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Fixes for Intel and container build fixes
2020-11-23
P
a
ul Bauer
Fix
e
s for Intel and
container bu
i
ld fixes
commit
|
commitdiff
|
tree
2020-10-05
Paul
Ba
u
e
r
Fix de
b
ug message l
o
c
a
tion
commit
|
commitdiff
|
tree
2020-09-10
Gille
s
Gouaillardet
fix check
_
a
ssi
g
n
_
i
n
t
eract
i
ons
_
ato
m
(
)
commit
|
commitdiff
|
tree
2020-06-16
Ar
t
em Zhmurov
A
d
d mi
s
sing
e
nd-of-li
n
e
in the GPU update as
s
ignment
.
.
.
commit
|
commitdiff
|
tree
2020-06-04
Artem
Z
h
m
u
rov
U
p
date the rel
e
as
e
n
o
tes
commit
|
commitdiff
|
tree
2020-04-29
A
r
t
e
m Z
h
murov
Fix the
n
umber of
s
teps ch
e
ck when checkpoint is
l
oad
e
d
commit
|
commitdiff
|
tree
2020-04-01
Mark Abraham
Fix minor bug with tools time-un
i
t co
n
version
s
commit
|
commitdiff
|
tree
2020-03-19
Szilárd Páll
Fix DL
B
initial st
a
te repor
t
in
g
commit
|
commitdiff
|
tree
2020-03-07
Paul Bauer
Add clang-
t
idy script
commit
|
commitdiff
|
tree
2020-03-02
Pa
u
l Bauer
Add Cuda build to gitlab CI
commit
|
commitdiff
|
tree
2020-02-22
D
avid van der Spoel
Fixed b
u
g
i
n
g
m
x
di
s
re du
e
t
o inconsistency in
input
.
commit
|
commitdiff
|
tree
2020-02-15
Szil
á
rd
Páll
Fix
gpuu
d
pate and gpucomm mat
r
ix docs
commit
|
commitdiff
|
tree
2020-01-24
S
zi
l
ár
d
Pál
l
Fix
d
ea
d
lock in PP-PME balanci
n
g st
a
rtup de
l
ay
commit
|
commitdiff
|
tree
2020-01-22
B
erk
H
ess
Clarify COM
M
/posres grom
p
p note
commit
|
commitdiff
|
tree
2019-12-30
Mark Abraham
Remove use of tuple in LINCS code f
o
r G
P
U
i
mpleme
n
tat
i
on
commit
|
commitdiff
|
tree
2019-12-20
Paul Bauer
Fix wrong header i
n
rele
a
se notes
commit
|
commitdiff
|
tree
2019-12-18
Alan Gr
a
y
Fix cond
i
tio
n
al
on
a
sse
r
tion for co
m
bining GPU Update
.
.
.
