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SIMD accelerated Urey-Bradley
2017-12-05
Magnus Lundborg
SIMD acce
l
erated Urey-Bradley
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix DD
e
x
a
ct
continuat
i
on bug
commit
|
commitdiff
|
tree
2017-12-04
Mark Abra
h
am
Fix free_gpu
commit
|
commitdiff
|
tree
2017-12-04
M
a
rk
A
b
r
ah
a
m
Merge
branch release-2016
i
nto release-2018
commit
|
commitdiff
|
tree
2017-12-04
Berk
H
e
s
s
U
p
date md
r
un signal help text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Only stop at nstlist steps wit
h
-repro
d
commit
|
commitdiff
|
tree
2017-12-04
Erik Li
n
da
h
l
F
ix
c
o
m
p
i
lation issues f
o
r AVX-512
commit
|
commitdiff
|
tree
2017-11-28
Mark
A
braham
GROMACS
2018 first beta release
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refactor
nbnxn exc
l
u
sion setting
commit
|
commitdiff
|
tree
2017-11-28
E
r
ik Lind
a
hl
Improve status messag
e
s
for SIMD che
c
k
s
commit
|
commitdiff
|
tree
2017-11-27
Szilárd Pá
l
l
Time FF
T
/gather in mixe
d
mode
commit
|
commitdiff
|
tree
2017-11-27
A
l
e
ksei Iupi
n
o
v
D
i
sabl
e
fa
i
ling
s
e
par
a
t
e
PME rank tests
commit
|
commitdiff
|
tree
2017-11-27
Paul
B
auer
A
d
d GP
U
tas
k
in
f
ormatio
n
to user-gui
d
e
commit
|
commitdiff
|
tree
2017-11-24
Alekse
i
Iupi
n
ov
Enable separate
P
ME GPU rank
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Activate
m
ixed mo
d
e of PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-24
Szilárd P
á
ll
Add GP
U
shar
i
n
g
post-submit config
commit
|
commitdiff
|
tree
2017-11-24
M
ark Abra
h
am
U
p
d
a
t
e developer guide
commit
|
commitdiff
|
tree
2017-11-24
M
ark A
b
r
aham
Activate PME on GPUs
commit
|
commitdiff
|
tree
2017-11-24
A
l
eks
e
i Iupinov
Remove outdated (already
i
mp
l
e
m
en
t
e
d
) pinning T
O
DO
commit
|
commitdiff
|
tree
2017-11-24
Ma
r
k Abraham
A
d
d PME inte
g
ra
t
ion
test
commit
|
commitdiff
|
tree
2017-11-24
Mark Abr
a
ham
Ex
t
end task as
s
i
gnment
c
ode
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Mention gmx_
i
nstall_head
e
rs() in the developer manual
commit
|
commitdiff
|
tree
2017-11-24
Aleksei Iupinov
Make FFT r
e
al-sp
a
ce g
r
id use CUDA pinning
for
m
i
x
ed
.
.
.
commit
|
commitdiff
|
tree
2017-11-24
Al
e
ksei Iup
i
no
v
Pin coordin
a
tes
,
forces
a
nd
c
harges for PME on GPU
commit
|
commitdiff
|
tree
2017-11-22
Pascal Merz
P
ro
o
f of conc
e
pt: Physical v
a
lidation suite
commit
|
commitdiff
|
tree
2017-11-21
E
rik Lindahl
Separate SI
M
D flag detection
from
m
a
n
ageme
n
t
commit
|
commitdiff
|
tree
2017-11-21
Mar
k
Abraham
Support pin
n
in
g
in Hos
t
A
llocator
commit
|
commitdiff
|
tree
2017-11-21
Viveca Lindah
l
Add
force co
r
r
ela
t
ion to AWH modu
l
e
commit
|
commitdiff
|
tree
2017-11-21
P
a
ul
Baue
r
Fi
r
st general
a
dditions to
t
h
e docu
m
entation
commit
|
commitdiff
|
tree
2017-11-19
Viveca Lindahl
Add AWH
s
ection to manual
.
commit
|
commitdiff
|
tree
2017-11-19
Viv
e
ca Lindahl
Add AWH biasing modul
e
+ tests
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
U
s
e Host
A
llocationPoli
c
y for chargeA
commit
|
commitdiff
|
tree
2017-11-17
Mark Abraham
A
dd checking
f
u
n
ction f
o
r whether a b
u
f
f
er is pinned
commit
|
commitdiff
|
tree
2017-11-17
Mark
A
braham
Improv
e
handlin
g
of PME G
P
U
force buff
e
r
commit
|
commitdiff
|
tree
2017-11-15
Aleksei Iupin
o
v
R
e
name an
d
expos
e
"ge
n
er
i
c" GPU m
e
mory transfer functions
commit
|
commitdiff
|
tree
2017-11-10
Mark Abrah
a
m
I
m
port cmake Modules/FindCUDA
.
cmake
commit
|
commitdiff
|
tree
2017-11-09
Aleksei Iupinov
Rename sync
h
ronous
G
P
U
tr
a
nsfer functions to m
a
tch
.
