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Improve mdrun performance user guide
2020-01-10
Szilárd
P
áll
Im
p
rove mdrun
performance user g
u
i
d
e
commit
|
commitdiff
|
tree
2019-12-04
C
hris
t
i
a
n Blau
Remove cutoff-sc
h
eme group fro
m
defa
u
lt mdout
.
m
d
p output
commit
|
commitdiff
|
tree
2019-10-31
Berk Hess
U
pdate GPU upda
t
e restrictions
commit
|
commitdiff
|
tree
2019-10-30
Jonathan Vincent
Up
d
ate
PME
CUDA spread/gather
commit
|
commitdiff
|
tree
2019-10-29
Artem
Z
hmu
r
ov
Switch the G
P
U
buffer o
p
s
o
n when up
d
ate is on GPU
commit
|
commitdiff
|
tree
2019-10-28
A
rtem Zhm
u
rov
Fix miss
i
n
g
coordinate D2H copy with GPU update and
.
.
.
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem Zhmurov
Add hav
e
CpuLocalForces flag to DomainLif
e
time
W
orkloa
d
commit
|
commitdiff
|
tree
2019-10-28
A
r
tem
Zh
m
urov
Allow using up
d
a
te flag
commit
|
commitdiff
|
tree
2019-10-22
Artem Zh
m
urov
Re
m
ove
unnecessar
y
CUDA stream
sync
h
r
onizatio
n
calls
commit
|
commitdiff
|
tree
2019-10-22
Ar
t
em Zhmurov
R
ename hav
e
PositionRestr
a
ints(
.
.
.
) to haveR
e
str
a
in
t
s
.
.
.
commit
|
commitdiff
|
tree
2019-10-21
Szi
l
árd
Páll
Remove
unsup
p
orted confi
g
s
from the gpuu
p
dat
e
m
a
trix
commit
|
commitdiff
|
tree
2019-10-21
Ala
n
Gray
GPU
Coordinate P
M
E/PP
Communications
commit
|
commitdiff
|
tree
2019-10-18
Alan Gr
a
y
G
P
U Receive for PME/PP GPU Force Communicatio
n
s
commit
|
commitdiff
|
tree
2019-10-18
P
a
ul Bauer
U
s
e
clang-
t
idy-8
commit
|
commitdiff
|
tree
2019-10-17
S
z
ilárd Páll
Fix clang-tid
y
warnin
g
s
i
n gpuhaloexcha
n
g
e
_i
m
pl
.
cuh
commit
|
commitdiff
|
tree
2019-10-15
Szil
á
rd Páll
Trigger synch
r
on
i
z
e
r when
local forces
are re
a
d
y
commit
|
commitdiff
|
tree
2019-10-15
A
rtem
Zhmur
o
v
Fi
x
the single-GPU update-
c
onstraint
s
commit
|
commitdiff
|
tree
2019-10-10
S
z
ilár
d
Páll
Fix condition
s
f
or building StatePro
p
a
ga
t
orDataGp
u
commit
|
commitdiff
|
tree
2019-10-10
Szilárd Páll
C
o
ns
t
ru
c
t a s
t
ruct wit
h
developmen
t
fe
a
t
ure flags
commit
|
commitdiff
|
tree
2019-10-03
Ber
k
Hess
F
i
x GPU atom
d
at
a
ini
t
timer issue
commit
|
commitdiff
|
tree
2019-10-02
Arte
m
Zhmur
o
v
Eliminate D2D copy in update
c
o
nstraints
commit
|
commitdiff
|
tree
2019-09-25
Szil
á
rd Páll
Merge remote
-
tracking branch 'origin/release-2019'
commit
|
commitdiff
|
tree
2019-09-18
Szilárd Páll
Se
t
up workload data stru
c
tures
commit
|
commitdiff
|
tree
2019-09-18
P
a
ul Bau
e
r
Fix MSVC war
n
i
n
g
commit
|
commitdiff
|
tree
2019-09-17
Pa
u
l Bauer
Add deprecation
n
ote for 32 bit
commit
|
commitdiff
|
tree
2019-09-16
Szilárd
P
áll
Re
f
acto
r
GPU buf ops-related launches in do_force()
commit
|
commitdiff
|
tree
2019-09-13
Sz
i
lárd Páll
Fix
G
PU X bu
f
fer ops
with empty domain
commit
|
commitdiff
|
tree
