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Small fixes to the DeviceStream
2020-03-20
A
rtem Zh
m
urov
S
m
al
l
f
i
xes to the De
v
ic
e
S
tre
a
m
commit
|
commitdiff
|
tree
2020-03-19
Artem Zhmurov
Store
DeviceInfo
r
mat
i
on inside the
D
eviceCon
t
ext class
commit
|
commitdiff
|
tree
2020-03-19
A
rte
m
Z
hmurov
Pass DeviceCon
t
e
xt ins
t
ead
o
f GP
U
runti
m
e data
when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Art
e
m Zhm
u
r
ov
Make some doxygen
e
rrors more clear
commit
|
commitdiff
|
tree
2020-03-13
Artem
Zhmurov
Combi
n
e
i
nitialization routines for GPUs
assi
g
ned to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Remove st
r
eam from GPU k
e
rnel launch config
commit
|
commitdiff
|
tree
2020-03-13
A
rtem Zhmurov
Use Devic
e
Stream in
i
t(
.
.
.
) f
u
nction to creat
e
streams
commit
|
commitdiff
|
tree
2020-03-13
A
r
tem
Z
h
m
urov
M
a
k
e
DeviceStream into a
class
commit
|
commitdiff
|
tree
2020-03-11
A
rtem
Z
h
m
urov
Fix the
p
ost-
s
ubmit
f
ailures
commit
|
commitdiff
|
tree
2020-03-11
Arte
m
Zhmurov
Take over man
a
gem
e
nt of OpenCL context fro
m
PME and
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Artem Zhmurov
Use init(
.
.
) function to buil
d
D
e
viceContext
commit
|
commitdiff
|
tree
2020-03-09
Artem Zhmurov
Make
D
eviceContext into
a proper clas
s
commit
|
commitdiff
|
tree
2020-03-05
Artem Zhmurov
F
inalize renaming of bEnerVir to computeEnergyAn
d
Viria
l
commit
|
commitdiff
|
tree
2020-03-04
Artem Zhmurov
Do not coun
t
PME o
n
l
y rank when initiali
z
ing NBNXM
commit
|
commitdiff
|
tree
2020-03-03
Artem
Z
hm
u
rov
Move
the PmePPC
o
m
m
Gpu i
n
itialization fr
o
m
forcerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zhm
u
rov
Update th
e
message on whether updat
e
a
n
d
c
onstra
i
nts
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Zhmurov
Fix the RVec to
floa
t
3 co
n
vers
i
on test
commit
|
commitdiff
|
tree
2020-02-22
Art
e
m Zhm
u
rov
Add missing heade
r
and disable f
a
ilin
g
tes
t
commit
|
commitdiff
|
tree
2020-02-21
A
r
tem Zhmurov
Refactor and enable RVec to float conversion test
commit
|
commitdiff
|
tree
2020-02-20
Arte
m
Z
h
murov
D
o
n
ot c
a
ll
PME GPU builder
in C
P
U co
d
e paths
commit
|
commitdiff
|
tree
2020-02-20
A
rtem Zh
m
urov
Use GROMACS
wrappers for EXPEC
T
_TH
R
OW/NO_THROW in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Art
e
m Zhmurov
U
se CUDA float3 vec
t
or type instea
d
of fvec
in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Ar
t
em Zh
m
u
r
ov
Clean up trivial function and
d
uplicati
n
g macros
e
s
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
A
rtem Zhmur
o
v
Fix the ni
g
h
tly failure
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmur
o
v
T
em
p
orary di
s
a
ble RVec->float3 conversion test to
f
ix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
Ar
t
em Zhmurov
Use RVec in
s
t
e
a
d of float for x,
v and f dev
i
ce
buffer
s
commit
|
commitdiff
|
tree
2020-02-06
Art
e
m Zhmurov
Move DeviceInfo into
G
PU
tra
i
ts
commit
|
commitdiff
|
tree
2020-02-05
Art
e
m
Z
hmurov
Make OpenCL DeviceVendor in
t
o enum cl
a
ss and
move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
A
r
tem Zh
m
u
r
ov
Move
non-bonded initi
a
lization
o
ut of the forcerec
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhmurov
Fix
t
ypo in
a
nd remov
e
a couple
of duplicates
f
ro
m
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Artem
Zhmurov
Enabl
e
GPU up
d
a
t
e for supported cas
e
s of F
E
P
commit
|
commitdiff
|
tree
2020-02-01
A
r
te
m
Z
hmurov
Couple
cool quo
t
es
commit
|
commitdiff
|
tree
2020-02-01
Arte
m
Zhmurov
Merge "
M
erge branch origin/release-2020 into master"
commit
|
commitdiff
|
tree
2020-01-30
A
rtem Zhmurov
C
l
e
an
i
ng booleans in NBNXM
i
n
O
p
enCL build
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmur
o
v
Reorganize GPU
s
t
uff initi
a
lization in
P
ME-only ranks
commit
|
commitdiff
|
tree
2020-01-29
Arte
m
Zhmurov
Split and mov
e
the checkD
e
v
i
ceBuffer
(
.