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
A
d
d
n
ote for
C
O
M
r
e
moval with posit
i
on
restraints
commit
|
commitdiff
|
tree
2019-12-17
Artem Zhm
u
r
ov
C
lea
n
-up b
u
f
f
er-ops CUDA kernels
commit
|
commitdiff
|
tree
2019-12-17
Szi
l
árd P
á
ll
Comment
the u
s
e of wai
t
Coordinates
C
opiedTo
D
e
v
ice
commit
|
commitdiff
|
tree
2019-12-17
Pau
l
B
auer
S
e
t correct
depen
d
ency f
o
r doc bu
i
l
d on
gmx
a
pi
commit
|
commitdiff
|
tree
2019-12-17
P
aul
B
aue
r
Fi
x
compiler
w
arning
a
bout extra ;
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Add
w
allcyc
l
e countin
g
to Stat
e
Propagato
r
D
a
taGpu
commit
|
commitdiff
|
tree
2019-12-11
A
r
tem Zhmurov
Enab
l
e most of the pullin
g
flavors with GPU update
commit
|
commitdiff
|
tree
2019-12-10
Artem Z
h
murov
S
e
t GPU
update to false
in case of
a
rerun
commit
|
commitdiff
|
tree
2019-11-29
A
r
tem Zhmurov
Make
L
e
ap-Frog CUDA ke
r
nel s
e
lection safer
commit
|
commitdiff
|
tree
2019-11-28
A
r
tem Zhm
u
rov
Fix pressure co
u
pling with GPU update
commit
|
commitdiff
|
tree
2019-11-27
Artem
Z
hmurov
Combin
e
two booleans i
n
md loop
commit
|
commitdiff
|
tree
2019-11-27
Mark Abr
a
ham
Disable GPU PME-PP com
m
unication with m
d
r
un
-pmef
f
t cpu
commit
|
commitdiff
|
tree
2019-11-26
Alan Gra
y
B
u
g fix for nonlocal D2H coordinate transf
e
r sync
h
r
o
n
izat
i
on
commit
|
commitdiff
|
tree
2019-11-23
Artem Zhmurov
New cool quo
t
e
commit
|
commitdiff
|
tree
2019-11-20
Alan
G
r
ay
M
ove
p
mePpCommG
p
u
r
eset ou
t
s
i
de d
o
_md
commit
|
commitdiff
|
tree
2019-11-19
Ma
r
k Abraham
Updated release
n
otes for CODATA
u
p
date
commit
|
commitdiff
|
tree
2019-11-19
Arte
m
Zhmu
r
ov
Fix icc-19 warning i
n
nightly matr
i
x
commit
|
commitdiff
|
tree
2019-11-13
Paul Bauer
Add build to
r
un clan
g
-format
u
pdate on
Jenkin
s
commit
|
commitdiff
|
tree
2019-11-03
Szilárd Páll
Impro
v
e SimulationWorkload doxyge
n
commit
|
commitdiff
|
tree
2019-10-30
Berk
Hess
Fix walls
with
G
P
U
update
commit
|
commitdiff
|
tree
2019-10-29
Berk
H
ess
Disable p
r
essure coupling with
GPU
update
commit
|
commitdiff
|
tree
2019-10-28
Szilárd
Páll
Extend Simulatio
n
Workl
o
ad
w
ith CPU flags
commit
|
commitdiff
|
tree
2019-10-21
Szilárd Páll
Override GMX_GPU_
D
D_COMMS if nonb
o
nd
e
ds are
o
ff
commit
|
commitdiff
|
tree
2019-10-18
Artem Zhmurov
R
emove excessiv
e
H2D and D2H co
o
rd
i
nat
e
s copies when
.
.
.
commit
|
commitdiff
|
tree
2019-10-17
Szilárd
P
áll
D
i
sable
G
MX_GPU_P
M
E_PP_C
O
M
MS
if
PME is no
t
offl
o
aded
commit
|
commitdiff
|
tree
2019-10-16
S
z
i
lárd
Páll
Fix initialization of
f
ield
i
n
P
M
E
d
ata structure
commit
|
commitdiff
|
tree
2019-10-16
Artem Z
h
murov
Link GPU force pr
o
ducer and consum
e
r tasks
commit
|
commitdiff
|
tree
2019-10-15
Alan Gray
PME/PP GPU Pimpl Class and GPU->CPU Communic
a
tion for
.
.
.
commit
|
commitdiff
|
tree
2019-10-15
Szilárd Páll
Link GPU
co
o
rdin
a
t
e prod
u
cer and consumer tasks
commit
|
commitdiff
|
tree
2019-10-14
A
r
tem Zhmurov
Add
s
eparate
c
onstructor
t
o
S
tatePropagatorDataGpu
.
.