2019-09-11
Artem
Zhmurov
D
eco
u
ple coor
d
in
a
t
es buffer mana
g
ement f
r
om bu
f
f
er
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
A
r
tem Zh
m
u
rov
Reorganize PME code:
commit
|
commitdiff
|
tree
2019-09-11
Szilárd Páll
F
ix gpucomm matrix
commit
|
commitdiff
|
tree
2019-09-06
Mark A
b
ra
h
am
C
l
ean up commrec un
i
formly
commit
|
commitdiff
|
tree
2019-09-04
Berk
H
ess
C
o
ll
e
ct setting
s
for DD in DDSett
i
ngs
commit
|
commitdiff
|
tree
2019-09-03
Berk H
e
ss
R
e
move
gmx_do
m
dec
_
t from dd_ch
o
o
s
e
_
gri
d
()
commit
|
commitdiff
|
tree
2019-09-03
Berk
H
ess
Extact UnitCellInfo from gmx_domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Mark Ab
r
aha
m
Move initializatio
n
of clFFT
commit
|
commitdiff
|
tree
2019-08-26
Mark Abraham
C
o
nverted a C
U
DA config to use clang host-on
l
y comp
i
lation
commit
|
commitdiff
|
tree
2019-08-23
Szilárd Páll
Fi
x
cl
a
ng tid
y
warnings
i
n CUDA bu
i
l
d
commit
|
commitdiff
|
tree
2019-08-21
Ma
r
k Abra
h
am
I
m
p
rove organization of
LINCS reporting
commit
|
commitdiff
|
tree
2019-08-15
Alan Gray
PME reduct
i
o
n
f
or CUDA F buff
e
r o
p
eration
s
commit
|
commitdiff
|
tree
2019-08-12
Szilárd Pá
l
l
Fix
h
w
loc find package naming and
quietness
i
ssues
commit
|
commitdiff
|
tree
2019-07-26
Berk
H
es
s
R
e
move sh_i
n
vrc6 from interactio
n
_const_t
commit
|
commitdiff
|
tree
2019-07-19
A
la
n
Gray
F b
u
ffer oper
a
ti
o
ns in C
U
DA
commit
|
commitdiff
|
tree
2019-07-16
Mark Abraham
Add gpubufferops test
m
a
tri
x
commit
|
commitdiff
|
tree
2019-07-11
Sz
i
lárd Pá
l
l
Use HostVect
o
r fo
r
Grid/GridSet
data need on-GPU
commit
|
commitdiff
|
tree
2019-07-04
Szilárd Pál
l
Bu
m
p
latest C
U
DA + gcc in the pre-s
u
bmit matrix
commit
|
commitdiff
|
tree
2019-07-04
Szil
á
rd Páll
F
i
x a -Wforma
t
-truncation warning in tng
commit
|
commitdiff
|
tree
2019-07-01
A
l
an Gray
Bug f
i
x
and sim
p
l
i
f
i
cation f
o
r CUDA X Buf
f
er Ops
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simplify GPU nbnxm
x c
o
nversion
commit
|
commitdiff
|
tree
2019-05-22
Al
a
n Gr
a
y
Code qu
a
l
i
ty improvement
s
for CUDA positio
n
buffer
op
s
commit
|
commitdiff
|
tree
2019-05-20
Szilá
r
d Páll
Improve X buffer ops kernel
commit
|
commitdiff
|
tree
2019-05-10
Alan Gray
Position buffer ops i
n
CUDA
commit
|
commitdiff
|
tree
2019-03-27
B
e
rk Hess
Fix
n
bnxm O
p
enC
L
with cl
u
st
e
r size
4
commit
|
commitdiff
|
tree
2019-02-07
Szilárd
Páll
Require a 64-bit pl
a
tfor
m
for OpenCL
commit
|
commitdiff
|
tree
2019-01-18
M
a
rk
A
braha
m
I
m
prove nvcc error reporting
commit
|
commitdiff
|
tree
2019-01-02
Szilárd Páll
Fix cl
a
ng 6 warning
commit
|
commitdiff
|
tree
2018-12-31
Szil
á
r
d
Páll
Fix
release n
o
tes typo
commit
|
commitdiff
|
tree
2018-12-20
S
z
ilárd Páll
Merge "Me
r
ge
branch relea
s
e
-
20
1
8 into release-2019
.
