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GROMACS 2021 first beta release
2020-10-12
Ar
t
e
m Zhmur
o
v
Fix the seedi
n
g of
P
RNG
whe
n
it
i
s used instead of
R
G
commit
|
commitdiff
|
tree
2020-10-09
Artem Zhmurov
Cool quote pick
i
n
g can
freeze wh
e
n
hardw
a
r
e
random
.
.
.
commit
|
commitdiff
|
tree
2020-10-08
Artem
Zhmuro
v
Ad
d
And
r
e
y
Alekseenk
o
t
o the list of authors
commit
|
commitdiff
|
tree
2020-10-06
Arte
m
Zhmurov
Remove unused canCompu
t
eOnG
p
u(
.
.
.
) function
f
rom device
.
.
.
commit
|
commitdiff
|
tree
2020-10-06
Artem
Z
hmurov
Simplify GPU usag
e
decision function signatures
commit
|
commitdiff
|
tree
2020-10-06
Artem Zhmurov
Use new GPU in
f
rast
r
ucture in MDLi
b
tests
commit
|
commitdiff
|
tree
2020-10-01
Artem
Z
hmurov
A
d
d
missing inc
l
u
d
e
into the test
s
c
o
mparison helper
commit
|
commitdiff
|
tree
2020-09-30
Artem Zhmurov
Restor
e
d
e
st
r
uctor
f
o
r
G
p
uTest and gmx
_
hw_info_t
commit
|
commitdiff
|
tree
2020-09-29
A
rt
e
m Zhmurov
Don't use
fah_fsync
commit
|
commitdiff
|
tree
2020-09-29
Artem Zh
m
ur
o
v
R
e
m
o
ve t
w
o-stag
e
initializa
t
i
o
n
in
D
ev
i
ceStream
commit
|
commitdiff
|
tree
2020-09-28
Arte
m
Zhmu
r
ov
add detection of C
P
X 5
3
0
0
w/
2
FMAs
commit
|
commitdiff
|
tree
2020-09-21
Artem Zhmurov
Do not
run PinnedMemoryCheck
e
rTest when there are no
.
.
.
commit
|
commitdiff
|
tree
2020-09-21
Arte
m
Z
hmurov
M
o
ve the message to
t
he depr
E
c
ation-poli
c
y f
i
le
commit
|
commitdiff
|
tree
2020-09-20
A
rtem
Zhm
u
rov
Set
active device when
the device
stream manager is
.
.
.
commit
|
commitdiff
|
tree
2020-09-20
Artem Zhmurov
A
llow using old env
i
ronment variables, but
p
rint deprecatio
n
.
.
.
commit
|
commitdiff
|
tree
2020-09-17
A
r
t
em Zhmurov
Remove
t
he CPU
h
ardware c
o
n
te
x
t from
t
he general list
.
.
.
commit
|
commitdiff
|
tree
2020-09-15
Artem Zh
m
urov
Use common devic
e
context head
e
r fo
r
O
p
en
C
L
commit
|
commitdiff
|
tree
2020-09-15
Art
e
m Zhmurov
Fix VSite out of
r
ange error me
s
sag
e
commit
|
commitdiff
|
tree
2020-09-14
Artem Zh
m
ur
o
v
Us
e
common d
e
vice context
header for OpenCL
commit
|
commitdiff
|
tree
2020-09-11
Artem Zhmurov
Define stubs fo
r
G
P
U data
s
tructures in SYCL to
m
ake
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
A
rtem Zhmurov
Use common devic
e
conte
x
t h
e
ader fo
r
O
p
e
nCL
commit
|
commitdiff
|
tree
2020-09-10
Arte
m
Zhmur
o
v
Use d
e
v
i
ce info
r
matio
n
obje
c
t instead o
f
id when pe
r
forming
.
.
.
commit
|
commitdiff
|
tree
2020-09-10
Artem Zhmurov
Unify
m
or
e
funct
i
ons in
C
UD
A
and
OpenCL imp
l
em
e
ntations
.
.
.
commit
|
commitdiff
|
tree
2020-09-09
Artem
Z
hmurov
R
es
t
ore GMX
_
FORCE_UPDATE_D
E
FAULT_GPU environment varible
.
