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Make PBC type enumeration into PbcType enum class
2020-01-09
A
rte
m
Z
hmuro
v
Make
P
BC type enumeration
into PbcTy
p
e enum class
commit
|
commitdiff
|
tree
2020-01-09
Alan Gray
F
i
x me
m
ory
a
ddress bug in GPU PM
E
coordi
n
ate address
.
.
.
commit
|
commitdiff
|
tree
2019-12-30
Mark
A
braham
Remove use of tuple in LINCS
c
ode for GPU
i
mple
m
entation
commit
|
commitdiff
|
tree
2019-12-20
Paul Bauer
Fix wrong
h
e
a
der in rel
e
ase notes
commit
|
commitdiff
|
tree
2019-12-18
Alan G
r
a
y
Fix cond
i
tional on assertion for
c
omb
i
ning GP
U
U
p
d
ate
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
B
e
rk Hess
A
d
d note f
o
r COM removal with position res
t
raints
commit
|
commitdiff
|
tree
2019-12-17
A
r
tem
Z
hmurov
Clean-u
p
buffer-ops CUDA kerne
l
s
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Pál
l
Comment
the use of wait
C
oordina
t
esCopiedTo
D
evice
commit
|
commitdiff
|
tree
2019-12-17
Paul
Bauer
Set co
r
rect depe
n
dency for doc bu
i
ld on
gmxap
i
commit
|
commitdiff
|
tree
2019-12-17
Paul Bauer
Fix compil
e
r warn
i
ng about extra
;
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Add wallcy
c
le counting t
o
StatePropagator
D
ataGp
u
commit
|
commitdiff
|
tree
2019-12-12
Paul Bauer
Merge branch 'ori
g
in/rele
a
se-2020' into master
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem
Z
hmu
r
ov
Enable most of the
pulling flavo
r
s
w
ith GPU
update
commit
|
commitdiff
|
tree
2019-12-10
A
rtem
Z
hmurov
Avoi
d
u
nnecessary reinterpret_cast of coordi
n
ates buffer
commit
|
commitdiff
|
tree
2019-12-10
Artem Zh
m
urov
Set GPU u
p
date to fals
e
in case of a
r
erun
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Make Leap-Frog C
U
DA kernel s
e
lect
i
o
n
saf
e
r
commit
|
commitdiff
|
tree
2019-11-28
Art
e
m
Z
hmurov
Fix pressure
c
oupling wi
t
h GPU
update
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmurov
C
o
mbi
n
e two
b
ooleans in md lo
o
p
commit
|
commitdiff
|
tree
2019-11-27
Mark Abraham
Di
s
able GPU PME-PP commun
i
c
ation with mdrun -p
m
e
f
f
t cpu
commit
|
commitdiff
|
tree
2019-11-26
Ala
n
G
r
ay
Bug fix for nonl
o
cal D2H coordinate
t
ransfer syn
c
hronization
commit
|
commitdiff
|
tree
2019-11-23
Artem Zh
m
u
r
ov
New cool quote
commit
|
commitdiff
|
tree
2019-11-20
Alan Gray
Move pmePpCommGpu rese
t
outsid
e
do_m
d
commit
|
commitdiff
|
tree
2019-11-19
Mark Abra
h
am
Updated rele
a
s
e
note
s
for CODATA update
commit
|
commitdiff
|
tree
2019-11-19
Artem
Zhmurov
Fix i
c
c-19 warn
i
ng in ni
g
htly m
a
tri
x
commit
|
commitdiff
|
tree
2019-11-15
Artem Zhmurov
Removing code d
u
plication
s
in StatePropagatorDataGpu
commit
|
commitdiff
|
tree
2019-11-13
Paul Bauer
A
d
d build to run cl
a
ng
-
format update on Jenkins
commit
|
commitdiff
|
tree
2019-11-03
S
z
il
á
rd Páll
I
m
prove Simula
t
io
n
Workload d
o
x
y
gen
commit
|
commitdiff
|
tree
2019-10-30
Berk
Hess
F
ix walls with GPU upda
t
e
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
Disabl
e
pres
s
ure coupling with GPU upd
a
te
commit
|
commitdiff
|
tree
2019-10-28
Szilárd Páll
Extend Simu
l
a
t
ionWorklo
a
d with CPU flags
commit
|
commitdiff
|
tree
2019-10-21
Szilá
r
d Páll
Over
r
ide GMX
_
GPU_
D
D
_COMM
S
if
n
onbonded
s
are
o
ff
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmur
o
v
Rem
o
ve excess
i
ve
H
2D a
n
d D2H
c
o
o
rdinates
copies
w
hen
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
Szilá
r
d Páll
D
isable GMX_GPU_PME_PP_COMMS
if P
M
E i
s
not offloaded
commit
|
commitdiff
|
tree
2019-10-16
Szilá
r
d P
á
ll
Fix
i
nitialization of field in PME data structure
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmurov
Link GPU for
c
e producer and co
n
sumer tasks
commit
|
commitdiff
|
tree
2019-10-15
A
l
an Gra
y
P
M
E/PP GPU Pimpl C
l
ass and
GPU->CPU Communic
a
tion for
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Szi