.
commit
|
commitdiff
|
tree
2019-10-13
Szilár
d
Pá
l
l
Enable StateProp
a
gatorGpuData for force t
r
ansfers
commit
|
commitdiff
|
tree
2019-10-13
Szi
l
árd Páll
Move b
u
ffer
o
ps / PME F reduct
i
on flags into S
t
epWor
k
loa
d
commit
|
commitdiff
|
tree
2019-10-12
Arte
m
Z
h
murov
Centralize management o
f
f
orces ready
o
n GPU
event
commit
|
commitdiff
|
tree
2019-10-12
Artem
Zh
m
uro
v
Change c
o
py
mode to
A
s
ync in PME only rank
commit
|
commitdiff
|
tree
2019-10-11
Arte
m
Zhm
u
rov
Wrong locality was
used
w
he
n
ignori
n
g the PME force
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
S
zil
á
rd
Páll
Migrate c
o
de to using Simulatio
n
Work
l
oa
d
flags
commit
|
commitdiff
|
tree
2019-10-10
S
z
ilárd
P
á
ll
R
e
m
ove incorrect GPU task de
p
e
nde
n
cy
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
Pass list of EventSynchronizers to
G
PU reduction
commit
|
commitdiff
|
tree
2019-10-10
P
au
l
B
a
ue
r
Basic population of
s
imulation workload
commit
|
commitdiff
|
tree
2019-10-10
Artem
Z
hmu
r
ov
Add
m
anagement f
o
r ve
l
ocities and forces
c
o
p
y even
t
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-10
S
z
ilárd Pá
l
l
Add management for coordinates copy events into
StateProp
a
ga
.
.
.
commit
|
commitdiff
|
tree
2019-10-07
A
rt
e
m Zhmurov
P
ass
t
h
e GPU strea
m
s to Sta
t
ePro
p
aga
t
orDataGpu constructor
commit
|
commitdiff
|
tree
2019-10-07
M
a
r
k
A
b
raham
E
x
t
end GPU traits
cl
a
s
s
commit
|
commitdiff
|
tree
2019-10-07
Artem
Z
hmurov
C
l
e
a
n up the comm
e
nt
s
sec
t
ions in Up
d
ate-Constrain
commit
|
commitdiff
|
tree
2019-10-07
Artem Zhmurov
Fix
a bug in G
P
U halo exc
h
ange initializati
o
n
commit
|
commitdiff
|
tree
2019-10-03
Berk
Hess
Use
g
m
x::Range for iZones in pair se
a
rc
h
commit
|
commitdiff
|
tree
2019-10-02
Carsten Ku
t
zner
Upd
a
te the
w
w
w link
to
th
e
Doxy
g
en documentati
o
n in
.
.
.
commit
|
commitdiff
|
tree
2019-09-30
S
zilárd Páll
Move PME GPU prog
r
am buildi
n
g later
commit
|
commitdiff
|
tree
2019-09-27
Ar
t
em Zh
m
uro
v
Slight improvemen
t
s to
G
P
U u
p
date/constrai
n
t
s
initialization
commit
|
commitdiff
|
tree
2019-09-27
Szi
l
árd Páll
Sw
i
tch GPU update off by default
commit
|
commitdiff
|
tree
2019-09-27
Art
e
m Zhmurov
Introduce
s
trea
m
managemen
t
to GP
U
Upda
t
e-
C
onstraints
commit
|
commitdiff
|
tree
2019-09-27
Berk
Hess
Extr
a
ct gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Ma
r
k Ab
r
aham
Sto
p
checking CUDA
version re
p
orte
d
b
y nvcc
commit
|
commitdiff
|
tree
2019-09-22
Artem Zhmurov
Dis
a
ble GPU update/constra
i
nts when ne
i
ther PME no
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Mark Ab
r
a
ham
Ma
k
e gm
x
_mul
t
isim_t a C++ obje
c
t
commit
|
commitdiff
|
tree
2019-09-10
Mark Abraham
Avoid warning in
n
o-mp
i
build
commit
|
commitdiff
|
tree
2019-09-10
Artem
Zhmurov
Making Devi
c
eBuffer availible in non-GP
U
bu
i
l
d
s
commit
|
commitdiff
|
tree
2019-09-10
Paul Bauer
Add
indication o
n
how to enable I
m
ageMagick con
v
ert
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
As
s
ert
the types of OpenCL k
e
r
nels argument
s
commit
|
commitdiff
|
tree
2019-08-25
A
r
tem Zh
m
urov
Ma
k
e use of recent changes
t
o
prepareK
e
r
nelArgu
m
ents
.