.
.
commit
|
commitdiff
|
tree
2018-12-18
Szil
á
r
d
Páll
M
e
rg
e
relea
s
e-2019 br
a
nch
into master
commit
|
commitdiff
|
tree
2018-12-18
Berk Hes
s
Use std::
v
ect
o
r
i
n L
I
N
CS
commit
|
commitdiff
|
tree
2018-12-17
Szilá
r
d Páll
Fix GMX_
B
UILD
_
OWN_FFTW_URL
C
Mak
e
cache entry
t
ype
commit
|
commitdiff
|
tree
2018-12-17
Paul
B
aue
r
Add ma
t
rix entry to test exter
n
a
l
F
F
T
W
b
uil
d
commit
|
commitdiff
|
tree
2018-12-17
P
a
ul B
a
uer
Fix F
F
T
W build
commit
|
commitdiff
|
tree
2018-12-13
Szilárd Páll
A
v
oid spurious timin
g
in
bo
n
ded GPU launch subcounter
commit
|
commitdiff
|
tree
2018-11-26
Mark A
b
raham
C
lean
u
p initial log out
p
ut
commit
|
commitdiff
|
tree
2018-11-22
Mark Abraham
Int
r
odu
c
e
PpForceWorkload
commit
|
commitdiff
|
tree
2018-11-07
S
z
ilárd Páll
Re
-
enable the armclang po
s
t
-submit buil
d
commit
|
commitdiff
|
tree
2018-11-07
Mark Abraham
Sup
p
r
es
s
cl
a
ng warnings about QM
M
M code
commit
|
commitdiff
|
tree
2018-11-01
Mark Abraham
Stop using hwloc on old ARM slave
commit
|
commitdiff
|
tree
2018-10-31
Berk Hess
Pin impor
t
ant buffers in CUDA bondeds
commit
|
commitdiff
|
tree
2018-10-22
Mark Abraham
Fix clang CU
D
A
warnings
commit
|
commitdiff
|
tree
2018-10-14
Szilárd Páll
Fix
m
ore clang-6 warni
n
gs in CUDA code
commit
|
commitdiff
|
tree
2018-10-08
Rola
n
d Schulz
F
i
x OCL compiler warn
i
ng
s
commit
|
commitdiff
|
tree
2018-10-08
Roland Schulz
Remove
majorit
y
of
OCL comma
n
d lin
e
c
on
s
tants
commit
|
commitdiff
|
tree
2018-10-07
Szilárd Páll
Use
n
ew
G
PU slave fo
r
A
MD Op
e
n
C
L verify runs
commit
|
commitdiff
|
tree
2018-10-05
R
oland Schul
z
Fix
m
ultipl
e
b
ugs
d
etected on W
i
ndows
commit
|
commitdiff
|
tree
2018-10-04
Roland Schulz
Use subgroup for warp_a
n
y
and CJ4 prefetch
commit
|
commitdiff
|
tree
2018-10-04
Ma
r
k Abraham
R
eplace CUDA call deprec
a
t
e
d
in CUDA 1
0
commit
|
commitdiff
|
tree
2018-09-27
Roland Schul
z
Recognize Int
e
l
GPU as c
o
mpatible
commit
|
commitdiff
|
tree
2018-09-13
Roland Sch
u
lz
Remove spar
c
6
4_hpc_ace n
o
n
b
onded kernels
commit
|
commitdiff
|
tree
2018-09-07
Mark A
b
raham
M
i
no
r
fixes
t
o GPU build
system
commit
|
commitdiff
|
tree
2018-08-27
Alekse
i
I
u
pinov
Prepare pme-g
p
u-t
y
pe
s
.
