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Improve mdrun performance user guide
2020-01-10
Szilárd Páll
I
mpro
v
e mdru
n
pe
r
forma
n
ce user
g
ui
d
e
commit
|
commitdiff
|
tree
2019-12-20
Szilá
r
d Pá
l
l
Enable
buffer ops whe
n
G
MX_GPU_DD_COMMS is set
commit
|
commitdiff
|
tree
2019-12-19
Szilárd Pál
l
PP-PME loa
d
ba
l
ancing impr
o
v
e
ments
commit
|
commitdiff
|
tree
2019-12-18
Szilárd
Páll
Allow x D2H
t
o overlap with GPU force compute
commit
|
commitdiff
|
tree
2019-12-17
Szi
l
ár
d
Páll
Comment th
e
use of waitCoordi
n
a
tesCopiedToDe
v
ice
commit
|
commitdiff
|
tree
2019-12-17
Szilárd Páll
Add
wallc
y
c
l
e
counting t
o
StatePr
o
pagat
o
r
D
ataGpu
commit
|
commitdiff
|
tree
2019-12-16
Sz
i
lárd Pá
l
l
Fix the GP
U
bonded
s
tre
a
m with 1 PP + 1 PME rank
commit
|
commitdiff
|
tree
2019-12-12
Szilárd Páll
A
llow overl
a
pping CPU force H
2
D w
i
th comp
u
te
commit
|
commitdiff
|
tree
2019-11-17
S
zilárd
Pál
l
Trigger
o
cl_nbnxm_kerne
l
s target with clang-tidy
commit
|
commitdiff
|
tree
2019-11-17
Szi
l
á
r
d P
á
ll
Fix clang-tidy 8
war
n
ing
s
in OpenCL nbnxm kern
e
ls
commit
|
commitdiff
|
tree
2019-11-03
Szilá
r
d Páll
I
m
prove
S
imulationW
o
rkload doxyg
e
n
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
Ren
a
me refer
e
nce checksum generating target
commit
|
commitdiff
|
tree
2019-11-01
Sz
i
lárd Pá
l
l
U
s
e "-"
in checksum-r
e
la
t
ed version su
f
fix
commit
|
commitdiff
|
tree
2019-11-01
Szilárd Páll
Im
p
r
ove
w
orkload dat
a
structures' docs
commit
|
commitdiff
|
tree
2019-10-28
Szilárd Páll
Extend SimulationWorkload wi
t
h CPU
f
lags
commit
|
commitdiff
|
tree
2019-10-21
Szilárd Páll
Remove un
s
upported configs from t
h
e gpu
u
pdate ma
t
rix
commit
|
commitdiff
|
tree
2019-10-21
Szil
á
rd Páll
Over
r
ide GMX_G
P
U_DD
_
COMMS if n
o
nbondeds a
r
e
off
commit
|
commitdiff
|
tree
2019-10-18
Szilárd Páll
Add
s
t
rict assertions on x synchronizer in PME
commit
|
commitdiff
|
tree
2019-10-18
Szilárd Pá
l
l
Fix
genion clang-8 warni
n
g
commit
|
commitdiff
|
tree
2019-10-17
Szilárd
P
áll
Fix clang-tid
y
warni
n
gs in g
p
uhaloexchange_impl
.
