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Update the release notes
2020-06-04
Artem Zhmurov
Update the release no
t
es
commit
|
commitdiff
|
tree
2020-04-29
A
rtem
Zhmurov
Fix the number of ste
p
s check
w
h
en
checkpoin
t
is
l
oa
d
ed
commit
|
commitdiff
|
tree
2020-04-01
Mark
Abraham
F
ix
m
inor bug wit
h
to
o
l
s ti
m
e-unit conversio
n
s
commit
|
commitdiff
|
tree
2020-03-19
S
z
il
á
rd Páll
F
ix DLB ini
t
ia
l
s
t
a
te r
e
po
r
ting
commit
|
commitdiff
|
tree
2020-03-07
Paul Ba
u
er
Add clang
-
t
i
dy scrip
t
commit
|
commitdiff
|
tree
2020-03-02
Paul Bauer
Add Cuda build to gitlab
C
I
commit
|
commitdiff
|
tree
2020-02-22
D
a
vid van
der Spo
e
l
Fixed
bug in
g
m
x
d
i
sre
due
t
o inc
o
nsis
t
enc
y
in input
.
commit
|
commitdiff
|
tree
2020-02-15
Szilárd Páll
F
i
x gpuudpate and gpucomm ma
t
r
i
x docs
commit
|
commitdiff
|
tree
2020-01-24
Szilá
r
d Páll
Fix deadlock
i
n
PP
-
PME balancing
s
t
artup
d
e
lay
commit
|
commitdiff
|
tree
2020-01-22
Be
r
k
Hess
Cl
a
rify COMM/posres grompp note
commit
|
commitdiff
|
tree
2019-12-30
Ma
r
k
A
b
raham
Remove use of tuple in
L
INCS code
f
or GPU impl
e
mentati
o
n
commit
|
commitdiff
|
tree
2019-12-20
Pau
l
B
a
uer
Fix wr
o
ng header
in release n
o
t
e
s
commit
|
commitdiff
|
tree
2019-12-18
Alan Gray
Fix
c
ondit
i
onal o
n
assertion for combining GPU Update
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
Be
r
k Hess
Ad
d
note fo
r
COM removal with positi
o
n
r
e
straints
commit
|
commitdiff
|
tree
2019-12-17
Artem
Z
hmurov
Clean-up buf
f
er-ops CUDA
k
e
rnel
s
commit
|
commitdiff
|
tree
2019-12-17
Szil
á
r
d Páll
Co
m
m
e
nt th
e
use
o
f
w
a
itCoordinate
s
CopiedToDevice
commit
|
commitdiff
|
tree
2019-12-17
Pa
u
l
B
a
uer
S
et co
r
rect dependenc
y
for doc build on
g
mx
a
pi
commit
|
commitdiff
|
tree
2019-12-17
Paul
Bauer
Fi
x
compiler warn
i
ng about extr
a
;
commit
|
commitdiff
|
tree
2019-12-17
Szilárd
P
á
ll
A
d
d
wa
l
lcycle counti
n
g to StatePropagatorD
a
t
a
G
pu
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem Zhmurov
E
nab
l
e most
o
f the pullin
g
flavo
r
s with GPU update
commit
|
commitdiff
|
tree
2019-12-10
Ar
t
em Zhmurov
Set GPU update to false in case of a rerun
commit
|
commitdiff
|
tree
2019-11-29
Artem Zh
m
urov
Make Le
a
p-Frog CU
D
A kernel s
e
lection safer
commit
|
commitdiff
|
tree
2019-11-28
Art
e
m Z
h
murov
Fix
pressure coup
l
ing
w
i
th GPU update
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
C
o
m
bine t
w
o booleans in md lo
o
p
commit
|
commitdiff
|
tree
2019-11-27
Mark Ab
r
aham
Disable
G
P
U PM
E
-P
P
commu
n
ication with mdrun
-pmefft cpu
commit
|
commitdiff
|
tree
2019-11-26
Alan Gray
Bug fix for nonlocal D2H coordinate
transfer
s
ynchronizat
i
on
commit
|
commitdiff
|
tree
2019-11-23
Ar
t
em Z
h
m
u
rov
New coo
l
quote
commit
|
commitdiff
|
tree
2019-11-20
A
l
an Gra
y
M
o
ve pme
P
pCommGpu reset outside do_md
commit
|
commitdiff
|
tree
2019-11-19
Mark Abr
a
ham
U
p
dated release notes
for
CODATA up
d
ate
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix ic
c
-19
war
n
ing in nigh
t
ly matrix
commit
|
commitdiff
|
tree
2019-11-13
Paul Bauer
Add bu
i
l
d
t
o
r
u
n clang-
f
ormat update on Jenki
n
s
commit
|
commitdiff
|
tree
2019-11-03
Szilárd Pá
l
l
Im
p
r
o
ve SimulationWorkload
doxygen
commit
|
commitdiff
|
tree
2019-10-30
Berk Hess
Fix walls with GPU update
commit
|
commitdiff
|
tree
2019-10-29
Be
r
k
Hess
Di
s
ab
l
e p
r
essure coupling
with GPU up
d
ate
commit
|
commitdiff
|
tree
2019-10-28
Szilárd Páll
E
xtend SimulationWorkload
w
i
t
h C
P
U flags
commit
|
commitdiff
|
tree