l
árd
P
á
ll
Link GPU coo
r
din
a
te
producer and consumer tasks
commit
|
commitdiff
|
tree
2019-10-14
Arte
m
Zhmuro
v
Add separ
a
t
e cons
t
ru
c
t
o
r
to
S
tate
P
r
o
pa
g
atorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szil
á
rd
P
áll
Enable St
a
t
e
Pr
o
p
agato
r
GpuD
a
ta for force transfers
commit
|
commitdiff
|
tree
2019-10-13
Szilárd Pál
l
Move buffe
r
o
p
s / PME F r
e
duction flags into
Step
W
orkload
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmuro
v
C
entralize management of forces
r
eady
on GPU event
commit
|
commitdiff
|
tree
2019-10-12
A
r
te
m
Zhmurov
C
hange copy m
o
de to Async in PME
only ran
k
commit
|
commitdiff
|
tree
2019-10-11
A
rtem Z
h
murov
Wrong locality was u
s
ed when
ignoring the PME
force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Pál
l
Migrate code to using SimulationWo
r
kload flags
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
Remov
e
incorrec
t
GPU task depende
n
cy
commit
|
commitdiff
|
tree
2019-10-10
Sz
i
lárd
Pál
l
Pass list
o
f Even
t
Synchr
o
n
i
ze
r
s to GPU red
u
ction
commit
|
commitdiff
|
tree
2019-10-10
Paul Bauer
Ba
s
ic populat
i
on of s
i
mulation workload
commit
|
commitdiff
|
tree
2019-10-10
Arte
m
Zhmu
r
ov
Add m
a
nagement f
o
r
velociti
e
s and fo
r
c
es
c
o
py event
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szil
á
rd Páll
A
dd m
a
nagement
f
or c
o
ordinates copy even
t
s into StatePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhm
u
rov
Pa
s
s the GPU stre
a
ms to Stat
e
Propagator
D
ataGpu c
o
nstructor
commit
|
commitdiff
|
tree
2019-10-07
Mark Abr
a
ham
Extend GPU
t
r
a
its cla
s
s
commit
|
commitdiff
|
tree
2019-10-07
A
rte
m
Z
hmurov
Clea
n
up
t
he
commen
t
s sections in U
p
date-Const
r
a
i
n
commit
|
commitdiff
|
tree
2019-10-07
Artem Zh
m
urov
Fix a bu
g
in GPU halo e
x
c
h
ange in
i
tialization
commit
|
commitdiff
|
tree
2019-10-03
B
e
r
k
Hess
U
s
e gmx::Range
f
or iZones i
n
pai
r
search
commit
|
commitdiff
|
tree
2019-10-02
Carste
n
K
utzner
Upda
t
e the www l
i
nk
t
o the Doxyge
n
documentation in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
S
zilárd Páll
M
o
ve PME
G
PU program building la
t
er
commit
|
commitdiff
|
tree
2019-09-27
Arte
m
Zh
m
urov
S
l
ight
i
mprovem
e
nts to GPU u
p
date/
c
onstraints initiali
z
ation
commit
|
commitdiff
|
tree
2019-09-27
Szilárd
P
áll
Switch GPU upd
a
te
off by
d
efa
u
lt
commit
|
commitdiff
|
tree
2019-09-27
Arte
m
Zhmu
r
o
v
Introduce str
e
am
mana
g
e
m
ent to
G
P
U Update-
C
onstraints
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extract gmx
:
:Range
commit
|
commitdiff
|
tree
2019-09-27
Mark Abraham
Stop checking CUDA
v
ersion reported by
nvcc
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhm
u
rov
Disable GPU update/constraint
s
when
n
either PM
E
n
o
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
a
r
k
Abraham
Make gmx_mul
t
i
s
im_t a C
+
+ object
commit
|
commitdiff
|
tree
2019-09-10
M
a
rk Abrah
a
m
Avoi
d
warni
n
g in no-m
p
i build
commit
|
commitdiff
|
tree
2019-09-10
Ar
t
e
m
Zhmurov
Making
D
ev
i
ceBuffer availibl
e
in non-GPU
b
uilds
commit
|
commitdiff
|
tree
2019-09-10
Paul
B
auer
Add indicat
i
on on how to enable ImageMagick convert
commit
|
commitdiff
|
tree
2019-09-09
Szilá
r
d Pál
l
Assert the types of
O
penC
L
k
ernels ar
g
uments
commit
|
commitdiff
|
tree
2019-08-25
Art
e
m
Z
h
m
urov
Make
u
se of
r
e
c
ent
c
ha
n
ges t
o
prepareKer
n
elArguments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Ar
t
em
Zhm
u
rov
Misceleneous improvem
e
nts to the Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-20
Ma
r
k
A
braham
Apply
c
lang-tidy-8
rea
d
ability-uppercase-literal-suffix
commit
|
commitdiff
|
tree
2019-08-20
Ma
r
k Abraham
Use potenti
a
l-s
h
if
t
as
d
efault modifier
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
Move b
o
n
d
ed function table into bo
n
ded
.
