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grompp: fix the -ref <file> option
2020-03-11
Szilá
r
d Páll
Reor
g
anize dip
o
l
e
calculati
o
n in do_fo
r
ce
commit
|
commitdiff
|
tree
2020-02-26
Szilárd Páll
Av
o
id mdru
n
terminate due to GP
U
sanity chec
k
err
o
rs
commit
|
commitdiff
|
tree
2020-02-26
S
z
ilárd Páll
Docum
e
nt NVIDIA Ope
n
C
L broken on V
o
lta a
n
d Tur
i
n
g
commit
|
commitdiff
|
tree
2020-02-26
Szilá
r
d Páll
Remove
o
utda
t
e
d P
M
E-GPU limitation in user
g
uide
commit
|
commitdiff
|
tree
2020-02-25
Szilárd
P
áll
Impr
o
ve GPU upda
t
e tasks
a
s
s
i
g
nme
n
t con
s
i
stency
commit
|
commitdiff
|
tree
2020-02-17
Szilárd Páll
A
dd simulati
o
n
workload f
l
ag f
o
r dip
o
le computa
t
ion
commit
|
commitdiff
|
tree
2020-02-15
S
z
ilárd Pál
l
F
ix gp
u
ud
p
ate a
n
d
gpucom
m
matrix docs
commit
|
commitdiff
|
tree
2020-02-11
Szi
l
árd
P
á
l
l
Fix incorrect GPU update ta
s
k assignm
e
nt fallback
commit
|
commitdiff
|
tree
2020-02-10
Szilárd Páll
A
void
dev flags in triggering gpu
u
pdate nightly
m
atrix
commit
|
commitdiff
|
tree
2020-02-10
Szilárd Páll
A
v
o
id
(
re)initializing
GPU update
without DD
commit
|
commitdiff
|
tree
2020-02-06
Szilárd Páll
Rem
o
ve mu
_
tot fr
o
m c
o
m
p
ute_global
s
()
commit
|
commitdiff
|
tree
2020-01-31
Szilá
r
d Páll
Eliminate
t
he legac
y
Flags manipulation in do_
f
orce()
commit
|
commitdiff
|
tree
2020-01-31
Szilárd P
á
l
l
R
e
move BufferOpsUs
e
Gpu enum
commit
|
commitdiff
|
tree
2020-01-29
Szilárd Páll
Smal
l
im
p
rovement in Open
C
L
e
rror handling
commit
|
commitdiff
|
tree
2020-01-24
Szilár
d
Páll
Add targ
e
t for o
f
f
line
PME OpenCL c
o
mpilation
commit
|
commitdiff
|
tree
2020-01-24
S
z
i
l
á
r
d
Páll
Fix deadlock in P
P
-PME
ba
l
anc
i
ng startup delay
commit
|
commitdiff
|
tree
2020-01-19
Szilárd Páll
T
e
mplate X buffe
r
ops
o
n
setFil
l
erCoord
s
commit
|
commitdiff
|
tree
2020-01-16
Szi
l
árd Páll
Fix PME run mode w
i
thout PME
commit
|
commitdiff
|
tree
2020-01-10
Szilárd Páll
I
m
prove m
d
run p
e
rforman
c
e user guide
commit
|
commitdiff
|
tree
2019-12-20
Szilárd
P
áll
Enable buffer ops when GMX_GPU_DD_COMMS i
s
set
commit
|
commitdiff
|
tree
2019-12-19
Szilá
r
d
Páll
P
P
-PME load ba
l
ancing improvem
e
nts
commit
|
commitdiff
|
tree
2019-12-18
Sz
i
lárd Páll
Allow x
D2H to ov
e
rlap with GPU forc
e
c
o
mput
e
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Pál
l
C
o
mment the use of waitC
o
ord
i
nate
s
C
o
p
i
edT
o
Device
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Add wallcycle counting to S
t
a
tePropagator
D
ata
G
p
u
commit
|
commitdiff
|
tree
2019-12-16
Szilárd Páll
Fi
x
the
G
PU bonded s
t
r
e
a
m w
i
th 1
PP + 1 PME
r
a
n
k
commit
|
commitdiff
|
tree
2019-12-12
Szilárd Páll
A
l
l
ow overlapping
CPU fo
r
ce
H
2
D with c
o
m
pute
commit
|
commitdiff