.
.
) funct
i
on
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
A
r
tem Zhmurov
Remove
the
re
s
t
o
f the d
e
vice coordinates m
a
nagement
.
.
.
commit
|
commitdiff
|
tree
2020-01-29
Artem Zhmurov
R
e
n
a
m
e Up
d
a
t
e
Constra
i
ntsC
u
da to Upd
a
te
C
onstraintsGpu
commit
|
commitdiff
|
tree
2020-01-23
Arte
m
Zhm
u
r
ov
F
i
x a co
u
ple of c
o
m
ma
s
in cool quo
t
es
commit
|
commitdiff
|
tree
2020-01-20
Artem Z
h
mur
o
v
Renam
e
Settl
e
Cu
d
a to
SettleGp
u
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
Rename LincsCu
d
a into LincsGpu
commit
|
commitdiff
|
tree
2020-01-20
Artem Zhmurov
R
ename LeapFrogCuda to Leap
F
rog
G
pu
commit
|
commitdiff
|
tree
2020-01-13
Artem Zh
m
urov
R
e
port if upd
a
te is running o
n
the GPU or on the CPU
commit
|
commitdiff
|
tree
2020-01-09
Artem Zhmurov
Change
signature
of the
setPbc
(
.
.
.
) method
i
n
update
.
.
.
commit
|
commitdiff
|
tree
2020-01-09
Art
e
m Zhmuro
v
Make
PBC
t
yp
e
e
n
umeration into PbcType enu
m
class
commit
|
commitdiff
|
tree
2019-12-31
Ar
t
em
Z
hmuro
v
Inform user why forcing GPU upda
t
e
is not
p
ossibl
e
commit
|
commitdiff
|
tree
2019-12-31
A
r
tem
Z
h
murov
Ad
d
descri
p
ti
o
n of GMX_F
O
RCE_UPDA
T
E_
D
E
F
AU
L
T_GPU de
v
.
.
.
commit
|
commitdiff
|
tree
2019-12-31
Artem Zh
m
urov
Fix
g
puupdate matr
i
x
commit
|
commitdiff
|
tree
2019-12-28
Artem Zh
m
uro
v
Cha
n
ge
t
he behavior of the GPU
u
pdate UI
commit
|
commitdiff
|
tree
2019-12-27
Art
e
m
Zhm
u
rov
Add a note to the
l
og f
i
le when
-update gpu was se
t
.
.
.
commit
|
commitdiff
|
tree
2019-12-27
Ar
t
e
m Zhmurov
Clean bad auto-format i
n
decid
e
gpu
u
sage doxygen
co
m
me
n
ts
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhm
u
rov
Clean-up bu
f
fer-ops CUDA
kerne
l
s
commit
|
commitdiff
|
tree
2019-12-13
Artem Zhmurov
Clean
u
p ou
t
dated comments
in md
.
c
pp
commit
|
commitdiff
|
tree
2019-12-12
Ar
t
em Zhmuro
v
Allow using GP
U
upda
t
e wit
h
D
D an
d
u
p
date g
r
oups
commit
|
commitdiff
|
tree
2019-12-11
Art
e
m
Zhmurov
Enabl
e
m
o
st of the
p
ulli
n
g flavor
s
with GPU
u
p
date
commit
|
commitdiff
|
tree
2019-12-11
Ar
t
em Zhmurov
Clarify what
s
etting zero to
s
ome
o
utput mdp options
.
.
.
commit
|
commitdiff
|
tree
2019-12-10
A
r
tem Zhmurov
Avoid unnec
e
ssary reint
e
rpret_c
a
st of coordinat
e
s buff
e
r
commit
|
commitdiff
|
tree
2019-12-10
A
rtem Zhmurov
Set G
P
U upd
a
te t
o
fa
l
s
e
in
case
of
a
rerun
commit
|
commitdiff
|
tree
2019-12-06
Art
e
m Zhmu
r
o
v
P
ass
a
r
ray ref
i
nstead of cas
t
ing to basic array in
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmur
o
v
Print Ope
n
CL e
r
r
o
r inf
o
in case of fai
l
ed as
s
er
t
ion
.
.
.