2019-10-21
S
zil
á
rd
P
áll
Override GM
X
_GPU_DD_
C
OMMS if
nonbondeds are
o
ff
commit
|
commitdiff
|
tree
2019-10-18
A
rtem Z
h
murov
Remove e
x
cessive H2D and D2H
c
oordinates copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
Szilárd Páll
Di
s
a
b
l
e
G
MX_GPU_PME_PP_C
O
MMS if PM
E
i
s
not o
f
f
l
o
aded
commit
|
commitdiff
|
tree
2019-10-16
Szilár
d
Páll
F
i
x in
i
tialization o
f
field
i
n
P
ME
d
ata structure
commit
|
commitdiff
|
tree
2019-10-16
A
rte
m
Zhmurov
Link GPU fo
r
ce prod
u
cer and consumer
t
asks
commit
|
commitdiff
|
tree
2019-10-15
Alan Gray
PME/PP GPU P
i
mpl Class an
d
GP
U
-
>CPU
C
ommunication f
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Szilárd Páll
Link
GPU coor
d
ina
t
e pro
d
ucer and c
o
nsu
m
er tasks
commit
|
commitdiff
|
tree
2019-10-14
A
r
t
em Zhmuro
v
Add
se
p
a
r
ate
c
on
s
tructor to S
t
at
e
Propag
a
torDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szi
l
á
rd Pál
l
E
n
a
b
le S
t
atePr
o
pagatorGpuData for force tr
a
nsfers
commit
|
commitdiff
|
tree
2019-10-13
Szilárd Páll
Move buffer ops / PME
F re
d
uct
i
on
fla
g
s
i
nto S
t
epWor
k
l
oad
commit
|
commitdiff
|
tree
2019-10-12
Artem Z
h
murov
Centr
a
lize manage
m
ent of forces
read
y
on GP
U
event
commit
|
commitdiff
|
tree
2019-10-12
Artem
Z
hmurov
Ch
a
nge copy mode to Async in PME
o
n
ly rank
commit
|
commitdiff
|
tree
2019-10-11
Artem
Z
hmuro
v
Wrong locality w
a
s use
d
when ign
o
ring
t
h
e
PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
S
z
ilárd Páll
Migrate
code to using SimulationWo
r
kload fl
a
g
s
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Pál
l
Remove incor
r
e
ct
GPU task depend
e
ncy
commit
|
commitdiff
|
tree
2019-10-10
Szilár
d
Páll
Pass l
i
st of EventS
y
nchronizers
t
o GPU reduction
commit
|
commitdiff
|
tree
2019-10-10
Paul Bauer
Basic pop
u
latio
n
of sim
u
latio
n
wo
r
kload
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmurov
Add man
a
gement for v
e
locities
a
nd forces copy
e
vents
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
A
dd m
a
nag
e
ment for coordi
n
a
tes copy events into Sta
t
ePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
P
a
ss
t
he GP
U
streams to StatePr
o
pagatorDataGpu c
o
n
s
t
r
u
c
tor
commit
|
commitdiff
|
tree
2019-10-07
M
a
rk
A
b
raham
Extend
G
P
U
t
raits cla
s
s
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
h
m
urov
C
l
e
an up the comments sections in Update-Const
r
ain
commit
|
commitdiff
|
tree
2019-10-07
A
rt
e
m Zhmuro
v
Fix a bug in GPU
h
a
l
o
exchan
g
e in
i
tializat
i
on
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use
g
m
x::Range f
o
r
i
Z
one
s
in
p
air search
commit
|
commitdiff
|
tree
2019-10-02
Carsten Kutzner
U
pdate
the www lin
k
to
the
Do
x
yge
n
documentation
in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
S
z
ilárd P
á
ll
M
ove PME GPU
p
r
ogram b
u
ild
i
n
g
l
ater
commit
|
commitdiff
|
tree
2019-09-27
Artem Zh
m
urov
Sligh
t
i
m
provem
e
nts to GPU update
/
co
n
straints
init
i
a
lization
commit
|
commitdiff
|
tree
2019-09-27
Szilárd Páll
Swi
t
ch
G
PU update o
f
f
b
y def
a
ult
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmurov
Introduce s
t
ream
m
anagement
t
o
GP
U
Update-Constraints
commit
|
commitdiff
|
tree
2019-09-27
B
erk Hess
Extract
gmx::
R
ange
commit
|
commitdiff
|
tree
2019-09-27
M
a
rk Abraham
Stop
c
he
c
king CUDA vers
i
on repor
t
e
d by nvcc
commit
|
commitdiff
|
tree
2019-09-22
Art
e
m
Zhm
u
rov
Di
s
able G
P
U
u
pda
t
e/co
n
straints when neit
h
er P
M
E nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Mark A
b
raham