h for
Open
C
L
commit
|
commitdiff
|
tree
2018-08-21
Szilárd
Páll
R
e
quest flushing denorms to
z
ero in O
p
enCL
commit
|
commitdiff
|
tree
2018-06-25
Aleksei Iupi
n
ov
Mo
v
e vectype_o
p
s
.
c
lh into gp
u
_u
t
ils
commit
|
commitdiff
|
tree
2018-06-25
Aleksei Iupinov
Move the PME GPU kernel launch functions in
t
o pme-gpu
.
.
.
commit
|
commitdiff
|
tree
2018-05-31
Aleksei
I
upinov
PME OpenCL 3D
FFT tr
a
nsf
o
rm is im
p
lemented, using clF
F
T
commit
|
commitdiff
|
tree
2018-05-30
Aleksei
I
upino
v
Make PME
GPU
s
tructures use
DeviceB
u
ffer
commit
|
commitdiff
|
tree
2018-05-29
Szilárd Pál
l
Sw
i
t
ch
t
o
C
UDA 9
.
2 +
gcc 7
commit
|
commitdiff
|
tree
2018-04-20
Szilárd Páll
Mi
n
or
f
ix f
o
r p
r
e-submit
matrix docs
commit
|
commitdiff
|
tree
2018-04-19
Szilárd
P
áll
Move th
e
P
ME GPU
c
l
earing to the
end of t
h
e
step
commit
|
commitdiff
|
tree
2018-04-18
Mark Abraham
Introduce gm
x
_used_in_
d
ebug
commit
|
commitdiff
|
tree
2018-04-13
Sz
i
lárd Páll
U
se trivalue opti
o
n for
G
MX_HWLOC
commit
|
commitdiff
|
tree
2018-03-20
Vedra
n
M
iletić
Docume
n
t matri
x
_convert f
u
nction in PB
C
commit
|
commitdiff
|
tree
2018-03-12
Szil
á
rd
Pál
l
Avoid icc-specific -march=core-av
x
2 flag with gcc/clang
commit
|
commitdiff
|
tree
2018-03-06
Szilárd Páll
Exten
d
"
F
inding out how to run mdrun bet
t
e
r" section
commit
|
commitdiff
|
tree
2018-03-06
Aleks
e
i Iupinov
Isolate PM
E
G
P
U
spline parameter indexing i
n
inline
.
.
.
commit
|
commitdiff
|
tree
2018-03-05
Alek
s
ei Iupin
o
v
Stop using cus
t
o
m FindOpenCL
.
cmake, per TODO
commit
|
commitdiff
|
tree
2018-03-05
Aleksei
Iupinov
Correct th
e
nbnxn_gp
u
_
c
ompile_ker
n
els() docs
commit
|
commitdiff
|
tree
2018-02-21
Szilárd Páll
Switch pre-subm
i
t CUDA 8
.
0 test to 9
.
0
commit
|
commitdiff
|
tree
2018-02-20
Szilár
d
Pál
l
Avoid aborting mdrun when
GPU sanity check detec
t
s
.
.
.
commit
|
commitdiff
|
tree
2018-02-18
Aleksei Iupinov
Replace *_free_bu
f
fered
calls
by f
r
eeDeviceBuffer
commit
|
commitdiff
|
tree
next