.
.
commit
|
commitdiff
|
tree
2020-09-07
Artem Zhmur
o
v
R
e
move in-body comment from
in
i
t_forcerec(
.
.
.
)
functio
n
commit
|
commitdiff
|
tree
2020-09-07
Artem
Z
h
murov
F
i
x clang-forma
t
commit
|
commitdiff
|
tree
2020-09-07
Artem Z
h
murov
Access the d
e
vice s
t
atus directly, remov
e
the
g
etter
commit
|
commitdiff
|
tree
2020-08-24
Artem
Z
hmurov
M
o
ve GPU devices ma
n
agement into hardwar
e
subfolder
commit
|
commitdiff
|
tree
2020-08-14
Artem Zh
m
urov
Fix DeviceStreamManager tests
commit
|
commitdiff
|
tree
2020-07-29
Artem Zhmur
o
v
R
e
vert c++
-
17 features that ar
e
n
o
t
supporte
d
by CUDA
.
.
.
commit
|
commitdiff
|
tree
2020-07-29
Artem Zhmurov
R
e
vert c++-17 features that are n
o
t supported by CUDA
.
.
.
commit
|
commitdiff
|
tree
2020-07-27
Artem
Zhmurov
F
i
x clang-tidy
warnin
g
commit
|
commitdiff
|
tree
2020-07-15
Artem Zhm
u
rov
Fix
t
he
s
usp
i
cious string l
i
te
r
al
e
rr
o
r in
G
PU statu
s
.
.
.
commit
|
commitdiff
|
tree
2020-07-07
Artem Zhmu
r
ov
M
a
ke cl_nbparam into
a
struct
commit
|
commitdiff
|
tree
2020-06-26
Artem Z
h
murov
Mak
e
hold
e
r for simulation c
o
nfig
u
ration
commit
|
commitdiff
|
tree
2020-06-25
A
r
tem
Z
h
mur
o
v
Make c
l
_nbparam into a
struc
t
commit
|
commitdiff
|
tree
2020-06-24
Artem
Z
h
murov
Fix mi
n
or nit-picks
commit
|
commitdiff
|
tree
2020-06-22
Artem Zhmurov
Remove
DeviceSt
r
eam include
f
rom GPU tr
a
its
commit
|
commitdiff
|
tree
2020-06-16
A
r
tem Zhmur
o
v
Add missin
g
end-of-line in t
h
e
GPU u
p
date assig
n
me
n
t
.
.
.
commit
|
commitdiff
|
tree
2020-06-12
Artem Z
h
mu
r
ov
Replace compil
e
_
c
pp_
a
s_cu
d
a(
.
.
.
) with CUDA run
t
ime
.
.
.
commit
|
commitdiff
|
tree
2020-06-09
Art
e
m
Zhmurov
Make
S
D stuff pri
v
a
te for update
.
cpp
commit
|
commitdiff
|
tree
2020-06-09
Ar
t
em Zhmurov
Mak
e
SD stuff privat
e
for
u
pdate
.
c
pp
commit
|
commitdiff
|
tree
2020-06-08
Artem Z
h
m
u
rov
M
o
ve constr
a
ints
relate
d
logic to const
r
aints fi
l
e
commit
|
commitdiff
|
tree
2020-06-08
Artem Zhmuro
v
U
n
ify Vd
W
and Elect
r
ost
a
tic kernel en
u
m
e
ration
s
in
.
.
.
commit
|
commitdiff
|
tree
2020-06-05
Artem Zhmurov
Move calcul
a
tion of kinetic ener
g
y to
m
d_support
commit
|
commitdiff
|
tree
2020-06-05
Artem Zhmurov
M
a
ke
a
error message l
e
ss confusing
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmurov
Make a er
r
o
r
mes
s
age
l
e
ss c
o
n
fusing
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhmurov
Update the r
e
l
ease
n
otes
commit
|
commitdiff
|
tree
2020-06-04
Artem Zhm
u
r
ov
Cool quote
commit
|
commitdiff
|
tree
2020-05-29
Ar
t
em Zhmurov
Unify initialization
o
f GPU and C
P
U SETTL
E
commit
|
commitdiff
|
tree
2020-05-26
Artem Zhmur
o
v
Re
m
o
ve the dependence on Co
n
straints o
b
ject on t_mdatoms
commit
|
commitdiff
|
tree
2020-05-25
Artem
Z
hmurov
Remove d
e
pendence on t_
m
datoms
f
rom
GPU version
of
.
