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Update the release notes
2020-06-04
Ar
t
em
Z
hmurov
Updat
e
the
release notes
commit
|
commitdiff
|
tree
2020-04-29
Artem
Z
hmurov
Fix the number of steps
c
h
ec
k
whe
n
c
h
eckp
o
int is loaded
commit
|
commitdiff
|
tree
2020-04-01
Mark
Abraham
Fi
x
m
inor bug
w
ith too
l
s time-uni
t
conversions
commit
|
commitdiff
|
tree
2020-03-19
Szi
l
á
r
d Páll
Fix DLB in
i
tia
l
state r
e
porting
commit
|
commitdiff
|
tree
2020-03-07
Paul Bauer
Add
c
lang-tidy s
c
ript
commit
|
commitdiff
|
tree
2020-03-02
P
aul B
a
ue
r
A
d
d Cuda
b
uil
d
to
g
itlab
C
I
commit
|
commitdiff
|
tree
2020-02-22
D
a
vid van d
e
r Spoe
l
Fixed bug
i
n gmx disre due to inconsi
s
ten
c
y in in
p
ut
.
commit
|
commitdiff
|
tree
2020-02-15
Szilá
r
d
P
á
l
l
Fix gp
u
u
d
pate
and gpucom
m
matri
x
d
o
cs
commit
|
commitdiff
|
tree
2020-01-24
Szilárd Páll
Fix deadlock i
n
P
P
-
P
M
E balancing startup
d
elay
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
C
larify COMM/posr
e
s grompp note
commit
|
commitdiff
|
tree
2019-12-30
Mar
k
Ab
r
aham
Remove use of
t
uple in LINCS code
f
or GPU im
p
l
ement
a
tion
commit
|
commitdiff
|
tree
2019-12-20
Paul
B
a
u
e
r
F
i
x wrong header in release
n
o
te
s
commit
|
commitdiff
|
tree
2019-12-18
Alan
Gray
Fix
conditional on assertion for
combinin
g
G
P
U Update
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
B
er
k
Hess
A
dd note for COM removal with position restraint
s
commit
|
commitdiff
|
tree
2019-12-17
Ar
t
em Zhmurov
C
lean-up buffer-o
p
s CUDA ker
n
els
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Comme
n
t the use o
f
wai
t
Co
o
rdinatesCopi
e
d
ToDevic
e
commit
|
commitdiff
|
tree
2019-12-17
P
a
u
l B
a
uer
Set correct d
e
pendency
f
or doc b
u
i
l
d
on gmxa
p
i
commit
|
commitdiff
|
tree
2019-12-17
Paul
Bauer
Fix com
p
iler
war
n
ing about extra ;
commit
|
commitdiff
|
tree
2019-12-17
Szilá
r
d Páll
A
dd wallc
y
cle counti
n
g
to S
t
ateP
r
opagatorDataGpu
commit
|
commitdiff
|
tree
2019-12-11
Art
e
m
Zhmu
r
ov
Enable most o
f
t
h
e
p
ullin
g
flav
o
rs with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-12-10
Artem
Z
h
murov
S
et GPU
u
pdate to false in ca
s
e
o
f a
r
erun
commit
|
commitdiff
|
tree
2019-11-29
Ar
t
e
m
Zhmurov
Make
L
eap-Fro
g
CU
D
A kernel selection s
a
fer
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhm
u
rov
Fix pres
s
ure coupling
wi
t
h GP
U
u
p
date
commit
|
commitdiff
|
tree
2019-11-27
Art
e
m Zhmu
r
ov
Combine
t
wo booleans
i
n md
l
oop
commit
|
commitdiff
|
tree
2019-11-27
Mar
k
Abraham
Disable G
P
U PME-PP commun
i
c
atio
n
with
mdru
n
-pmefft
c
p
u
commit
|
commitdiff
|
tree
2019-11-26
Al
a
n
Gray
Bug fix for
nonlocal
D
2H
c
oordinate tra
n
sfer
synchronization
commit
|
commitdiff
|
tree
2019-11-23
Artem Z
h
murov
New cool quot
e
commit
|
commitdiff
|
tree
2019-11-20
Alan G
r
ay
Move pmePpCom
m
Gpu reset outside do_md
commit
|
commitdiff
|
tree
2019-11-19
Mark Abra
h
am
Updated
release notes for CO
D
ATA
update
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix icc-19 warning in nightly matr
i
x
commit
|
commitdiff
|
tree
2019-11-13
Paul Bauer
Add
b
u
ild to run clang-format upd
a
te o
n
J
en
k
ins
commit
|
commitdiff
|
tree
2019-11-03
Sz
i
lár
d
Páll
Impro
v
e Si
m
ula
t
io
n
W
orkl
o
ad doxygen
commit
|
commitdiff
|
tree
2019-10-30
Berk Hess
Fi
x
w
al
l
s w
i
t
h
GPU upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
Berk
H
ess
Disab
l
e
p
ressure c
o
u
p
ling
w
ith GPU
u
pda
t
e
commit
|
commitdiff
|
tree
2019-10-28
Szilár
d
P
á
ll
E
x
tend SimulationWorkloa
d
with CPU flags
commit
|
commitdiff
|
tree
2019-10-21
S
zilár
d
Pál
l
Over
r
ide GMX_GPU_
D
D_COMMS if nonbo
n
deds a
r
e off
commit
|
commitdiff
|
tree
2019-10-18
Arte
m
Zh
m
u
rov
Remove
e
xcessive H2D and D2H
c
oordinates copies
w
h
e
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
S
zi
l
árd
P
áll
Disab
l
e GMX_GPU_PME_PP_COMMS if PME is
not of
f
loaded
commit
|
commitdiff
|
tree
2019-10-16
Szi
l
ár
d
Páll
Fix initi
a
l
iz
a
tion of field in PME data st
r