.
.
commit
|
commitdiff
|
tree
2019-08-25
Artem Zhmurov
M
i
sceleneous im
p
rovements to
the Leap F
r
og
tests
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Appl
y
clang-t
i
dy-8 reada
b
il
i
ty-uppercase
-
li
t
eral
-
suffix
commit
|
commitdiff
|
tree
2019-08-20
Ma
r
k Abr
a
ham
Us
e
pot
e
n
tial-shift as
default m
o
d
i
fi
e
r
commit
|
commitdiff
|
tree
2019-08-09
B
erk He
s
s
Move bonded funct
i
on t
a
ble into bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-08
Mark Abra
h
am
Initialize gmx_ekindat
a
_t and t_vc
m
proper
l
y
commit
|
commitdiff
|
tree
2019-08-06
Art
e
m Z
h
mu
r
ov
Fix for cmake
l
ists in mdlib
t
ests
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Change the
f
ile structure in c
o
nst
r
aints tests
commit
|
commitdiff
|
tree
2019-07-31
Szilá
r
d
P
áll
Store wcycle
p
o
i
nter in n
o
nbon
d
ed
_
verlet_t
commit
|
commitdiff
|
tree
2019-07-26
A
r
tem Zhmuro
v
Remove PImpl s
c
affold
i
ng f
r
o
m
CUDA version of SETTLE
commit
|
commitdiff
|
tree
2019-07-05
Kevin Boyd
Change error message wh
e
n att
e
mpting to offload to
.
.
.
commit
|
commitdiff
|
tree
2019-07-05
Artem Zhmurov
Remo
v
e PImpl s
c
affolding
f
rom
CUDA version of LINCS
commit
|
commitdiff
|
tree
2019-07-04
Artem Zhmurov
Use
r
eallo
c
ateDevic
e
Buffer(
.
.
.
) in CUDA version of
.
.
.
commit
|
commitdiff
|
tree
2019-07-03
Artem Z
h
murov
Early
e
xit for CUDA version
s
of SETT
L
E and
L
INCS
commit
|
commitdiff
|
tree
2019-07-03
Artem Zhmurov
Mem
o
ry management fixes in CUDA version of
L
INCS
commit
|
commitdiff
|
tree
2019-06-28
Szilárd Pál
l
Separate C
P
U NB kernel and buffe
r
clearing subcounters
commit
|
commitdiff
|
tree
2019-06-28
M
agnus Lu
n
dbo
r
g
Fused G
P
U bonded kernels
commit
|
commitdiff
|
tree
2019-06-18
Artem Zhm
u
rov
Combine CUDA Leap-Frog, LINCS an
d
S
ETTLE
.
I
.
commit
|
commitdiff
|
tree
2019-05-24
Artem
Z
hmurov
C
larify which of the main energy terms
ar
e
printed
.
commit
|
commitdiff
|
tree
2019-05-13
Paul Bauer
Fix ma
t
h format
t
ing in r
e
ference manual
commit
|
commitdiff
|
tree
2019-05-12
Arte
m
Z
hm
u
r
o
v
CUDA ver
s
ion
of L
e
ap-Frog inte
g
rator
w
ith basic tests
commit
|
commitdiff
|
tree
2019-05-06
M
a
rk
A
braham
Improve how mdrun -noappen
d
names
o
utput files
commit
|
commitdiff
|
tree
2019-05-02
Artem Zhmurov
Use test w
i
th parameters for
E
nergyOutput
commit
|
commitdiff
|
tree
2019-04-30
Arte
m
Zhmurov
CUD
A
versi
o
n
o
f
SETTLE al
g
orithm with basic tests
commit
|
commitdiff
|
tree
next