cuh
commit
|
commitdiff
|
tree
2019-10-17
Szilá
r
d
Páll
Eliminate spurio
u
s GPU->
C
P
U copy
commit
|
commitdiff
|
tree
2019-10-17
Szilárd Páll
Di
s
a
ble GMX_GPU
_
PME_PP_COMMS if PME
i
s not
o
ffl
o
aded
commit
|
commitdiff
|
tree
2019-10-16
Szilárd
P
á
l
l
Fi
x
initia
l
ization of fie
l
d i
n
P
ME data
str
u
c
ture
commit
|
commitdiff
|
tree
2019-10-16
Szilárd Pá
l
l
Ma
k
e
t
he wait on non
b
onded G
P
U results cond
i
ti
o
nal
commit
|
commitdiff
|
tree
2019-10-15
S
zilárd Páll
Trigger synchro
n
izer when l
o
cal forc
e
s are
ready
commit
|
commitdiff
|
tree
2019-10-15
Szilá
r
d Páll
Lin
k
GPU coordinate producer and
consumer tasks
commit
|
commitdiff
|
tree
2019-10-13
S
zilárd Páll
E
n
able StateP
r
opagatorGpuD
a
ta for
f
orc
e
transfers
commit
|
commitdiff
|
tree
2019-10-13
Szilár
d
Páll
M
ove b
u
f
fer
o
ps / PME F redu
c
tion flags
i
nt
o
StepWo
r
kload
commit
|
commitdiff
|
tree
2019-10-10
S
zilárd Páll
Migrate code to using Simulat
i
onWorkload flag
s
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Pál
l
R
emove incorrect
GPU task depende
n
cy
commit
|
commitdiff
|
tree
2019-10-10
Szi
l
ár
d
Páll
F
ix conditions for
b
uilding
S
t
atePro
p
agatorDataGpu
commit
|
commitdiff
|
tree
2019-10-10
Szilárd
P
á
ll
Constru
c
t a struct with develo
p
ment feature flag
s
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Pál
l
P
ass list of Eve
n
tSynchroniz
e
rs to GPU reduction
commit
|
commitdiff
|
tree
2019-10-10
S
zilá
r
d
Pá
l
l
A
d
d management
f
or coordinates cop
y
events into StatePropaga
.
.
.
commit
|
commitdiff
|
tree
2019-10-09
Szil
á
rd P
á
l
l
Add GP
U
even
t
to mark th
a
t coordinate update i
s
done
commit
|
commitdiff
|
tree
2019-09-30
Szilá
r
d Páll
M
ove PME G
P
U program building later
commit
|
commitdiff
|
tree
2019-09-30
Szilárd Pál
l
Ma
k
e the wait
on PME GPU r
e
sults c
o
ndition
a
l
commit
|
commitdiff
|
tree
2019-09-27
Szi
l
árd Páll
Swi
t
c
h
GPU
update off by default
commit
|
commitdiff
|
tree
2019-09-25
S
zil
á
rd Páll
M
erge remote-tracking branch 'origin/release-20
1
9'
commit
|
commitdiff
|
tree
2019-09-18
Szil
á
r
d
P
áll
Set
up
w
orkload data structu
r
es
commit
|
commitdiff
|
tree
2019-09-16
S
zilá
r
d Páll
Refact
o
r GPU buf ops-related launches
i
n do_force()
commit
|
commitdiff
|
tree
2019-09-16
Szilárd
P
áll
E
limin
a
te unnec
e
s
sa
r
y GPU stream
d
epende
n
cy call
commit
|
commitdiff
|
tree
2019-09-13
Szilárd Páll
Fix
GPU X
b
u
f
fer
o
p
s
w
ith empty domain
commit
|
commitdiff
|
tree
2019-09-12
Szilárd Pá
l
l
Reorgani
z
e on-GPU
P
ME
force
r
educt
i
on flag h
a
ndli
n
g
commit
|
commitdiff
|
tree
2019-09-11
Szilá
r
d Páll
Fix gpucom
m
ma
t
rix
commit
|
commitdiff
|
tree
2019-09-10
Szilárd Páll
Eliminate raw for
c
e
f
l
a
gs in
d
o_for
c
e_
l
o
w
level(
)
commit
|
commitdiff
|
tree
2019-09-10
Szi
l
árd
P
áll
Use
t
h
read-MP
I
in th
e
gpucomm matrix
commit
|
commitdiff
|
tree
2019-09-09
S
z
ilárd
Páll
A
sse
r
t
the type
s
of
O
p
e
nCL kernels argume
n
ts
commit
|
commitdiff
|
tree
2019-09-09
S
zil
á
rd Páll
Pa
s
s gmx::For
c
eFlags to
C
PU nb
n
xm
dispatc
h
code
commit
|
commitdiff
|
tree
2019-09-09
Szilárd P
á
l
l
Pass the new g
m
x
::Forc
e
Flags to t
h
e nbnxm module
commit
|
commitdiff
|
tree
2019-09-06
Szilár
d
P
á
ll
Add gpuupdate and g
p
ucomm
O
nDemand tokens
commit
|
commitdiff
|
tree
2019-09-04
Szi
l
árd Pá
l
l
B
ump ARM
H
PC toolchain i
n
post-su
b
mit t
o
v19
.