ucture
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmurov
Link GPU force producer and
c
onsum
e
r tasks
commit
|
commitdiff
|
tree
2019-10-15
Alan G
r
ay
PM
E
/PP
G
PU Pimpl Class a
n
d
GPU->CPU C
o
mmunication
f
or
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Szilárd Páll
Link GPU coordinat
e
pro
d
ucer and consumer t
a
sks
commit
|
commitdiff
|
tree
2019-10-14
Artem Zhmu
r
ov
A
d
d
s
e
parate
c
o
ns
t
ructor to
S
tatePro
p
agatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szilár
d
Páll
Enable StatePropagatorGpuD
a
ta
f
or
fo
r
ce
t
ra
n
sfers
commit
|
commitdiff
|
tree
2019-10-13
Szilárd Páll
M
o
ve buffer ops / PM
E
F reduction
flags in
t
o
StepWor
k
load
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Centralize management of force
s
read
y
on GP
U
event
commit
|
commitdiff
|
tree
2019-10-12
Ar
t
em Zhmurov
Change copy mode to A
s
y
nc in
P
M
E
o
nly rank
commit
|
commitdiff
|
tree
2019-10-11
Artem Zhmuro
v
Wrong locality was u
s
ed w
h
e
n ignori
n
g the PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Pá
l
l
Migrate
code to using Simu
l
ationWorkload flag
s
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
Remove incorrec
t
GPU task dependency
commit
|
commitdiff
|
tree
2019-10-10
Szil
á
r
d
Páll
Pa
s
s
l
ist
o
f
EventS
y
nchroni
z
e
r
s
to GPU reduction
commit
|
commitdiff
|
tree
2019-10-10
Paul Bauer
Basic population of simulation wo
r
kload
commit
|
commitdiff
|
tree
2019-10-10
Artem Zh
m
urov
Ad
d
management
for velocities and f
o
rces copy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
A
d
d
m
anagement
f
or coordinates
c
opy eve
n
ts into StatePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
Art
e
m Zh
m
uro
v
Pass
t
he GPU streams
t
o StateProp
a
g
a
t
o
rDat
a
Gpu con
s
tructor
commit
|
commitdiff
|
tree
2019-10-07
Ma
r
k A
b
raha
m
Extend GPU traits clas
s
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Clean u
p
the c
o
mments sections in Update-Constrain
commit
|
commitdiff
|
tree
2019-10-07
Art
e
m Z
h
muro
v
Fix a bug in GPU h
a
lo exchange initializat
i
on
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use gmx::Range fo
r
iZones in p
a
i
r search
commit
|
commitdiff
|
tree
2019-10-02
C
arste
n
Kutzner
Update the www
l
ink to the
D
o
xygen doc
u
mentation i
n
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
Szilár
d
Páll
M
o
ve P
M
E GPU p
r
ogram building lat
e
r
commit
|
commitdiff
|
tree
2019-09-27
Artem
Z
hmurov
Slig
h
t im
p
r
o
vements to GPU updat
e
/c
o
nstraint
s
i
n
itialization
commit
|
commitdiff
|
tree
2019-09-27
Szilár
d
Pál
l
Switch GPU update of
f
by defaul
t
commit
|
commitdiff
|
tree
2019-09-27
Artem Zhmur
o
v
Int
r
oduce stream management to GPU Updat
e
-Constraints
commit
|
commitdiff
|
tree
2019-09-27
Berk
Hess
Extr
a
ct gmx:
:
Ran
g
e
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Stop
checking CUDA
v
ersion reported b
y
nvcc
commit
|
commitdiff
|
tree
2019-09-22
Art
e
m Zhmuro
v
Disable
G
PU update/c
o
nstra
i
nts
wh
e
n neither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Ma
r
k Abraham
Ma
k
e gm
x
_mult
i
sim_t a C++ object
commit
|
commitdiff
|
tree
2019-09-10
Mark Abraha
m
Avoid warning in
n
o
-mpi build
commit
|
commitdiff
|
tree
2019-09-10
Artem Zhmur
o
v
Making
DeviceBu
f
f
e
r availible
in no
n
-GPU bu
i
lds
commit
|
commitdiff
|
tree
2019-09-10
Paul
B
a
uer
Add indica
t
io
n
on ho
w
to enable ImageMagick
c
onvert
commit
|
commitdiff
|
tree
2019-09-09
S
z
i
l
árd Páll
A
s
sert the types of OpenCL
kernels a
r
gument
s
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Ma
k
e us
e
of rece
n
t
c
hang
e
s to prepareKer
n
el
A
rguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Ar
t
e
m Zh
m
urov
Misceleneous improve
m
e
nts to
t
he Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Apply clang-tidy-
8
readability-
u
p
percas
e
-
literal-suffix
commit
|
commitdiff
|
tree
2019-08-20
Mark
Abra
h
am
Use potential-shi
f
t as
d
efa
u
lt mo
d
ifier
commit
|
commitdiff
|
tree
2019-08-09
Be
r
k H
e
ss
Move bonded function table
i
nto b
o
nded
.