cpp
commit
|
commitdiff
|
tree
2019-08-08
Mark A
b
raha
m
Init
i
ali
z
e gmx_ekin
d
ata_
t
and t_vcm prope
r
ly
commit
|
commitdiff
|
tree
2019-08-06
A
rtem Zhmurov
F
ix
f
or cmake list
s
in
mdlib tests
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhm
u
rov
Change the file structure in con
s
t
r
a
ints tests
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
Páll
Store wcycle pointer in nonbonded_ver
l
et_t
commit
|
commitdiff
|
tree
2019-07-26
Artem Zhmurov
Remove P
I
m
p
l
s
c
affolding fro
m
CUDA version
of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Kevin Boyd
Cha
n
ge error message when attempting to offloa
d
to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Artem Z
h
muro
v
Remove
PImpl
scaffolding from CUDA version
of LINCS
commit
|
commitdiff
|
tree
2019-07-04
Artem
Z
h
murov
Use reallocateD
e
viceBuffer(
.
.
.
) in CU
D
A
version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Early
exit
f
or CUDA v
e
rsions
of
S
ETTLE
a
n
d
LIN
C
S
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em Zh
m
urov
Memory m
a
nagemen
t
f
i
xes in CUDA version of LINCS
commit
|
commitdiff
|
tree
2019-06-28
Szilárd Páll
Se
p
arate CPU NB kernel and buffer clear
i
ng subc
o
unters
commit
|
commitdiff
|
tree
2019-06-28
Magnus
Lund
b
o
r
g
Fused GPU bonded kerne
l
s
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhmu
r
ov
Combine CUDA
L
eap-Frog, LINCS and
S
ETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
Ar
t
em Zhm
u
rov
C
l
arif
y
wh
i
ch of the mai
n
en
e
r
g
y terms are
printed
.
commit
|
commitdiff
|
tree
2019-05-13
Paul Bauer
Fix math
format
t
ing in re
f
erence
ma
n
ual
commit
|
commitdiff
|
tree
2019-05-12
Artem Zhmurov
CUDA version of Leap-Frog integrator wi
t
h basic tests
commit
|
commitdiff
|
tree
2019-05-06
Mark Abraham
Improve how mdrun -
n
oappen
d
names output files
commit
|
commitdiff
|
tree
2019-05-02
Arte
m
Zhmur
o
v
Us
e
test with p
a
rameters fo
r
Ener
g
yOutp
u
t
commit
|
commitdiff
|
tree
2019-04-30
Artem Zhmurov
CUDA version of SETTLE al
g
orithm with basic
tests
commit
|
commitdiff
|
tree
2019-04-29
Arte
m
Zhmurov
Fi
x
for the C
U
DA vers
i
on of
LINCS
commit
|
commitdiff
|
tree
2019-04-28
Artem Zh
m
urov
CUDA version of LINCS con
s
t
r
a
i
nts
.
commit
|
commitdiff
|
tree
2019-04-04
C
arsten Ku
t
zne
r
Early exit from mdrun if gro
u
p scheme
i
s de
t
ect
e
d in
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
Remov
e
isPressureCou
p
lingStep
(
.
.
.
)
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
R
e
move isTemperat
u
reCouplingSt
e
p(
.
.
.
)
commit
|
commitdiff
|
tree
2019-03-13
A
r
tem Zh
m
u
rov
B
asic routi
n
es to handle perio
d
ic boundary
.
commit
|
commitdiff
|
tree
2019-02-19
Artem Zhmu
r
ov
PBC setup f
o
r
G
P
U is moved into pbcu
t
i
l
s
.
commit
|
commitdiff
|
tree
2019-02-13
Ar
t
e
m
Zhmurov
Ignore V
i
sual S
t
u
d
io C
o
de me
t
adat
a
.
commit
|
commitdiff
|
tree