3
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
Add
bac
k
a
clan
g
-tidy exce
p
tion
commit
|
commitdiff
|
tree
2019-09-04
Szilárd Pá
l
l
Cent
r
alize m
o
re M
D
/force shedule flags
commit
|
commitdiff
|
tree
2019-08-28
Szi
l
ár
d
P
áll
Add clang-tidy nightly test
with SIMD
+ OpenCL
commit
|
commitdiff
|
tree
2019-08-28
Szi
l
ár
d
Páll
Move no
n
bonded GPU
wait timing into
t
he
GPU module
commit
|
commitdiff
|
tree
2019-08-25
Szi
l
árd Páll
clan
g
-tidy 8 fixes for the
GPU h
o
st
c
o
de-path
commit
|
commitdiff
|
tree
2019-08-25
Szilárd Pá
l
l
Furt
h
er fixes
for cla
n
g-t
i
dy clang version 8
commit
|
commitdiff
|
tree
2019-08-23
Szilárd Páll
Fix clang-tidy warnin
g
s in the OpenCL bu
i
ld
commit
|
commitdiff
|
tree
2019-08-23
Szilárd Páll
F
ix clang tidy warnin
g
s in CUDA build
commit
|
commitdiff
|
tree
2019-08-19
Szilá
r
d Páll
Bum
p
clang-
c
uda post-subm
i
t compiler/CUDA version
commit
|
commitdiff
|
tree
2019-08-19
Szilárd Pál
l
Switch to ARM HP
C
toolchain v19
.
2 in post-submit
commit
|
commitdiff
|
tree
2019-08-19
Szil
á
rd Pál
l
W
o
rk ar
o
und clang CUDA device code
c
odegen
b
u
g
commit
|
commitdiff
|
tree
2019-08-16
Szilárd Páll
Fix
sim_util
.
c
pp copyright header
commit
|
commitdiff
|
tree
2019-08-15
Sz
i
lárd Páll
Fix O
p
enCL gather reduction
commit
|
commitdiff
|
tree
2019-08-12
S
zilárd P
á
ll
Fix hwloc find pack
a
g
e nami
n
g and qui
e
tne
s
s
i
ssue
s
commit
|
commitdiff
|
tree
2019-07-31
S
z
ilárd Páll
Store wcycl
e
pointer in no
n
bon
d
ed_verlet_t
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Páll
Fixes for F bu
f
fer ops
c
hange
commit
|
commitdiff
|
tree
2019-07-31
S
z
ilá
r
d Páll
Move
cyc
l
e counting into the GPU
bo
n
ded module
commit
|
commitdiff
|
tree
2019-07-31
S
z
ilá
r
d P
á
l
l
Re
p
ort wh
e
n developme
n
t fe
a
ture flags are u
s
ed
commit
|
commitdiff
|
tree
2019-07-31
S
zilárd Páll
M
ove
end of s
t
ep
G
PU task
l
a
unches to a function
commit
|
commitdiff
|
tree
2019-07-25
Szilárd Páll
O
nly stop the CUDA profiler if there are devices
commit
|
commitdiff
|
tree
2019-07-22
Szilárd Páll
C
o
n
dit
i
onally pin G
P
U
-related g
r
id data
commit
|
commitdiff
|
tree
2019-07-11
Szilárd
P
áll
U
s
e Hos
t
Vector for
Grid/
G
ridSet data
n
ee
d
o
n
-GPU
commit
|
commitdiff
|
tree
2019-07-08
Szil
á
rd Páll
Eliminate a us
e
of do
u
ble pre
c
i
sion in t
h
e
GPU bonded
.
.