cpp
commit
|
commitdiff
|
tree
2019-08-08
M
ark Ab
r
aham
Initialize gmx
_
ekindata
_
t and t_
v
cm properly
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhm
u
r
ov
Fix for cmake li
s
ts
i
n md
l
ib
te
s
ts
commit
|
commitdiff
|
tree
2019-07-31
Ar
t
em Zhmurov
Chan
g
e
t
he file structure in constrain
t
s
t
ests
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Stor
e
wcycle poi
n
ter in nonbonded_
v
er
l
et
_
t
commit
|
commitdiff
|
tree
2019-07-26
Ar
t
em Zhmu
r
ov
Rem
o
ve
PIm
p
l
scaffolding from CUDA
v
ersion of
SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Kevin Boyd
Change
e
rror
message wh
e
n att
e
mpting to offlo
a
d
to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Ar
t
e
m
Zhmurov
Remo
v
e
PImpl sca
f
fo
l
d
i
ng from
CUDA version o
f
L
INCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmurov
Use reallocateDeviceBuffer(
.
.
.
)
i
n
CUD
A
version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Earl
y
exit fo
r
CUDA versions of SETT
L
E
an
d
LINC
S
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
M
emory management fixes in
CUDA version
o
f LINCS
commit
|
commitdiff
|
tree
2019-06-28
Szilárd
Páll
Separate
C
PU N
B
k
ernel and buff
e
r
clear
i
ng subco
u
nters
commit
|
commitdiff
|
tree
2019-06-28
Magn
u
s Lundborg
Fuse
d
GPU bonde
d
kernels
commit
|
commitdiff
|
tree
2019-06-18
Art
e
m
Zhmurov
C
o
mbine CUDA
L
eap-Frog
,
LI
N
CS a
n
d SETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
Arte
m
Zh
m
u
r
ov
Cla
r
i
f
y
w
hich of the m
a
i
n en
e
r
g
y terms
ar
e
printed
.
commit
|
commitdiff
|
tree
2019-05-13
Paul Bauer
Fix
m
ath formatti
n
g
in
r
eference m
a
nua
l
commit
|
commitdiff
|
tree
2019-05-12
Art
e
m Zhmurov
CU
D
A ve
r
s
ion of Leap-Frog integrator with basic tests
commit
|
commitdiff
|
tree
2019-05-06
Mark
A
braham
Improve how mdrun -noa
p
pend names output files
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhmurov
Us
e
te
s
t with para
m
e
t
er
s
for Energy
O
utput
commit
|
commitdiff
|
tree
2019-04-30
A
r
t
em Zhm
u
rov
CUDA ve
r
sio
n
of
S
ETTLE
a
lgorithm with basic tests
commit
|
commitdiff
|
tree
2019-04-29
Arte
m
Zhmurov
Fix for the CUDA version of
L
INCS
commit
|
commitdiff
|
tree
2019-04-28
Art
e
m Zhm
u
rov
CUDA v
e
rsion of LINCS cons
t
raints
.
commit
|
commitdiff
|
tree
2019-04-04
Ca
r
sten
K
utzner
E
ar
l
y
e
x
i
t f
r
om mdrun i
f
gro
u
p schem
e
is detected in
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
Remov
e
isP
r
essureCoupli
n
g
S
tep(
.
.
.
)
commit
|
commitdiff
|
tree
next