|
tree
2019-11-17
S
z
ilárd Páll
Trigger ocl_nbnxm_k
e
r
nels target with clang-tidy
commit
|
commitdiff
|
tree
2019-11-17
Szilárd Páll
Fix
clan
g
-tidy 8
w
arning
s
in OpenCL nbnxm kernels
commit
|
commitdiff
|
tree
2019-11-03
Sz
i
lárd Pál
l
I
m
prove
S
imulationW
o
rklo
a
d
dox
y
gen
commit
|
commitdiff
|
tree
2019-11-01
Szilá
r
d Páll
Ren
a
me re
f
erenc
e
checks
u
m gener
a
ting ta
r
get
commit
|
commitdiff
|
tree
2019-11-01
Szilá
r
d
P
á
l
l
U
se "
-
"
in
c
hecksum-related version suffix
commit
|
commitdiff
|
tree
2019-11-01
Szi
l
á
rd Páll
Impr
o
ve
w
o
rkload
d
ata structures
'
docs
commit
|
commitdiff
|
tree
2019-10-28
Szilárd Pál
l
Extend S
i
m
ulationWorkload w
i
th
CPU flags
commit
|
commitdiff
|
tree
2019-10-21
Szil
á
rd Pál
l
R
emove unsupported configs
f
rom the gpuupda
t
e
ma
t
rix
commit
|
commitdiff
|
tree
2019-10-21
Szilárd
P
áll
Override GMX_GPU_D
D
_COMMS if nonbo
n
deds
a
re off
commit
|
commitdiff
|
tree
2019-10-18
Szil
á
rd Páll
Add strict assertions on
x
synchronizer
in
P
ME
commit
|
commitdiff
|
tree
2019-10-18
Szilárd Páll
Fix genion clang-8 warning
commit
|
commitdiff
|
tree
2019-10-17
Szilá
r
d Páll
Fix clang-tidy warning
s
in gpuhaloex
c
hange_impl
.
cuh
commit
|
commitdiff
|
tree
2019-10-17
S
zilá
r
d Páll
El
i
m
i
n
ate spurious GPU->CPU copy
commit
|
commitdiff
|
tree
2019-10-17
Szilárd Páll
Dis
a
bl
e
G
MX_
G
PU_P
M
E
_
PP_COMMS
i
f P
M
E is not of
f
loa
d
ed
commit
|
commitdiff
|
tree
2019-10-16
Szilárd Pál
l
F
ix initialization of
fiel
d
i
n
P
ME d
a
ta struc
t
ure
commit
|
commitdiff
|
tree
2019-10-16
Sz
i
lárd Páll
Make the
wait
o
n no
n
bonded
G
PU res
u
lts
c
onditio
n
al
commit
|
commitdiff
|
tree
2019-10-15
Szi
l
árd Páll
T
rigger
s
ynchronizer when
l
ocal force
s
a
r
e ready
commit
|
commitdiff
|
tree
2019-10-15
S
zilá
r
d Páll
Link GPU c
o
ordi
n
ate produ
c
er
and consu
m
er t
a
sks
commit
|
commitdiff
|
tree
2019-10-13
S
zilárd Páll
Enable S
t
a
te
P
ropagatorGpuData
f
or force tra
n
sf
e
rs
commit
|
commitdiff
|
tree
2019-10-13
Sz
i
lá
r
d Páll
Mo
v
e
buffer ops / PME F redu
c
tion fla
g
s
into StepWorkload
commit
|
commitdiff
|
tree
2019-10-10
Szilárd
P
áll
Migrat
e
code to usin
g
Si
m
ulationWorkload
fla
g
s
commit
|
commitdiff
|
tree
2019-10-10
Sz
i
lárd Páll
Remove inco
r
r
e
ct GPU task dependency
commit
|
commitdiff
|
tree
2019-10-10
S
zilár
d
P
á
ll
F
ix cond
i
ti
o
n
s
for buildin
g
StatePropagato
r
Data
G
pu
commit
|
commitdiff
|
tree
2019-10-10
Sz
i
l
á
rd P
á
l
l
Construc
t
a stru
c
t
with d
e
ve
l
opment feature
f
lags
commit
|
commitdiff
|
tree
2019-10-10
Szilár
d
Páll
Pass list of
EventSynchro
n
i
z
ers to GPU
r
educ
t
ion
commit
|
commitdiff
|
tree
2019-10-10
Szilárd
Páll
Add ma
n
age
m
ent for coordinates copy events into S
t
atePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Szilárd P
á