.
.
commit
|
commitdiff
|
tree
2017-11-09
Mark Ab
r
aham
Prepared
t_mdato
m
s for using vect
o
r
commit
|
commitdiff
|
tree
2017-11-09
Mark Abra
h
am
Introduce HostAlloca
t
i
onPolicy
commit
|
commitdiff
|
tree
2017-11-09
Roland Schulz
ICC
s
ho
u
ld use ZM
M
if code anyh
o
w uses ZMM
commit
|
commitdiff
|
tree
2017-11-07
Ma
r
k Ab
r
aha
m
Reform gmx
_
pme_p
p
allo
c
and
use vector
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Introduce gmxopencl
.
h
commit
|
commitdiff
|
tree
2017-11-07
Mark Abraham
Test clang on ARM
i
n nightly matr
i
x
commit
|
commitdiff
|
tree
2017-11-07
Szilárd
P
á
ll
A
dd wallcycle ti
m
er
for
t
h
e P
M
E
GPU F reduction
commit
|
commitdiff
|
tree
2017-11-07
Szilárd Páll
Split off nbnxn G
P
U timing a
n
d staging reduction
commit
|
commitdiff
|
tree
2017-11-07
Mark Abra
h
am
I
m
prove PME includes
commit
|
commitdiff
|
tree
2017-11-07
S
zil
á
rd Páll
D
edupl
i
cate
CUDA and OpenCL timer stru
c
t
commit
|
commitdiff
|
tree
2017-11-06
Da
v
id van der Spoel
Fixed check for water in gen_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-03
Mark Abraham
Merge "M
e
rge
b
ranch relea
s
e
-2016"
commit
|
commitdiff
|
tree
2017-11-02
David
v
an der Spoel
New
mdp
input fo
r
electric fields
.
commit
|
commitdiff
|
tree
2017-11-02
Aleksei Iupin
o
v
Replace math
.
h by
c
m
ath in
c
l
u
des
i
n
cpp
f
iles
commit
|
commitdiff
|
tree
2017-11-02
Mark Abraham
Merge branch release-2016
commit
|
commitdiff
|
tree
2017-11-01
Paul Bauer
Small change to LaTeX manual
g
e
neration
commit
|
commitdiff
|
tree
2017-11-01
Mark Abraham
Fix thread-MPI ra
n
k
choice for orientatio
n
restraints
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iu
p
ino
v
Remove unused PME GPU declar
a
ti
o
ns
commit
|
commitdiff
|
tree
2017-11-01
Aleksei Iu
p
inov
M
o
ve pme_gpu_fini
s
h_computat
i
on() documen
t
ation to
.
.
.
commit
|
commitdiff
|
tree
2017-11-01
Paul Ba
u
e
r
F
i
xing
missing references in web
d
o
cumenta
t
ion
commit
|
commitdiff
|
tree
2017-11-01
A
l
eksei Iupinov
Fix
erro
n
eous PME GPU "ste
p
"
n
amings
commit
|
commitdiff
|
tree
2017-11-01
Mark
A
braha
m
I
m
p
rove
handling of GPU IDs
commit
|
commitdiff
|
tree
2017-11-01
Aleks
e
i Iupinov
Simplify PM
E
GPU
synchroni
z
at
i
on co
d
e
commit
|
commitdiff
|
tree
2017-10-31
Alek
s
ei Iup
i
nov
R
eus
e
epbcXY
l
ogic
commit
|
commitdiff
|
tree
2017-10-31
Sz
i
l
á
r
d
Pá
l
l
Fi
x
nstl
i
st incr
e
a
se warn
i
n
g
prin
t
commit
|
commitdiff
|
tree
2017-10-31
Szilárd Páll
Check CUDA
a
v
a
ila
b
le/compiled code compatibility
commit
|
commitdiff
|
tree
2017-10-30
Al
e
ksei Iupinov
Fix referenc
e
m
o
de
b
uild
unused fu
n
c
t
ion
w
arnings
commit
|
commitdiff
|
tree
2017-10-30
Berk Hess
Remove
u
n
used sign parameter from dih_an
g
le()
commit
|
commitdiff
|
tree
2017-10-30
Roland S
c
hulz
A
rr
a
yRef: Rep
l
ace fromVect
o
r with su
b
A
rr
a
y
commit
|
commitdiff
|
tree
2017-10-30
David van de
r
Sp
o
el
Added option -
w
ater t
i
ps3p to
pdb2gmx
.
