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Remove use of tuple in LINCS code for GPU implementation
2019-12-30
Mark
Abraham
Remo
v
e use of t
u
p
le i
n
L
I
NCS code for
G
P
U implementation
commit
|
commitdiff
|
tree
2019-12-20
P
aul Bau
e
r
Fix wrong hea
d
e
r i
n
release not
e
s
commit
|
commitdiff
|
tree
2019-12-18
Alan Gray
Fix
c
o
n
ditiona
l
on a
s
sertion for combin
i
ng GPU Up
d
a
t
e
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
Be
r
k Hess
Add note for COM removal with po
s
iti
o
n restraints
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhmurov
Cl
e
an-up
b
uff
e
r-ops C
U
DA kernel
s
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Comment the use
of wait
C
oordinatesCopiedToDevice
commit
|
commitdiff
|
tree
2019-12-17
Paul Bauer
Set correct d
e
p
e
nde
n
cy
f
or
d
o
c
build on gmxapi
commit
|
commitdiff
|
tree
2019-12-17
P
aul Bauer
Fix c
o
mp
i
ler w
a
rn
i
n
g ab
o
ut extra
;
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Pá
l
l
Add
wa
l
lcycle count
i
ng to StatePropag
a
torData
G
p
u
commit
|
commitdiff
|
tree
2019-12-11
Artem Z
h
murov
Ena
b
le most
o
f
t
he p
u
llin
g
flavo
r
s with GPU up
d
ate
commit
|
commitdiff
|
tree
2019-12-10
A
r
t
em
Zhmurov
Set GPU update
to false
in c
a
se of a r
e
run
commit
|
commitdiff
|
tree
2019-11-29
Artem Zh
m
u
r
ov
Ma
k
e Leap
-
Fr
o
g CUDA kernel selection safe
r
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmurov
Fix pressure couplin
g
wi
t
h
GP
U
u
pd
a
te
commit
|
commitdiff
|
tree
2019-11-27
A
r
te
m
Zhmurov
Comb
i
n
e
two
boo
l
eans in md loop
commit
|
commitdiff
|
tree
2019-11-27
Mark A
b
raham
Disable GPU PME-PP communication wi
t
h
mdrun -pmefft cpu
commit
|
commitdiff
|
tree
2019-11-26
Alan Gray
Bug fix for nonlocal D2H coordinate t
r
ansfer
s
y
nch
r
onization
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
N
e
w c
o
o
l qu
o
te
commit
|
commitdiff
|
tree
2019-11-20
Alan Gray
Mo
v
e pmePpCommGpu
r
eset ou
t
sid
e
do_md
commit
|
commitdiff
|
tree
2019-11-19
Ma
r
k
A
braham
Upd
a
ted release not
e
s for
C
O
D
ATA u
p
date
commit
|
commitdiff
|
tree
2019-11-19
Artem Zh
m
urov
Fix
i
cc-19
wa
r
ning in nightl
y
matr
i
x
commit
|
commitdiff
|
tree
2019-11-13
Paul Bauer
Ad
d
build to run cla
n
g-f
o
rmat update on Jenkins
commit
|
commitdiff
|
tree
2019-11-03
Szilárd Páll
I
mprove SimulationWorklo
a
d
d
o
x
ygen
commit
|
commitdiff
|
tree
2019-10-30
Berk Hess
Fix walls wi
t
h GPU update
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Disable pressure coupling with GPU
upd
a
te
commit
|
commitdiff
|
tree
2019-10-28
S
zilárd Páll
Exten
d
S
i
mulationWorkload with CP
U
f
lags
commit
|
commitdiff
|
tree
2019-10-21
Szilárd Páll
Override GMX_GPU_DD_COMMS if nonbond
e
ds ar
e
off
commit
|
commitdiff
|
tree
2019-10-18
Artem
Z
hmurov
Remove excessive H2D
a
nd D2
H
coordin
a
tes copies w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
Szilá
r
d Páll
Disable GMX_GPU_PM
E
_PP_COM
M
S if
P
ME is not offload
e
d
commit
|
commitdiff
|
tree
2019-10-16
Szilárd
P
áll
F
i
x i
n
i
t
i
a
liza
t
io
n
o
f field in PME dat
a
structure
commit
|
commitdiff
|
tree
2019-10-16
Artem Zh
m
urov
Link
GPU force produce
r
and consume
r
tasks
commit
|
commitdiff
|
tree
2019-10-15
A
l
a
n
Gray
PME/PP
G
PU
P
impl Class and GP
U
->CP
U
Co
m
muni
c
ation for
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Szilá
r
d Páll