.
.
commit
|
commitdiff
|
tree
2020-05-23
Artem Zhmurov
Remove de
p
endence on t_m
d
atoms
from pull code
commit
|
commitdiff
|
tree
2020-05-22
Ar
t
e
m
Zhmuro
v
Remove dep
e
ndence
o
f
constrain
t
s on t_mdatom
s
commit
|
commitdiff
|
tree
2020-05-22
Art
e
m Zhmuro
v
Remove depend
e
nce of
c
onstr
a
in
t
s on
t_mdatoms
commit
|
commitdiff
|
tree
2020-05-15
Artem Zhm
u
rov
U
n
i
f
y CUDA and
O
p
enCL
l
ookup-table creation
commit
|
commitdiff
|
tree
2020-05-11
Arte
m
Zhmu
r
ov
Remove
t
he
duplicating n
o
te from the release
n
otes
commit
|
commitdiff
|
tree
2020-05-11
Art
e
m Zhmurov
U
n
ify CUDA an
d
OpenCL lo
o
ku
p
-
tab
l
e creation
commit
|
commitdiff
|
tree
2020-05-05
Artem Zhmurov
Unify CU
D
A and OpenCL lookup-
t
able cr
e
ation
commit
|
commitdiff
|
tree
2020-05-04
Ar
t
em Zhm
u
rov
Unify CUDA and
OpenCL lookup-tab
l
e
c
reation
commit
|
commitdiff
|
tree
2020-04-29
Ar
t
em Zhmu
r
ov
F
i
x
the num
b
er of ste
p
s
c
heck wh
e
n check
p
o
int is
l
oaded
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Fix the
r
emova
l
of COM
v
elocity in case of GPU update
commit
|
commitdiff
|
tree
2020-04-27
Artem Zhmurov
Move P
B
C s
e
t
up ou
t
of the launchKe
r
n
el(
.
.
.
) in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-04-20
A
rte
m
Z
h
murov
Fix the numb
e
r
of steps ch
e
ck
w
h
en ch
e
ckpoint
i
s loaded
commit
|
commitdiff
|
tree
2020-04-16
Artem Zh
m
u
rov
New cool quote
commit
|
commitdiff
|
tree
2020-04-16
A
rtem Zhmurov
Unify CUDA a
n
d
Ope
n
C
L
loo
k
up-tabl
e
creati
o
n
commit
|
commitdiff
|
tree
2020-03-25
Artem Zhmurov
Make use of the Devi
c
eStrea
m
Manager
commit
|
commitdiff
|
tree
2020-03-23
Artem
Zhmur
o
v
Intr
o
d
uce DeviceStreamManager
commit
|
commitdiff
|
tree
2020-03-20
Artem Zhmur
o
v
Add
OpenCL error report
i
ng to GPU region timer
commit
|
commitdiff
|
tree
2020-03-20
Ar
t
em
Zhmurov
Small fixes to the DeviceStrea
m
commit
|
commitdiff
|
tree
2020-03-19
A
rtem
Zhmur
o
v
Store DeviceI
n
formation inside
the DeviceContext class
commit
|
commitdiff
|
tree
2020-03-19
Art
e
m
Zhmurov
Pass DeviceContext
i
n
stead of GPU r
u
ntime
da
t
a
when
.
.
.
commit
|
commitdiff
|
tree
2020-03-18
Artem Zhmurov
Make some doxygen errors more cl
e
a
r
commit
|
commitdiff
|
tree
2020-03-13
A
r
tem Zhmurov
Combine initia
l
ization routines for GPUs assi
g
n
ed to
.
.
.
commit
|
commitdiff
|
tree
2020-03-13
Artem Zhmurov
Remove
s
tream from GPU kernel launch config
commit
|
commitdiff
|
tree
2020-03-13
Artem
Z
hm
u
rov
U
se Dev
i
ceSt
r
e
am init(
.
