
-
up
d
ate gpu
was set
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Artem Zhmurov
Clean
b
ad auto-fo
r
mat in decideg
p
uusage doxygen co
m
me
n
t
s
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmu
r
ov
Clean-up buffer-ops CUDA kernels
commit
|
commitdiff
|
tree
2019-12-13
A
r
tem
Zhmurov
Clean
up outd
a
ted comme
n
ts in md
.
cpp
commit
|
commitdiff
|
tree
2019-12-12
Art
e
m Zhmurov
A
l
lo
w
using GPU update with DD and
update
g
roups
commit
|
commitdiff
|
tree
2019-12-11
Artem Zhmu
r
ov
Enab
l
e most
o
f th
e
pulling flavors with
GPU update
commit
|
commitdiff
|
tree
2019-12-11
Arte
m
Z
h
murov
Cl
a
rify
wha
t
setting z
e
ro
t
o some
o
utput mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
Artem Zhmurov
Set GPU
u
pdate to false in case
o
f a
rerun
commit
|
commitdiff
|
tree
2019-12-06
A
r
tem Zh
m
urov
P
a
ss
a
rray ref
i
n
stead
of casting to basic ar
r
ay in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
em
Zhm
u
rov
Print OpenCL e
r
ror info
i
n ca
s
e
o
f f
a
iled as
s
erti
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
M
ake Leap-Fr
o
g CUDA k
e
rnel select
i
on safer
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmur
o
v
Rename so
m
e variable
s
in GPU Up
d
at
e
commit
|
commitdiff
|
tree
2019-11-28
Artem Z
h
mur
o
v
C
l
ear d
e
vic
e
f
o
rce
b
u
ffer
i
f it wa
s
real
l
oc
a
ted
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhmu
r
ov
Fix pressure coup
l
ing with GPU up
d
ate
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Zhmurov
Combin
e
t
wo bo
o
leans in
md loop
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Zh
m
urov
Add me
t
hod for coordinates s
c
a
ling into
G
PU up
d
ate
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Zhm
u
rov
Use
same matrix for Parri
n
el
l
o-Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem
Zhmur
o
v
Fix index mapping is
s
ue with LINCS
on GPU
commit
|
commitdiff
|
tree
2019-11-23
Arte
m
Z
h
muro
v
New co
o
l quote
commit
|
commitdiff
|
tree
2019-11-20
Art
e
m Zhmurov
Add D2H copies for the checkpoin
t
ing
commit
|
commitdiff
|
tree
2019-11-20
A
r
tem Zh
m
urov
Move
t
he
copy of the vel
o
citie
s
for the outp
u
t closer
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
F
i
x icc
-
19 wa
r
ning in nightl
y
matr
i
x
commit
|
commitdiff
|
tree
2019-10-31
Art
e
m
Zhmurov
Remove e
x
cessive H2D
and D2H c
o
pies of forces
w
hen
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Z
h
murov
Dis
a
ble GPU u
p
date when
c
oor
d
inate
s
swa
p
ping i
s
enable
d
commit
|
commitdiff
|
tree
2019-10-29
A
r
tem Zhmurov
Switch the GPU buffer
ops
o
n
when u
p
date is on
GPU
commit
|
commitdiff
|
tree
2019-10-28
Artem
Zhmurov
Fix missing coordinate
D
2H c
o
py with GPU update and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Art
e
m Zhmurov
Add haveCpuLocalForces flag to Domain
L
ifetimeWorkload
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmu
r
ov
Allow using upda
t
e flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Zhmurov
Slight improvements
to decideWhet
h
e
r
To
U
se
G
puForUpdate
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
A
r
tem Zhm
u
r
o
v
Remove unnecessary CUDA stream synchronization c
a
lls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Rename havePositionRestraints(
.
.
.
) t
o
haveRestraints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Art
e
m
Z
hmurov
Up
d
a
t
e the copyright message
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Ar
t
em Zhmurov
A
dd env
i
ro
n
ment variable that cha
n
g
e
s
t
he meaning of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
r
tem Zhm
u
rov
Remove exces
s
i
v
e H2
D
and D2H co
o
rd
i
nate
s
copies
when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
r
tem Zhmu
r
ov
Remove
e
xcessive H2D
a
nd D2H
c
opies
of velocities when
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmurov
Li
n
k GPU f
o
rce
producer and
consumer tasks
commit
|
commitdiff
|
tree
2019-10-15
Artem Zhmu
r
ov
Fix the si
n
gle-GPU up
d
ate-c
o
nst
r
aints
commit
|
commitdiff
|
tree
2019-10-14
Artem
Z
h
m
u
r
o
v
Add separate constructor to Sta
t
eP
r
opagatorDat
a
Gpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Cent
r
alize
m
a
nagement of
forces ready o
n
GPU event
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmu
r
ov
C
h
a
n
ge
c
o
py mode to
Asyn
c
in PM
E
o
n
ly rank
commit
|
commitdiff
|
tree
2019-10-12
Artem
Zhmu
r
ov
Centralize managemen
t
of coord
i
n
at
e
s ready
o
n GPU event
commit
|
commitdiff
|
tree
2019-10-11
Artem Z
h
murov
W
r
o
ng
l
ocality
w
as use
d
when ignoring the PME for
c
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Art
e
m Zhmurov
Add management
f
or velocities and force
s
c
opy ev
e
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem
Z
hmurov
Fix for the r
e
cent nightly f
a
i
l
u
r
e
commit
|
commitdiff
|
tree
2019-10-07
A
rtem Z
h
m
u
rov
Pa
s
s the GPU
st
r
e
a
ms
to St
a
tePropaga
t
orDataGpu
c
onstructor
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmu
r
ov
Cle
a
n up t
h
e comments sections i
n
Update-Constr
a
in
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhm
u
rov
Fix a bug in GPU h
a
l
o
exchange init
i
alizati
o
n
commit
|
commitdiff
|
tree
2019-10-03
Artem Zhmurov
Fix the bu
g
with
o
ffloadin
g
the
P
ME-only ran
k
s to
GPU
commit
|
commitdiff
|
tree
2019-10-02
Artem Zhmurov
E
l
iminate
D
2D copy in up
d
a
t
e c
o
n
s
traints
commit
|
commitdiff
|
tree
2019-10-01
Artem Zhmurov
StatePropagatorDat
a
Gpu obj
e
ct t
o
manag
e
GP
U
forces
.