L
ink GPU coo
r
din
a
te p
r
oducer an
d
consu
m
e
r ta
s
ks
commit
|
commitdiff
|
tree
2019-10-14
Arte
m
Zhmurov
Add s
e
parate cons
t
r
u
cto
r
to St
a
te
P
ropagat
o
rDa
t
aGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szil
á
rd Páll
E
n
able St
a
tePropa
g
atorGpuData for
f
o
rce transfer
s
commit
|
commitdiff
|
tree
2019-10-13
Sz
i
lárd
P
áll
Move buffer
o
ps / PME F reduction
flags into Ste
p
Workload
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
C
e
nt
r
alize manageme
n
t of forces ready on GPU even
t
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Chan
g
e copy mode to Asy
n
c in PME only
r
ank
commit
|
commitdiff
|
tree
2019-10-11
Artem Zh
m
urov
Wrong local
i
ty
w
as
used when ignoring the PME
for
c
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Sz
i
l
árd Páll
Migrate code to using Si
m
ulationWorklo
a
d
f
lags
commit
|
commitdiff
|
tree
2019-10-10
S
zil
á
rd Páll
Remove incorrect GPU tas
k
dependency
commit
|
commitdiff
|
tree
2019-10-10
Szilárd P
á
ll
Pass
lis
t
of EventSync
h
r
onizers
t
o GP
U
reduction
commit
|
commitdiff
|
tree
2019-10-10
Paul Ba
u
er
Basic popu
l
ation of simulation worklo
a
d
commit
|
commitdiff
|
tree
2019-10-10
Artem Zhmu
r
ov
Ad
d
m
a
nag
e
ment for velociti
e
s and fo
r
ces
c
opy events
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
Add mana
g
eme
n
t for co
o
rdinat
e
s copy ev
e
n
t
s
i
n
to StatePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
A
r
tem Zhmurov
P
ass
the GPU streams to
S
tatePr
o
pagatorDataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
Mark
A
b
r
a
h
a
m
E
xtend GPU traits
class
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Clean u
p
the com
m
ents sections in
Up
d
ate-Constr
a
in
commit
|
commitdiff
|
tree
2019-10-07
Arte
m
Zhmurov
Fi
x
a b
u
g
in
GPU
halo exchange initialization
commit
|
commitdiff
|
tree
2019-10-03
Berk H
e
ss
Use gmx::R
a
nge for
i
Z
ones i
n
p
a
ir search
commit
|
commitdiff
|
tree
2019-10-02
Carsten Ku
t
zner
Up
d
a
te the w
w
w link to the Doxygen documentation in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
Szilá
r
d Páll
Move PME GPU prog
r
am
b
uilding later
commit
|
commitdiff
|
tree
2019-09-27
Artem Z
h
mur
o
v
S
light
i
mp
r
ove
m
e
nts to GPU update/constraints initialization
commit
|
commitdiff
|
tree
2019-09-27
Szilárd P
á
ll
Switch G
P
U update off by de
f
aul
t
commit
|
commitdiff
|
tree
2019-09-27
A
rtem Zh
m
urov
Introduc
e
s
t
r
e
am man
a
gemen
t
to GPU Updat
e
-C
o
ns
t
raints
commit
|
commitdiff
|
tree
2019-09-27
B
erk Hess
Extract gm
x
::Ran
g
e
commit
|
commitdiff
|
tree
2019-09-27
Mark Abr
a
ham
S
top checkin
g
CUDA
vers
i
o
n
rep
o
rted
b
y nvcc
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmu
r
ov
Disab
l
e GPU update/
c
o
n
straints when n
e
ither PME nor
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Mark Abraham
M
a
ke gmx_mu
l
ti
s
im_t a C++ objec
t
commit
|
commitdiff
|
tree
2019-09-10
Mark Abraham
Avo
i
d
warning in no-mpi build
commit
|
commitdiff
|
tree
2019-09-10
Artem Z
h
murov
Making DeviceBuffer ava
i
li
b
le in
non-GPU
builds
commit
|
commitdiff
|
tree
2019-09-10
Paul Bauer
A
d
d indication
o
n how to enable Ima
g
e
Magi
c
k c
o
nvert
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
A
ssert the
types o
f
OpenCL
kernels arguments
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
Make use of recent changes to