ll
Add GPU eve
n
t
t
o m
a
rk that coordinate update is done
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
Move PME GPU program bu
i
ldin
g
late
r
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Páll
M
a
ke the
wait on
P
ME GPU
result
s
co
n
ditional
commit
|
commitdiff
|
tree
2019-09-27
S
zilárd
P
áll
Switch GPU update off by default
commit
|
commitdiff
|
tree
2019-09-25
Szilá
r
d Páll
Merge remote-tracking branch '
o
rig
i
n/release-2019'
commit
|
commitdiff
|
tree
2019-09-18
Szilárd Páll
Set up wor
k
load
d
a
ta structu
r
e
s
commit
|
commitdiff
|
tree
2019-09-16
Szilárd Páll
Refacto
r
GPU buf op
s
-
related
l
a
u
nches
i
n
d
o_force(
)
commit
|
commitdiff
|
tree
2019-09-16
Szilár
d
Páll
Eliminate unnec
e
ssa
r
y G
P
U
stream d
e
pendency call
commit
|
commitdiff
|
tree
2019-09-13
Sz
i
lárd Páll
Fix GPU X buffer ops wit
h
e
mpty domain
commit
|
commitdiff
|
tree
2019-09-12
Szilárd
P
áll
R
e
organi
z
e on-GPU
P
M
E force reducti
o
n flag ha
n
dling
commit
|
commitdiff
|
tree
2019-09-11
S
z
il
á
rd Páll
Fix gpucomm matrix
commit
|
commitdiff
|
tree
2019-09-10
Szilárd P
á
l
l
Eliminate
r
a
w
force flag
s
in d
o
_
force_lowle
v
el()
commit
|
commitdiff
|
tree
2019-09-10
Szilár
d
Páll
Use
t
h
r
ead-
M
PI
in the
g
pucom
m
matrix
commit
|
commitdiff
|
tree
2019-09-09
Szilárd Páll
As
s
ert t
h
e types of OpenCL kerne
l
s
argument
s
commit
|
commitdiff
|
tree
2019-09-09
Szilárd P
á
ll
Pass
gmx::Forc
e
Flags to CPU n
b
nxm disp
a
t
ch code
commit
|
commitdiff
|
tree
2019-09-09
Szi
l
á
rd P
á
l
l
Pass the new gmx::ForceFlags
t
o
the nbnxm m
o
du
l
e
commit
|
commitdiff
|
tree
2019-09-06
Szilárd
P
ál
l
Add
g
puup
d
ate and gp
u
comm OnDemand tokens
commit
|
commitdiff
|
tree
2019-09-04
Szi
l
árd Páll
Bump ARM HP
C
toolchain in post-s
u
bmit to
v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
S
z
ilárd Pál
l
Add ba
c
k a clan
g
-t
i
dy except
i
on
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
C
e
n
tralize more MD
/
fo
r
ce
s
hedule flag
s
commit
|
commitdiff
|
tree
2019-08-28
Szi
l
árd
Páll
Add clang-tidy n
i
ghtly test
with SIMD + OpenCL
commit
|
commitdiff
|
tree
2019-08-28
Szilár
d
P
áll
M
o
ve
n
o
nbonded GPU wai
t
timing into the GPU modu
l
e
commit
|
commitdiff
|
tree
2019-08-25
Sz
i
lárd Páll
cl
a
ng-t
i
dy
8
fixes for
t
he
GPU host code-path
commit
|
commitdiff
|
tree
2019-08-25
Sz
i
lárd Páll
Further
f
ixe
s
for clang-ti
d
y clang ve
r
sion
8
commit
|
commitdiff
|
tree
2019-08-23
Szilárd
Páll
Fix clang-t
i
dy warning
s
in
the Ope
n
CL bu
i
ld
commit
|
commitdiff
|
tree
2019-08-23
Szilárd Páll
Fix
c
lan
g
t
idy
warnings in CUDA build
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
Bump clang-cuda post-s
u
bmit
c
ompiler/CUDA version
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
Sw
i
tch to
A
RM HPC to
o
lcha
i
n v19
.