.
.
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Slight improveme
n
ts t
o
GP
U
update/const
r
aints initi
a
l
i
z
ation
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Introduce st
r
eam management to GPU Update-Constrain
t
s
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmur
o
v
Dis
a
b
l
e
GPU update/c
o
nstraint
s
when neither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Art
e
m Zhmurov
Change
Padd
e
d
Vector to Pad
d
edHost
V
ector for f
o
rce
C
P
U
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Z
h
murov
F
ix for the p
o
st-submit failure
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmurov
Decou
p
le GPU
f
o
r
ce buffer manag
e
ment from
buffer o
p
s
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhm
u
rov
Decouple coordinates b
u
ffer
management
fro
m
b
u
ffer
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmu
r
ov
Reorganiz
e
PME
cod
e
:
commit
|
commitdiff
|
tree
2019-09-10
Artem Zhmurov
Mak
i
ng DeviceBuffer availible in non
-
GPU bui
l
ds
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add Parrinello-Rahm
a
n
p
ressur
e
cou
p
ling to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
A
dd temperature coupling to CU
D
A Leap-Frog integrator
commit
|
commitdiff
|
tree
2019-08-25
Art
e
m Z
h
murov
Make u
s
e of rec
e
nt
c
hanges to prepareKernelArguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Misc
e
leneous
i
mprovement
s
t
o the Leap Frog
t
ests
commit
|
commitdiff
|
tree
2019-08-14
A
r
tem Zhmurov
BugF
i
x: Zeroing the
padded area o
f
coor
d
inates vectors
.
.
.
commit
|
commitdiff
|
tree
2019-08-13
Artem Zhmurov
Make use of reference data
i
n integr
a
tor te
s
ts
commit
|
commitdiff
|
tree
2019-08-13
Art
e
m Zhmurov
Make use of reference data in SETTLE tests
commit
|
commitdiff
|
tree
2019-08-09
A
r
te
m
Zhmurov
Prepare
U
p
d
ate and Constra
i
nts for Doma
i
n Decomposition
commit
|
commitdiff
|
tree
2019-08-09
A
rt
e
m Zhmu
r
ov
Ref
a
c
t
oring of the SETTLE test
s
commit
|
commitdiff
|
tree
2019-08-08
Artem
Zhm
u
rov
Ref
a
cto
r
Leap-Frog t
e
sts and connect them to CPU version
commit
|
commitdiff
|
tree
2019-08-06
Artem
Z
hmurov
Fix for cmake lis
t
s in mdlib tests
commit
|
commitdiff
|
tree
2019-08-06
Artem Z
h
mur
o
v
Remove PI
m
pl scaffold
i
ng from CUDA v
e
rsion of Leap
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Artem
Zh
m
u
r
ov
Chang
e
the file structure in
c
onstraints tes
t
s
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Introduce function
tha
t
checks if the
c
omputations
.
.
.
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmurov
Re
m
ove
PImpl scaffolding from
CUDA versi
o
n of SE
T
TLE
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmurov
Remove PImpl scaffolding from CUDA version o
f
LINCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmurov
Use reallocateDeviceBuffer(
.
.
.
)
in CUDA
version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Art
e
m Zhmurov
Early
exit for C
U
DA v
e
rsions of SETTLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
A
rtem Z
h
murov
Memory
m
anagement fix
e
s in CUDA vers
i
on of
L
INCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhm
u
rov
Combine CUD
A
L
e
ap-Frog,
LINCS and SETTLE
.
I
I
.
commit
|
commitdiff
|
tree
2019-06-18
Ar
t
e
m
Z
hmurov
C
o
m
b
ine CUDA
L
e
a
p-Frog
,
LINCS an
d
SETTL
E
.
I
.
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmurov
Bug fix:
C
onstraints
t
ests are n
o
t ins
t
ant
i
ated wi
t
h
.
.
.
commit
|
commitdiff
|
tree
2019-05-24
A
r
te
m
Zhmurov
C
l
arify
w
hich of the mai
n
ene
r
gy terms a
r
e
printed
.
commit
|
commitdiff
|
tree
2019-05-24
Artem Zh
m
ur
o
v
Clarify the EnergyOutpu
t
III
commit
|
commitdiff
|
tree
2019-05-24
Artem Zhmurov
Clari
f
y the EnergyOutput II
commit
|
commitdiff
|
tree
2019-05-13
Artem Zhmurov
Clarify
t
h
e
En
e
r
g
yO
u
tpu
t
I
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmuro
v
CUDA vers
i
on of
L
eap-Frog integrat
o
r
w
ith basic tests
commit
|
commitdiff
|
tree
next