commit
|
commitdiff
|
tree
2017-10-30
Aleksei I
u
pinov
Brin
g
PME GPU/CUDA inte
r
nal structure na
m
es
t
o CamelCase
commit
|
commitdiff
|
tree
2017-10-27
Mark Abrah
a
m
F
ix hw detec
t
ion more
commit
|
commitdiff
|
tree
2017-10-26
M
a
rk Abraham
New quote
commit
|
commitdiff
|
tree
2017-10-20
Mark Abr
a
ham
Clarify do
c
s f
o
r Fmax in E
M
commit
|
commitdiff
|
tree
2017-10-20
Mark
Abraham
M
e
rg
e
bran
c
h r
e
lease-2016
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix
w
a
rnin
g
fo
r
confout
with pe
r
iodic
m
o
l
ecules
commit
|
commitdiff
|
tree
2017-10-16
Mark A
b
raham
Merge branch
relea
s
e
-2016
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improve vs
i
te
p
arallel
chec
k
ing
commit
|
commitdiff
|
tree
2017-10-13
Aleksei Iupinov
Re
l
ax PME spli
n
e
c
omput
a
tion
t
olerance in double precis
i
on
.
.
.
commit
|
commitdiff
|
tree
2017-10-13
Mark Abraham
U
p
date tests for C++11 c
o
m
p
iler
and
s
tandard libr
a
ry
commit
|
commitdiff
|
tree
2017-10-13
Roland Schulz
Specialize ArrayRef f
o
r SimdReal
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Intr
o
duced h
e
ader for communication to
/
from PME
r
anks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupinov
Fix clang warn
i
ngs for PM
E
CUDA
ker
n
el
s
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iup
i
nov
Relax PME solving test complex grid tolerance
commit
|
commitdiff
|
tree
2017-10-11
Mark Abraham
Cl
e
an
e
d
up e
w
a
ldcoeff for PME-only ranks
commit
|
commitdiff
|
tree
2017-10-11
Aleksei Iupino
v
P
M
E solving -
CUDA kerne
l
+
unit t
e
sts
commit
|
commitdiff
|
tree
2017-10-11
Paul Bauer
Change to modules
for buil
d
of
w
eb documentation
commit
|
commitdiff
|
tree
2017-10-11
Aleksei I
u
pinov
PM
E
force gathe
r
ing - C
U
DA kernel
+
unit tes
t
s
commit
|
commitdiff
|
tree
2017-10-11
A
lek
s
ei Iupinov
PME s
p
line+s
p
r
e
ad
CUDA
kernel and un
i
t
t
ests
commit
|
commitdiff
|
tree
2017-10-11
M
a
rk Abraham
Use
clang-
5
in Jenkin
s
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disabl
e
ARM Neo
n
native
rsqrt iteration
commit
|
commitdiff
|
tree
2017-10-09
A
l
eksei I
u
p
inov
P
M
E GPU/CU
D
A data framework
.
commit
|
commitdiff
|
tree
2017-10-07
Mark Ab
r
aham
Te
l
l
c
ppcheck that
.
cpp
and
.
cu files are c++
commit
|
commitdiff
|
tree
2017-10-07
R
oland Sch
u
lz
Refact
o
r l
o
ad+SimdLoad*ProxyInternal to reduce duplica
t
ion
commit
|
commitdiff
|
tree
2017-10-06
B
e
rk
H
e
ss
A
dd SIMD int
r
i
n
s
ics version
o
f simp
l
e upda
t
e
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Improve Padd
e
dR
V
ecVector res
i
zing
commit
|
commitdiff
|
tree
2017-10-06
Aleksei Iupinov
A
d
d t
i
ming accumulation capabi
l
i
t
y into
G
pu
R
egio
n
Timer
commit
|
commitdiff
|
tree
2017-10-05
Ber
k
H
e
s
s
Make SIMD ambiguous te
s
t work with fl
o
at/dou
b
l
e
o
nly
commit
|
commitdiff
|
tree
2017-10-05
S
zilárd Páll
Fix pair
list
a
rray assertion
commit
|
commitdiff
|
tree
2017-10-05
Szilárd Páll
A
v
oid -Wm
i
ssing-pro
t
otypes warnings in clang CUDA builds
commit
|
commitdiff
|
tree
2017-10-05
Roland Schulz
F
ix th
a
t
exp(load(x)) is ambiguous
commit
|
commitdiff
|
tree
2017-10-04
Mar
k
Ab
r
ah
a
m
En
a
ble g
r
oup-scheme
S
IMD wi
t
h GMX_SIMD=
A
VX2_128
commit
|
commitdiff
|
tree
2017-10-04
Aleksei Iupin
o
v
Add GpuReg
i
onTimer class
commit
|
commitdiff
|
tree
next