2
i
n
post-su
b
mit
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Páll
W
o
rk
around clang
CU
D
A d
e
vic
e
co
d
e codegen
b
ug
commit
|
commitdiff
|
tree
2019-08-16
S
z
i
l
árd
P
á
l
l
Fix
sim_util
.
cpp copyright header
commit
|
commitdiff
|
tree
2019-08-15
S
zilárd Páll
Fix Op
e
nCL
g
a
ther red
u
ction
commit
|
commitdiff
|
tree
2019-08-12
Szilárd Páll
Fix hwloc
find packag
e
na
m
ing an
d
q
u
ietness i
s
sues
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
Páll
Sto
r
e
w
c
y
cle p
o
i
nter
i
n
n
onbonded_verl
e
t_t
commit
|
commitdiff
|
tree
2019-07-31
S
z
ilárd Páll
Fix
e
s for F buffer ops
c
h
a
nge
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
Páll
Mov
e
cycle
c
ountin
g
into t
h
e GPU bond
e
d mod
u
le
commit
|
commitdiff
|
tree
2019-07-31
S
z
i
l
árd
P
á
l
l
R
eport when development fea
t
ure fl
a
gs a
r
e used
commit
|
commitdiff
|
tree
2019-07-31
Szilár
d
Páll
Move end of step GPU task launches to a fu
n
c
t
ion
commit
|
commitdiff
|
tree
2019-07-25
Szilár
d
Pál
l
Only
s
top the CUDA
p
rofiler i
f
there are devices
commit
|
commitdiff
|
tree
2019-07-22
Szilárd Páll
Conditionally
p
in GPU-related grid
dat
a
commit
|
commitdiff
|
tree
2019-07-11
Szi
l
árd Páll
U
se HostVector for
G
r
id/GridSet data need on-GPU
commit
|
commitdiff
|
tree
2019-07-08
Szilá
r
d Páll
Elimi
n
ate
a
u
s
e
of double precision in the G
P
U bonded
.
.
.
commit
|
commitdiff
|
tree
2019-07-04
Szi
l
árd Pá
l
l
Bump latest CUDA + gcc
in
t
he
pre-submit matrix
commit
|
commitdiff
|
tree
2019-07-04
Szilárd Páll
Fix a
-Wformat-trunca
t
ion
warning in tng
commit
|
commitdiff
|
tree
2019-07-01
Szilárd
Páll
Refactor tracking of GPU sho
r
t
-
ran
g
e
work
/
s
kipping
commit
|
commitdiff
|
tree
2019-06-30
Szi
l
á
r
d Páll
Cre
a
t
e
dedicated s
u
bcounter
f
or nonbonded F
E
P
commit
|
commitdiff
|
tree
2019-06-28
Szilár
d
P
á
ll
Sepa
r
ate CPU NB
k
e
rnel
and
b
uffe
r
cleari
n
g subcounter
s
commit
|
commitdiff
|
tree
2019-06-27
Szilárd Pá
l
l
Re
m
o
v
e al
r
e
a
dy resolved
p
o
s
t-submit ma
t
rix TODO
commit
|
commitdiff
|
tree
2019-06-24
Szilárd Páll
Only us
e
AVX512 in
own-FFTW if GROMACS also uses it
commit
|
commitdiff
|
tree
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