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmuro
v
Make Leap-Frog CUDA kerne
l
selection safer
commit
|
commitdiff
|
tree
2019-11-29
Artem Zhmurov
Rename so
m
e variables in GPU
U
pdate
commit
|
commitdiff
|
tree
2019-11-28
Ar
t
em Zhm
u
r
o
v
C
l
ear devic
e
f
orce buffer if i
t
w
a
s realloc
a
ted
commit
|
commitdiff
|
tree
2019-11-28
Artem Zhmu
r
ov
Fix p
r
essure coupling with
G
PU update
commit
|
commitdiff
|
tree
2019-11-27
A
r
tem Zhmurov
C
ombine two booleans in md
l
oop
commit
|
commitdiff
|
tree
2019-11-27
Artem Zhmuro
v
Add meth
o
d for coordinat
e
s s
c
al
i
ng into GPU
update
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Artem Zhmurov
Remov
e
the PBC manage
m
ent fr
o
m LI
N
CS, SE
T
TLE and
Leap
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Ar
t
e
m Zhmuro
v
Use sa
m
e matrix for Parrinello-Rahman and Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-11-25
Artem Z
h
m
urov
F
ix
i
n
dex m
a
pping
i
ss
u
e with LINCS on GPU
commit
|
commitdiff
|
tree
2019-11-23
A
r
t
e
m
Zhmur
o
v
New cool q
u
ote
commit
|
commitdiff
|
tree
2019-11-20
A
r
t
e
m Zhm
u
rov
Ad
d
D2H c
o
pies for the
c
h
eckpointin
g
commit
|
commitdiff
|
tree
2019-11-20
Artem Zhmurov
Move the copy o
f
the velocities f
o
r
the output clos
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-11-19
Artem Zhmurov
Fix icc-19
warning in nightly
m
a
t
rix
commit
|
commitdiff
|
tree
2019-11-15
Artem Zhmuro
v
R
emovin
g
co
d
e duplications in StatePropagato
r
DataGp
u
commit
|
commitdiff
|
tree
2019-11-13
Art
e
m Zhmurov
U
s
e same matrix for Parrin
e
l
lo-
R
ahman
a
nd Berendsen
.
.
.
commit
|
commitdiff
|
tree
2019-10-31
Artem Zhmur
o
v
Remove e
x
ce
s
sive
H2
D
and
D2H c
o
pies of f
o
rces when
.
.
.
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Di
s
able GPU upd
a
te
w
hen coordinates swapping
is
e
n
a
bled
commit
|
commitdiff
|
tree
2019-10-29
Artem Zhmurov
Switch the GPU buffer ops on whe
n
upda
t
e
is on
G
P
U
commit
|
commitdiff
|
tree
2019-10-28
Artem
Zhmuro
v
F
ix m
i
ssing
coordinate
D
2H copy with
GPU
u
pdate and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
Artem Zhmurov
Add h
a
veCpuLocalForces
flag to DomainLife
t
imeWor
k
l
oad
commit
|
commitdiff
|
tree
2019-10-28
Ar
t
e
m Zhmur
o
v
Allow u
s
ing update flag
commit
|
commitdiff
|
tree
2019-10-23
Artem Z
h
murov
Slig
h
t i
m
pr
o
vements to decideWheth
e
r
To
U
se
G
pu
F
orUpdat
e
.
.
.
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
Remove unnece
s
sary CUDA stream
sync
h
ron
i
za
t
ion calls
commit
|
commitdiff
|
tree
2019-10-22
Artem Zhmurov
R
ename havePo
s
itionRestra
i
nts(
.
.
.
) to
haveR
e
straints
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Ar
t
em
Z
hmurov
Update the copyright me
s
s
a
g
e
1. Add
Artem Zhmurov
to the list of contributors.
commit
|
commitdiff
|
tree
2019-10-21
Artem Zhmu
r
ov
A
d
d
e
n
vi
r
on
m
e
nt varia
b
le
t
h
at cha
n
ge
s
the meaning of
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
rtem
Z
hmurov
Remove ex
c
essiv
e
H2D and D2H co
o
rdinates copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-18
A
r
tem Zhmuro
v
Remove
excessiv
e
H
2
D and D2H copie
s
of velo
c
ities w
h
en
.
.
.
commit
|
commitdiff
|
tree
2019-10-16
Artem Zhmu
r
ov
Link GPU force producer and
c
o
n
sumer
t
a
sks
commit
|
commitdiff
|
tree
2019-10-15
Artem
Zhmurov
Fix the single
-
GPU updat
e
-
c
onstraints
commit
|
commitdiff
|
tree
2019-10-14
Artem
Zhm
u
r
o
v
Add separate construct
o
r
t
o
State
P
ropagatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-12
Artem Zhmurov
Centralize man
a
gem
e
nt of forces r
e
ady on GPU e
v
ent
commit
|
commitdiff
|
tree
2019-10-12
A
rtem Zhmurov
C
h
ange
c
o
p
y m
o
d
e
to
A
syn
c
i
n
PME only ra
n
k
commit
|
commitdiff
|
tree
2019-10-12
Artem
Zhmuro
v
Centralize management of coordinates ready on GPU event
commit
|
commitdiff
|
tree
2019-10-11
Ar
t
em Zhmurov
Wron
g
locality was used when ig
n
o
r
i
ng the PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
A
r
tem
Z
hmurov
Add management f
o
r vel
o
c
i
ti
e
s
and forces
c
opy eve
n
ts
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Artem Zhmur
o
v
Fix for th
e
r
ecent
ni
g
htly failure
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Pass the GPU streams to StatePropa
g
atorDa
t
aGpu const
r
u
c
t
o
r
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
C
le
a
n up
t
he comments
sections in Up
d
a
t
e
-
Co
n
strain
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
hmur
o
v
Fix a
bug in G
P
U halo exchange ini
t
ialization
commit
|
commitdiff
|
tree
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