p
repare
K
ern
e
lAr
g
uments
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmur
o
v
Misceleneous improvement
s
to the Leap Frog tests
commit
|
commitdiff
|
tree
2019-08-20
Mark Abra
h
am
Apply clang-tidy-8 readability-uppercase-
l
iteral-suffix
commit
|
commitdiff
|
tree
2019-08-20
Mark Abr
a
ha
m
Use potential-shift as default
m
o
difie
r
commit
|
commitdiff
|
tree
2019-08-09
Berk H
e
ss
Mo
v
e bonded functio
n
ta
b
l
e into bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-08
Mark
Abr
a
ham
Initiali
z
e gmx_ekindata_t
and t_vc
m
p
r
ope
r
ly
commit
|
commitdiff
|
tree
2019-08-06
Artem Zhmur
o
v
Fix f
o
r cmake lists in mdlib tests
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhm
u
ro
v
Ch
a
nge the file s
t
ructure i
n
c
onstraints test
s
commit
|
commitdiff
|
tree
2019-07-31
S
zilárd Páll
S
t
ore wcyc
l
e
p
o
inter
i
n no
n
bonded_ver
l
et_t
commit
|
commitdiff
|
tree
2019-07-26
Artem
Zhmurov
Remove
P
Imp
l
sc
a
ffolding from CU
D
A
v
er
s
ion of
SETTLE
commit
|
commitdiff
|
tree
2019-07-05
K
e
vin Boyd
Change error messag
e
wh
e
n attempting
to offload to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmu
r
o
v
Remove PImpl
scaffoldin
g
from
C
UDA
v
ersi
o
n
of LINCS
commit
|
commitdiff
|
tree
2019-07-04
A
r
tem Zh
m
urov
Use re
a
llocateDeviceBuffer
(
.
.
.
) in
CUDA version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Ar
t
em
Zhmu
r
ov
Early exit for
CUDA versions of
SE
T
TLE and LINCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmuro
v
Memory m
a
nagement
f
ix
e
s in CU
D
A
version
of LINCS
commit
|
commitdiff
|
tree
2019-06-28
Szi
l
árd Páll
Sep
a
rate C
P
U NB k
e
rnel
an
d
buffer cle
a
ring
subcou
n
ters
commit
|
commitdiff
|
tree
2019-06-28
Magnus Lund
b
org
F
u
sed GPU bonded kernels
commit
|
commitdiff
|
tree
2019-06-18
A
r
tem
Z
hmu
r
ov
Combine CUDA Lea
p
-F
r
o
g
, LI
N
CS a
n
d
S
ETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
Artem
Zhm
u
r
o
v
Clarify
w
h
ich
o
f the main
en
e
rgy te
r
ms are pr
i
nted
.
commit
|
commitdiff
|
tree
2019-05-13
Paul Baue
r
Fix math
forma
t
ting in
r
eference manu
a
l
commit
|
commitdiff
|
tree
2019-05-12
Art
e
m
Zhmuro
v
CUDA version of Leap-Frog integra
t
or
w
it
h
b
a
s
ic t
e
sts
commit
|
commitdiff
|
tree
2019-05-06
Mark Abraham
I
mprove how mdrun -noappend names ou
t
pu
t
files
commit
|
commitdiff
|
tree
2019-05-02
A
r
t
em Zhmurov
Use test with paramete
r
s for Ene
r
gyOutput
commit
|
commitdiff
|
tree
2019-04-30
Artem
Z
hmurov
CUDA
version
of
SET
T
LE algorithm with basic te
s
ts
commit
|
commitdiff
|
tree
2019-04-29
Ar
t
em Zhmurov
Fix for the CUDA versi
o
n of L
I
NCS
commit
|
commitdiff
|
tree
2019-04-28
Artem Zhmurov
CUDA
v
e
rsion
of LINCS
c
on
s
traints
.
commit
|
commitdiff
|
tree
2019-04-04
Carsten Kutzner
E
a
rly exit
f
rom mdrun if group sc
h
eme is de
t
ected
i
n
.
.
.
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
Remov
e
isPressureCouplingSte
p
(
.
.
.
)
commit
|
commitdiff
|
tree
2019-04-04
Artem Zhmurov
Re
m
o
v
e isTemperature
C
oupli
n
gStep
(
.
.
.
)
commit
|
commitdiff
|
tree
2019-03-13
A
rtem Zhmurov
Basic routines to handle peri
o
d
ic boundar
y
.
commit
|
commitdiff
|
tree
2019-02-19
A
rt
e
m
Zhmurov
PBC se
t
up for
GP
U
is moved into pbcutils
.
commit
|
commitdiff
|
tree
2019-02-13
Artem Zhmurov
Ignore V
i
sual Studio Code metadata
.
commit
|
commitdiff
|
tree