.
commit
|
commitdiff
|
tree
2019-07-04
Szi
l
árd Páll
B
u
mp latest CUDA + gcc
i
n the pre-submit matrix
commit
|
commitdiff
|
tree
2019-07-04
Szil
á
rd
Páll
F
i
x
a -Wformat-truncati
o
n wa
r
ning in
tng
commit
|
commitdiff
|
tree
2019-07-01
S
z
ilár
d
Páll
Refa
c
tor t
r
acking o
f
GPU
short
-
range work/skipping
commit
|
commitdiff
|
tree
2019-06-30
Szilár
d
Páll
Cr
e
ate
dedi
c
a
ted
subcounter for nonbon
d
ed
F
EP
commit
|
commitdiff
|
tree
2019-06-28
Szilárd
P
áll
Separate
CPU N
B
kerne
l
and buffer c
l
earing subcoun
t
ers
commit
|
commitdiff
|
tree
2019-06-27
Szilá
r
d Páll
Rem
o
ve
already resolved p
o
st-submit
m
atrix TODO
commit
|
commitdiff
|
tree
2019-06-24
S
z
i
lárd Pá
l
l
Only use AVX512 in own-FFTW if GROMACS also u
s
es it
commit
|
commitdiff
|
tree
2019-06-19
Szilárd Páll
Disable PME GPU on Apple Ope
n
CL
commit
|
commitdiff
|
tree
2019-05-29
Szilárd Páll
T
e
mplate x buffer ops call o
n
whether GPU is
used
commit
|
commitdiff
|
tree
2019-05-23
Sz
i
lá
r
d Páll
Fix
m
ulit
p
le link refs in dev-manu
a
l
commit
|
commitdiff
|
tree
2019-05-20
Sz
i
lárd
Páll
Improve X
b
uffer ops k
e
rnel
commit
|
commitdiff
|
tree
2019-04-25
Szilárd Páll
Fix clang war
n
ing abo
u
t NULL use
commit
|
commitdiff
|
tree
2019-04-25
Szilár
d
P
á
ll
Avoid u
s
i
n
g AtomL
o
cality::Count a
s
a val
i
d value
commit
|
commitdiff
|
tree
2019-04-24
Sz
i
l
á
r
d Páll
Fix
C
UDA fallback shmem gather redu
c
tion
commit
|
commitdiff
|
tree
2019-04-18
Szilá
r
d Páll
Fix wa
r
nin
g
s & conso
l
idate decla
r
ations
commit
|
commitdiff
|
tree
2019-04-16
Szilárd
Páll
Mov
e
functions operating on ene
r
data
out of for
c
e
.
cpp
commit
|
commitdiff
|
tree
2019-04-16
Szilárd Páll
R
emove "coarse load balanc
i
ng
v
ars" from
forcerec
commit
|
commitdiff
|
tree
2019-04-16
S
zilár
d
Páll
Grou
p
scheme r
e
l
a
ted cleanup
commit
|
commitdiff
|
tree
2019-04-16
Szilárd Pál
l
Remove Group sc
h
eme
n
e
ighbor search wrapper
commit
|
commitdiff
|
tree
2019-04-15
Szilárd Páll
Add user
guide
not
e
on AVX512 throttle in G
P
U
r
uns
commit
|
commitdiff
|
tree
2019-04-05
S
z
ilárd Páll
Revert "Tempora
r
ily d
i
sab
l
e AR
M
H
P
C
c
ompiler in post
.
.
.
commit
|
commitdiff
|
tree
2019-04-05
Szilárd Pál
l
Rev
e
rt
"
Temporarily dis
a
ble ARM HPC c
o
m
p
iler
in
p
ost
.
.
.
commit
|
commitdiff
|
tree
2019-04-02
Szilárd Páll
Tempo
r
ari
l
y dis
a
ble
A
RM H
P
C compiler
in post-submit
commit
|
commitdiff
|
tree
2019-04-02
Szilárd
Páll
Temporarily
d
isable
A
RM H
P
C c
o
mpiler in post-su
b
m
i
t
commit
|
commitdiff
|
tree
2019-03-28
Szilár
d
Páll
Better
d
ocum
e
nt
G
M
X_OPENMP_MAX_THRE
A
DS
commit
|
commitdiff
|
tree
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