Make gmx_multisim_t a C++ ob
j
ect
commit
|
commitdiff
|
tree
2019-09-10
Ma
r
k Abraham
Avoid warning in no-mpi build
commit
|
commitdiff
|
tree
2019-09-10
Artem
Z
h
murov
Making
D
eviceBuf
f
er
a
vai
l
ib
l
e
i
n
n
on-
G
PU
b
uilds
commit
|
commitdiff
|
tree
2019-09-10
Paul Bauer
Add i
n
dication
on how to
enable I
m
ag
e
Ma
g
ick
convert
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
A
s
sert t
h
e
types of Ope
n
CL kernels
argument
s
commit
|
commitdiff
|
tree
2019-08-25
A
r
tem Zhmu
r
ov
Make use
o
f re
c
ent changes
to prep
a
reKernelArgum
e
nts
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Misce
l
eneous improvem
e
nts to the Leap Frog
t
e
sts
commit
|
commitdiff
|
tree
2019-08-20
Mark A
b
raham
Apply cla
n
g-tidy-8 re
a
dabil
i
ty-up
p
e
r
ca
s
e-literal-suffix
commit
|
commitdiff
|
tree
2019-08-20
Mark Abra
h
am
Use
potenti
a
l-shif
t
a
s
d
ef
a
ult mod
i
f
i
e
r
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
Move bonded function
table int
o
bonded
.
cp
p
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
Initialize gmx_e
k
indata_t
a
nd t_vcm p
r
ope
r
ly
commit
|
commitdiff
|
tree
2019-08-06
Art
e
m
Z
hmurov
Fix for c
m
ake
list
s
in mdlib
tests
commit
|
commitdiff
|
tree
2019-07-31
A
r
t
em Zhmur
o
v
Chang
e
the file st
r
ucture in cons
t
rain
t
s
t
ests
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Store wcycle pointer in no
n
bonded_verlet_
t
commit
|
commitdiff
|
tree
2019-07-26
A
rt
e
m Zhmurov
Remove PImpl scaffo
l
ding fro
m
CUD
A
v
e
rsion of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Kevin
Boyd
C
hange error me
s
sage
w
hen a
t
tempting to
o
fflo
a
d to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Artem
Z
h
murov
Remo
v
e PImpl scaffolding fr
o
m CUDA version of
LI
N
CS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmu
r
ov
Use real
l
ocateDevic
e
Buffe
r
(
.
.
.
) in
C
UDA version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Art
e
m Z
h
murov
Ea
r
ly
e
xit
for CUDA ver
s
ions
o
f
S
ETTLE a
n
d LINCS
commit
|
commitdiff
|
tree
2019-07-03
A
r
tem
Zhmurov
Me
m
ory
man
a
g
ement fixes i
n
CUDA version of LINCS
commit
|
commitdiff
|
tree
2019-06-28
Szil
á
rd Páll
Separate CPU NB kernel and buffe
r
clearing sub
c
ounters
commit
|
commitdiff
|
tree
2019-06-28
M
a
gn
u
s Lun
d
borg
Fus
e
d GPU bonded kernels
commit
|
commitdiff
|
tree
2019-06-18
Artem Z
h
mu
r
ov
Combine C
U
D
A Leap
-
Frog, LI
N
CS and SETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
A
rtem Zhmuro
v
Clarif
y
which
of the mai
n
ener
g
y terms are
p
ri
n
ted
.
commit
|
commitdiff
|
tree
2019-05-13
Paul
Bau
e
r
F
i
x
math formatting in reference manual
commit
|
commitdiff
|
tree
2019-05-12
Ar
t
em Zhmurov
CUDA version
o
f Lea
p
-
F
rog integrat
o
r
wi
t
h basic t
e
sts
commit
|
commitdiff
|
tree
2019-05-06
Mark Abra
h
am
Improve how mdrun -noappend names outp
u
t files
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhm
u
rov
Use test w
i
t
h para
m
eters
f
or EnergyOutput
commit
|
commitdiff
|
tree
2019-04-30
Artem Zhmurov
CUDA versio
n
o
f SETT
L
E algor
i
thm with basic tes
t
s
commit
|
commitdiff
|
tree
2019-04-29
Ar
t
e
m
Zhmurov
Fix for the
CUDA
v
ersion of L
I
N
C
S
commit
|
commitdiff
|
tree
2019-04-28
Artem Zhmur
o
v
CUDA version of LINCS co
n
strai
n
ts
.
commit
|
commitdiff
|
tree
2019-04-04
Carsten
K
u
t
zner
Early exi
t
f
r
o
m mdrun if gro
u
p scheme is
d
etected
in
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
A
r
te
m
Zhmurov
Rem
o
ve
i
sPressureCo
u
plingStep(
.
.
.
)
commit
|
commitdiff
|
tree
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