.
.
) func
t
ion to cr
e
ate s
t
reams
commit
|
commitdiff
|
tree
2020-03-13
A
r
tem Zhmurov
Make Dev
i
ceStream into a
class
commit
|
commitdiff
|
tree
2020-03-11
A
r
tem Zhmur
o
v
Fix
the post-submit failures
commit
|
commitdiff
|
tree
2020-03-11
A
r
tem Zhmurov
Take over management of
O
p
enCL
c
ont
e
x
t
from PME
a
n
d
.
.
.
commit
|
commitdiff
|
tree
2020-03-10
Artem Zhmurov
Use init(
.
.
) fu
n
cti
o
n to build Dev
i
ceContext
commit
|
commitdiff
|
tree
2020-03-09
Artem
Z
h
mur
o
v
M
a
ke Devic
e
C
o
ntext into a pr
o
per
c
lass
commit
|
commitdiff
|
tree
2020-03-05
Arte
m
Z
hmurov
Finalize renaming o
f
bEnerVi
r
to co
m
puteEn
e
rg
y
AndVirial
commit
|
commitdiff
|
tree
2020-03-04
Arte
m
Zh
m
u
rov
Do not count
PME only rank when in
i
tializing N
B
N
X
M
commit
|
commitdiff
|
tree
2020-03-03
Artem Zhmurov
Move th
e
Pme
P
P
C
o
m
m
G
p
u
i
niti
a
lization from fo
r
cerec
.
.
.
commit
|
commitdiff
|
tree
2020-03-02
Artem Zh
m
urov
Update the mess
a
ge o
n
whether
u
p
d
at
e
and const
r
aints
.
.
.
commit
|
commitdiff
|
tree
2020-02-25
Artem Zhmurov
Fix th
e
RVec to float3 c
o
nversion test
commit
|
commitdiff
|
tree
2020-02-22
Art
e
m
Z
h
murov
Add m
i
ssing header a
n
d disab
l
e
f
ailing test
commit
|
commitdiff
|
tree
2020-02-21
Artem Zhmurov
Refacto
r
and enable RVec to float
c
o
nve
r
s
i
o
n t
e
st
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmurov
Do not
c
all PME GPU
b
uild
e
r i
n
CPU
code paths
commit
|
commitdiff
|
tree
2020-02-20
Arte
m
Z
hmuro
v
U
s
e GROMACS
w
ra
p
pers for EXPECT
_
THROW/NO
_
T
HROW in PME
.
.
.
commit
|
commitdiff
|
tree
2020-02-20
Artem Zhmu
r
ov
Use CUDA floa
t
3
vector type
instead of
fvec in GPU
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Arte
m
Z
hmurov
C
lean up trivi
a
l funct
i
o
n
a
n
d duplicating m
a
croses
.
.
.
commit
|
commitdiff
|
tree
2020-02-11
Art
e
m Zhmurov
Fix t
h
e ni
g
h
t
ly failure
commit
|
commitdiff
|
tree
2020-02-08
Artem Zhmuro
v
Tempo
r
a
r
y disab
l
e
R
Vec->float3
c
o
n
version test to fix
.
.
.
commit
|
commitdiff
|
tree
2020-02-06
A
rte
m
Zhmurov
Use
R
Vec instead o
f
float f
o
r
x, v
and f device
b
uff
e
rs
commit
|
commitdiff
|
tree
2020-02-06
Artem Zh
m
u
rov
Move Devi
c
e
In
f
o into G
P
U traits
commit
|
commitdiff
|
tree
2020-02-05
Artem Zhm
u
rov
M
ake Open
C
L DeviceVendor into enum class a
n
d move to
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Artem
Z
h
murov
Move non-bon
d
ed initializa
t
ion out of the forcerec
commit
|
commitdiff
|
tree
2020-02-05
Ar
t
e
m
Zh
m
u
r
ov
Fix typo
in
an
d
remove a couple of duplicates f
r
om
.
.
.
commit
|
commitdiff
|
tree
2020-02-03
Ar
t
em Zhmurov
E
n
able GPU update for su
p
p
orted cases of FEP
commit
|
commitdiff
|
tree
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